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Abdelazeem NM, Gouhar SA, Fahmy CA, Elshahid ZA, El-Hussieny M. Evaluation of newly synthesized 2-(thiophen-2-yl)-1H-indole derivatives as anticancer agents against HCT-116 cell proliferation via cell cycle arrest and down regulation of miR-25. Sci Rep 2024; 14:20045. [PMID: 39209915 PMCID: PMC11362284 DOI: 10.1038/s41598-024-68815-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
In the present study, we prepared new sixteen different derivatives. The first series were prepared (methylene)bis(2-(thiophen-2-yl)-1H-indole) derivatives which have (indole and thiophene rings) by excellent yield from the reaction (2 mmol) 2-(thiophen-2-yl)-1H-indole and (1 mmol) from aldehyde. The second series were synthesized (2-(thiophen-2-yl)-1H-indol-3-yl) methyl) aniline derivatives at a relatively low yield from multicomponent reaction of three components 2-(thiophen-2-yl)-1H-indole, N-methylaniline and desired aldehydes. The anticancer effect of the newly synthesized derivatives was determined against different cancers, colon, lung, breast and skin. The counter screening was done against normal Epithelial cells (RPE-1). The effect on cell cycle and mechanisms underlying of the antitumor effect were also studied. All new compounds were initially tested at a single dose of 100 μg/ml against this panel of 5 human tumor cell lines indicated that the compounds under investigation exhibit selective cytotoxicity against HCT-116 cell line and compounds (4g, 4a, 4c) showed potent anticancer activity against HCT-116 cell line with the inhibitory concentration IC50 values were, 7.1±0.07, 10.5± 0.07 and 11.9± 0.05 μΜ/ml respectively. Also, the active derivatives caused cell cycle arrest at the S and G2/M phase with significant(p < 0.0001) increase in the expression levels of tumor suppressors miR-30C, and miR-107 and a tremendous decrease in oncogenic miR-25, IL-6 and C-Myc levels. It is to conclude that the anticancer activity could be through direct interaction with tumor cell DNA like S-phase-dependent chemotherapy drugs. Which can interact with DNA or block DNA synthesis such as doxorubicin, cisplatin, or 5-fluorouracil and which were highly effective in killing the cancer cells. This data ensures the efficiency of the 3 analogues on inducing cell cycle arrest and preventing cancer cell growth. The altered expressions explained the molecular mechanisms through which the newly synthesized analogues exert their anticancer action.
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Affiliation(s)
- Nagwa M Abdelazeem
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Dokki, 12622, Cairo, Egypt
| | - Shaimaa A Gouhar
- Medical Biochemistry Department, Medicine and Clinical Studies Research Institute, National Research Centre, Dokki, 12622, Cairo, Egypt
| | - Cinderella A Fahmy
- Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences, National Research Centre, Dokki, 12622, Cairo, Egypt
- Biochemistry Department, Biotechnology Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Zeinab A Elshahid
- Chemistry of Natural and Microbial Products, National Research Centre, Dokki, 12622, Cairo, Egypt.
| | - Marwa El-Hussieny
- Organometallic and Organometalloid Chemistry Department, National Research Centre, Dokki, 12622, Cairo, Egypt.
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202
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Sharma P, Sethi RS. In Vivo Exposure of Deltamethrin Dysregulates the NFAT Signalling Pathway and Induces Lung Damage. J Toxicol 2024; 2024:5261994. [PMID: 39239465 PMCID: PMC11377118 DOI: 10.1155/2024/5261994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/23/2024] [Accepted: 08/10/2024] [Indexed: 09/07/2024] Open
Abstract
Deltamethrin is an insecticide used to control harmful agricultural insects that otherwise damage crops and to control vector-borne diseases. Long-term exposure to deltamethrin results in the inflammation of the lungs. The present study elucidates the molecular mechanism underlying the deltamethrin-induced lung damage. The lung samples were extracted from the Swiss albino mice following the treatment of low (2.5 mg/kg) and high (5 mg/kg) doses of deltamethrin. The mRNA expression of TCR, IL-4, and IL-13 showed upregulation, while the expression of NFAT and FOS was downregulated following a low dose of deltamethrin. Moreover, the expression of TCR was downregulated with the exposure of a high dose of deltamethrin. Furthermore, the immunohistochemistry data confirmed the pattern of protein expression for TCR, FOS, IL-4, and IL-13 following a low dose of deltamethrin exposure. However, no change was seen in the TCR, NFAT, FOS, JUN, IL-4, and IL-13 immunopositive cells of the high-dose treatment group. Also, ELISA results showed increased expression of IL-13 in the BAL fluid of animals exposed to low doses of deltamethrin. Overall, the present study showed that deltamethrin exposure induces lung damage and immune dysregulation via dysregulating the NFAT signalling pathway.
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Affiliation(s)
- Prakriti Sharma
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - R S Sethi
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
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203
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Cooney I, Schubert HL, Cedeno K, Fisher ON, Carson R, Price JC, Hill CP, Shen PS. Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway. Nat Commun 2024; 15:7505. [PMID: 39209885 PMCID: PMC11362554 DOI: 10.1038/s41467-024-51835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.
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Affiliation(s)
- Ian Cooney
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Karina Cedeno
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Olivia N Fisher
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| | - Peter S Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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204
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Majidiani H, Pourseif MM, Kordi B, Sadeghi MR, Najafi A. TgVax452, an epitope-based candidate vaccine targeting Toxoplasma gondii tachyzoite-specific SAG1-related sequence (SRS) proteins: immunoinformatics, structural simulations and experimental evidence-based approaches. BMC Infect Dis 2024; 24:886. [PMID: 39210269 PMCID: PMC11361240 DOI: 10.1186/s12879-024-09807-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND The highly expressed surface antigen 1 (SAG1)-related sequence (SRS) proteins of T. gondii tachyzoites, as a widespread zoonotic parasite, are critical for host cell invasion and represent promising vaccine targets. In this study, we employed a computer-aided multi-method approach for in silico design and evaluation of TgVax452, an epitope-based candidate vaccine against T. gondii tachyzoite-specific SRS proteins. METHODS Using immunoinformatics web-based tools, structural modeling, and static/dynamic molecular simulations, we identified and screened B- and T-cell immunodominant epitopes and predicted TgVax452's antigenicity, stability, safety, adjuvanticity, and physico-chemical properties. RESULTS The designed protein possessed 452 residues, a MW of 44.07 kDa, an alkaline pI (6.7), good stability (33.20), solubility (0.498), and antigenicity (0.9639) with no allergenicity. Comprehensive molecular dynamic (MD) simulation analyses confirmed the stable interaction (average potential energy: 3.3799 × 106 KJ/mol) between the TLR4 agonist residues (RS09 peptide) of the TgVax452 in interaction with human TLR4, potentially activating innate immune responses. Also, a dramatic increase was observed in specific antibodies (IgM and IgG), cytokines (IFN-γ), and lymphocyte responses, based on C-ImmSim outputs. Finally, we optimized TgVax452's codon adaptation and mRNA secondary structure for efficient expression in E. coli BL21 expression machinery. CONCLUSION Our findings suggest that TgVax452 is a promising candidate vaccine against T. gondii tachyzoite-specific SRS proteins and requires further experimental studies for its potential use in preclinical trials.
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MESH Headings
- Protozoan Proteins/immunology
- Protozoan Proteins/genetics
- Protozoan Proteins/chemistry
- Toxoplasma/immunology
- Toxoplasma/genetics
- Toxoplasma/chemistry
- Protozoan Vaccines/immunology
- Protozoan Vaccines/genetics
- Antigens, Protozoan/immunology
- Antigens, Protozoan/genetics
- Antigens, Protozoan/chemistry
- Animals
- Computational Biology
- Mice
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/genetics
- Female
- Antibodies, Protozoan/immunology
- Mice, Inbred BALB C
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/chemistry
- Humans
- Molecular Dynamics Simulation
- Immunodominant Epitopes/immunology
- Immunodominant Epitopes/genetics
- Immunodominant Epitopes/chemistry
- Toxoplasmosis/prevention & control
- Toxoplasmosis/immunology
- Immunoinformatics
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Affiliation(s)
- Hamidreza Majidiani
- Healthy Aging Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran.
- Department of Basic Medical Sciences, Neyshabur University of Medical Sciences, Neyshabur, Iran.
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology (RCPN), Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
- Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
- Engineered Biomaterial Research Center (EBRC), Khazar University, Baku, Azerbaijan.
| | - Bahareh Kordi
- Department of Agricultural Science, Technical and Vocational University (TVU), Tehran, Iran
| | - Mohammad-Reza Sadeghi
- Research Center for Pharmaceutical Nanotechnology (RCPN), Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Najafi
- Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
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205
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Tummala H, Walne AJ, Badat M, Patel M, Walne AM, Alnajar J, Chow CC, Albursan I, Frost JM, Ballard D, Killick S, Szitányi P, Kelly AM, Raghavan M, Powell C, Raymakers R, Todd T, Mantadakis E, Polychronopoulou S, Pontikos N, Liao T, Madapura P, Hossain U, Vulliamy T, Dokal I. The evolving genetic landscape of telomere biology disorder dyskeratosis congenita. EMBO Mol Med 2024:10.1038/s44321-024-00118-x. [PMID: 39198715 DOI: 10.1038/s44321-024-00118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 09/01/2024] Open
Abstract
Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome, caused by genetic mutations that principally affect telomere biology. Approximately 35% of cases remain uncharacterised at the genetic level. To explore the genetic landscape, we conducted genetic studies on a large collection of clinically diagnosed cases of DC as well as cases exhibiting features resembling DC, referred to as 'DC-like' (DCL). This led us to identify several novel pathogenic variants within known genetic loci and in the novel X-linked gene, POLA1. In addition, we have also identified several novel variants in POT1 and ZCCHC8 in multiple cases from different families expanding the allelic series of DC and DCL phenotypes. Functional characterisation of novel POLA1 and POT1 variants, revealed pathogenic effects on protein-protein interactions with primase, CTC1-STN1-TEN1 (CST) and shelterin subunit complexes, that are critical for telomere maintenance. ZCCHC8 variants demonstrated ZCCHC8 deficiency and signs of pervasive transcription, triggering inflammation in patients' blood. In conclusion, our studies expand the current genetic architecture and broaden our understanding of disease mechanisms underlying DC and DCL disorders.
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Affiliation(s)
- Hemanth Tummala
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK.
- Barts Health NHS Trust, London, UK.
| | - Amanda J Walne
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Mohsin Badat
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
| | - Manthan Patel
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Abigail M Walne
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Jenna Alnajar
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Chi Ching Chow
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Ibtehal Albursan
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Jennifer M Frost
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - David Ballard
- Department of Analytical, Environmental & Forensic Sciences, Kings College London, Franklin-Wilkins Building, Stamford Street, London, SE1 9NH, UK
| | - Sally Killick
- Department of Haematology, Royal Bournemouth Hospital NHS Foundation Trust, Bournemouth, BH7 7DW, UK
| | - Peter Szitányi
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Prague, Czech Republic
| | - Anne M Kelly
- Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Manoj Raghavan
- Clinical Haematology, Queen Elizabeth Hospital, Edgbaston, Birmingham, B15 2TH, UK
| | - Corrina Powell
- Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B15 2TG, UK
| | - Reinier Raymakers
- University Medical Center Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Tony Todd
- Department of Haematology, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
| | - Elpis Mantadakis
- Department of Pediatrics' University General Hospital of Alexandroupolis, Democritus University of Thrace Faculty of Medicine, 6th Kilometer Alexandroupolis-Makris, 68 100 Alexandroupolis, Thrace, Greece
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Athens, Greece
| | - Nikolas Pontikos
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, Gower St, London, WC1E 6BT, UK
| | - Tianyi Liao
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Pradeep Madapura
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Upal Hossain
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
| | - Tom Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Inderjeet Dokal
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
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206
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Villamayor-Belinchón L, Sharma P, Gordiyenko Y, Llácer JL, Hussain T. Structural basis of AUC codon discrimination during translation initiation in yeast. Nucleic Acids Res 2024:gkae737. [PMID: 39193907 DOI: 10.1093/nar/gkae737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 08/08/2024] [Accepted: 08/27/2024] [Indexed: 08/29/2024] Open
Abstract
In eukaryotic translation initiation, the 48S preinitiation complex (PIC) scans the 5' untranslated region of mRNAs to search for the cognate start codon (AUG) with assistance from various eukaryotic initiation factors (eIFs). Cognate start codon recognition is precise, rejecting near-cognate codons with a single base difference. However, the structural basis of discrimination of near-cognate start codons was not known. We have captured multiple yeast 48S PICs with a near-cognate AUC codon at the P-site, revealing that the AUC codon induces instability in the codon-anticodon at the P-site, leading to a disordered N-terminal tail of eIF1A. Following eIF1 dissociation, the N-terminal domain of eIF5 fails to occupy the vacant eIF1 position, and eIF2β becomes flexible. Consequently, 48S with an AUC codon is less favourable for initiation. Furthermore, we observe hitherto unreported metastable states of the eIF2-GTP-Met-tRNAMet ternary complex, where the eIF2β helix-turn-helix domain may facilitate eIF5 association by preventing eIF1 rebinding to 48S PIC. Finally, a swivelled head conformation of 48S PIC appears crucial for discriminating incorrect and selection of the correct codon-anticodon pair during translation initiation.
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Affiliation(s)
| | - Prafful Sharma
- Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India
| | | | - Jose L Llácer
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
- Centro para Investigación Biomédica en Red sobre Enfermedades Raras CIBERER-ISCIII, Valencia, Spain
| | - Tanweer Hussain
- Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India
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207
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Frey L, Ghosh D, Qureshi BM, Rhyner D, Guerrero-Ferreira R, Pokharna A, Kwiatkowski W, Serdiuk T, Picotti P, Riek R, Greenwald J. On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation. eLife 2024; 12:RP93562. [PMID: 39196271 DOI: 10.7554/elife.93562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.
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Affiliation(s)
- Lukas Frey
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Dhiman Ghosh
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Bilal M Qureshi
- Scientific Center for Optical and Electron Microscopy, Zürich, Switzerland
| | - David Rhyner
- Institute of Molecular Physical Science, Zürich, Switzerland
| | | | - Aditya Pokharna
- Institute of Molecular Physical Science, Zürich, Switzerland
| | | | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, Zürich, Switzerland
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208
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Westhorpe R, Roske JJ, Yeeles JTP. Mechanisms controlling replication fork stalling and collapse at topoisomerase 1 cleavage complexes. Mol Cell 2024:S1097-2765(24)00658-0. [PMID: 39236719 DOI: 10.1016/j.molcel.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/14/2024] [Accepted: 08/02/2024] [Indexed: 09/07/2024]
Abstract
Topoisomerase 1 cleavage complexes (Top1-ccs) comprise a DNA-protein crosslink and a single-stranded DNA break that can significantly impact the DNA replication machinery (replisome). Consequently, inhibitors that trap Top1-ccs are used extensively in research and clinical settings to generate DNA replication stress, yet how the replisome responds upon collision with a Top1-cc remains obscure. By reconstituting collisions between budding yeast replisomes, assembled from purified proteins, and site-specific Top1-ccs, we have uncovered mechanisms underlying replication fork stalling and collapse. We find that stalled replication forks are surprisingly stable and that their stability is influenced by the template strand that Top1 is crosslinked to, the fork protection complex proteins Tof1-Csm3 (human TIMELESS-TIPIN), and the convergence of replication forks. Moreover, nascent-strand mapping and cryoelectron microscopy (cryo-EM) of stalled forks establishes replisome remodeling as a key factor in the initial response to Top1-ccs. These findings have important implications for the use of Top1 inhibitors in research and in the clinic.
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Affiliation(s)
- Rose Westhorpe
- Protein and Nucleic Acid Chemistry Division, Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Johann J Roske
- Protein and Nucleic Acid Chemistry Division, Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Joseph T P Yeeles
- Protein and Nucleic Acid Chemistry Division, Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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209
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Watanabe R, Song C, Takemura M, Murata K. Subnanometer structure of medusavirus capsid during maturation using cryo-electron microscopy. J Virol 2024:e0043624. [PMID: 39194243 DOI: 10.1128/jvi.00436-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024] Open
Abstract
Medusavirus is a giant virus classified into an independent family of Mamonoviridae. Amoebae infected with medusavirus release immature particles in addition to virions. These particles were suggested to exhibit the maturation process of this virus, but the structure of these capsids during maturation remains unknown. Here, we apply a block-based reconstruction method in cryo-electron microscopy (cryo-EM) single particle analysis to these viral capsids, extending the resolution to 7-10 Å. The maps reveal a novel network composed of minor capsid proteins (mCPs) supporting major capsid proteins (MCPs). A predicted molecular model of the MCP fitted into the cryo-EM maps clarified the boundaries between the MCP and the underlining mCPs, as well as between the MCP and the outer spikes, and identified molecular interactions between the MCP and these components. Several structural changes of the mCPs under the fivefold vertices of the immature particles were observed, depending on the presence or absence of the underlying internal membrane. In addition, the lower part of the penton proteins on the fivefold vertices was also missing in mature virions. These dynamic conformational changes of mCPs indicate an important function in the maturation process of medusavirus.IMPORTANCEThe structural changes of giant virus capsids during maturation have not thus far been well clarified. Medusavirus is a unique giant virus in which infected amoebae release immature particles in addition to mature virus particles. In this study, we used cryo-electron microscopy to investigate immature and mature medusavirus particles and elucidate the structural changes of the viral capsid during the maturation process. In DNA-empty particles, the conformation of the minor capsid proteins changed dynamically depending on the presence or absence of the underlying internal membranes. In DNA-full particles, the lower part of the penton proteins was lost. This is the first report of structural changes of the viral capsid during the maturation process of giant viruses.
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Affiliation(s)
- Ryoto Watanabe
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Chihong Song
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Masaharu Takemura
- Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Kazuyoshi Murata
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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210
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Bettin EB, Grassmann AA, Dellagostin OA, Gogarten JP, Caimano MJ. Leptospira interrogans encodes a canonical BamA and three novel noNterm Omp85 outer membrane protein paralogs. Sci Rep 2024; 14:19958. [PMID: 39198480 PMCID: PMC11358297 DOI: 10.1038/s41598-024-67772-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 07/15/2024] [Indexed: 09/01/2024] Open
Abstract
The Omp85 family of outer membrane proteins are ubiquitously distributed among diderm bacteria and play essential roles in outer membrane (OM) biogenesis. The majority of Omp85 orthologs are bipartite and consist of a conserved OM-embedded 16-stranded beta-barrel and variable periplasmic functional domains. Here, we demonstrate that Leptospira interrogans encodes four distinct Omp85 proteins. The presumptive leptospiral BamA, LIC11623, contains a noncanonical POTRA4 periplasmic domain that is conserved across Leptospiraceae. The remaining three leptospiral Omp85 proteins, LIC12252, LIC12254 and LIC12258, contain conserved beta-barrels but lack periplasmic domains. Two of the three 'noNterm' Omp85-like proteins were upregulated by leptospires in urine from infected mice compared to in vitro and/or following cultivation within rat peritoneal cavities. Mice infected with a L. interrogans lic11254 transposon mutant shed tenfold fewer leptospires in their urine compared to mice infected with the wild-type parent. Analyses of pathogenic and saprophytic Leptospira spp. identified five groups of noNterm Omp85 paralogs, including one pathogen- and two saprophyte-specific groups. Expanding our analysis beyond Leptospira spp., we identified additional noNterm Omp85 orthologs in bacteria isolated from diverse environments, suggesting a potential role for these previously unrecognized noNterm Omp85 proteins in physiological adaptation to harsh conditions.
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Affiliation(s)
- Everton B Bettin
- Department of Medicine, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030-3715, USA
| | - André A Grassmann
- Department of Medicine, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030-3715, USA
| | - Odir A Dellagostin
- Biotechnology Unit, Technological Development Center, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Melissa J Caimano
- Department of Medicine, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030-3715, USA.
- Department of Pediatrics, University of Connecticut Health, Farmington, CT, USA.
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, USA.
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211
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Duarte ML, Eto C, Mazzon RR, Melocco G, Esposito F, Lincopan N, Ferreira FA. Emergence of methicillin-resistant Staphylococcus aureus (MRSA) RdJ clone (CC5-ST105-SCCmecII-t002) in Santa Catarina, Brazil. Microb Pathog 2024; 195:106903. [PMID: 39208961 DOI: 10.1016/j.micpath.2024.106903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
The emergence of highly successful genetic lineages of methicillin-resistant Staphylococcus aureus (MRSA) poses a challenge in human healthcare due to increased morbidity and mortality rates. The RdJ clone (CC5-ST105-SCCmecII-t002 lineage), previously identified in Rio de Janeiro, Brazil, was linked to bloodstream infections and features a mutation in the aur gene (encoding aureolysin). Additionally, clinical isolates derived from this clone were more effective at evading monocytic immune responses. This study aimed to detect the RdJ clone among clinical MRSA isolated in Santa Catarina (SC) and examine its antimicrobial resistance and phagocytosis evasion capabilities. Our findings revealed the RdJ clone in 20 % of MRSA isolates, all exhibiting multiresistance. RdJ clone isolates from SC did not demonstrate a decreased rate of phagocytosis compared to CC5 non-RdJ isolates. Structural analysis suggests that the aur mutation is unlikely to significantly impact aureolysin activity. Genomic analysis of one isolate unveiled a genetic variant of the RdJ clone, sharing lineage and gene distribution but lacking the aur mutation. This study enhances the understanding of the clinical and epidemiologic risks associated with the RdJ clone and the biological mechanisms underlying its spreading in SC.
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Affiliation(s)
- Matheus Luís Duarte
- Laboratory of Bacterial Molecular Genetics (GeMBac), Department of Microbiology, Immunology and Parasitology, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade88040-960, Florianópolis, SC, Brazil
| | - Carolina Eto
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, 88040-960, Florianópolis, SC, Brazil
| | - Ricardo Ruiz Mazzon
- Laboratory of Bacterial Molecular Genetics (GeMBac), Department of Microbiology, Immunology and Parasitology, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade88040-960, Florianópolis, SC, Brazil
| | - Gregory Melocco
- Laboratory of Resistome and Therapeutic Alternatives, Institute of Biomedical Sciences, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes, Butantã, 05508-000, São Paulo, SP, Brazil
| | - Fernanda Esposito
- Laboratory of Resistome and Therapeutic Alternatives, Institute of Biomedical Sciences, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes, Butantã, 05508-000, São Paulo, SP, Brazil
| | - Nilton Lincopan
- Laboratory of Resistome and Therapeutic Alternatives, Institute of Biomedical Sciences, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes, Butantã, 05508-000, São Paulo, SP, Brazil
| | - Fabienne Antunes Ferreira
- Laboratory of Bacterial Molecular Genetics (GeMBac), Department of Microbiology, Immunology and Parasitology, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade88040-960, Florianópolis, SC, Brazil.
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212
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Wroblewski E, Patel N, Javed A, Mata CP, Chandler-Bostock R, Nair LBG, Ulamec SM, Clark S, Phillips SEV, Ranson NA, Twarock R, Stockley PG. Visualizing viral RNA packaging signals in action. J Mol Biol 2024:168765. [PMID: 39214281 DOI: 10.1016/j.jmb.2024.168765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Here we confirm, using genome-scale RNA fragments in assembly competition assays, that multiple sub-sites (Packaging Signals, PSs) across the 5́ two-thirds of the gRNA of Satellite Tobacco Necrosis Virus-1 make sequence-specific contacts to the viral CPs helping to nucleate formation of its T=1 virus-like particle (VLP). These contacts explain why natural virions only package their positive-sense genomes. Asymmetric cryo-EM reconstructions of these VLPs suggest that these interactions occur between amino acid residues in the N-terminal ends of the CP subunits and the gRNA PS loop sequences. The base-paired stems of PSs also act non-sequence-specifically by electrostatically promoting the assembly of CP trimers. Importantly, alterations in PS-CP affinity result in an asymmetric distribution of bound PSs inside VLPs, with fuller occupation of the higher affinity 5́ PS RNAs around one vertex, decreasing to an RNA-free opposite vertex within the VLP shell. This distribution suggests that gRNA folding regulates cytoplasmic genome extrusion so that the weakly bound 3́ end of the gRNA, containing the RNA polymerase binding site, extrudes first. This probably occurs after cation-loss induced swelling of the CP-shell, weakening contacts between CP subunits. These data reveal for the first time in any virus how differential PS folding propensity and CP affinities support the multiple roles genomes play in virion assembly and infection. The high degree of conservation between the CP fold of STNV-1 and those of the CPs of many other viruses suggests that these aspects of genome function will be widely shared.
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Affiliation(s)
- Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nikesh Patel
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Abid Javed
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rebecca Chandler-Bostock
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lekshmi B G Nair
- York Centre for Complex Systems Analysis, University of York, YO10 5DD, United Kingdom; Departments of Mathematics and Biology, University of York, YO10 5DD, United Kingdom
| | - Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Samuel Clark
- York Centre for Complex Systems Analysis, University of York, YO10 5DD, United Kingdom; Departments of Mathematics and Biology, University of York, YO10 5DD, United Kingdom
| | - Simon E V Phillips
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, YO10 5DD, United Kingdom; Departments of Mathematics and Biology, University of York, YO10 5DD, United Kingdom.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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213
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Burdette LA, Leach SA, Kennedy N, Ikwuagwu BC, Summers JS, Tullman-Ercek D. Characterization and engineering of the type 3 secretion system needle monomer from Salmonella through the construction and screening of a comprehensive mutagenesis library. mSphere 2024; 9:e0036724. [PMID: 39109886 DOI: 10.1128/msphere.00367-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/21/2024] [Indexed: 08/29/2024] Open
Abstract
Protein production strategies in bacteria are often limited due to the need for cell lysis and complicated purification schemes. To avoid these challenges, researchers have developed bacterial strains capable of secreting heterologous protein products outside the cell, but secretion titers often remain too low for commercial applicability. Improved understanding of the link between secretion system structure and its secretory abilities can help overcome the barrier to engineering higher secretion titers. Here, we investigated this link with the PrgI protein, the monomer of the secretory channel of the type 3 secretion system (T3SS) of Salmonella enterica. Despite detailed knowledge of the PrgI needle's assembly and structure, little is known about how its structure influences its secretory capabilities. To study this, we recently constructed a comprehensive codon mutagenesis library of the PrgI protein utilizing a novel one-pot recombineering approach. We then screened this library for functional T3SS assembly and secretion titer by measuring the secretion of alkaline phosphatase using a high-throughput activity assay. This allowed us to construct a first-of-its-kind secretion fitness landscape to characterize the PrgI needle's mutability at each position as well as the mutations which lead to enhanced T3SS secretion. We discovered new design rules for building a functional T3SS as well as identified hypersecreting mutants. This work can be used to increase understanding of the T3SS's assembly and identify further targets for engineering. This work also provides a blueprint for future efforts to engineer other complex protein assemblies through the construction of fitness landscapes.IMPORTANCEProtein secretion offers a simplified alternative method for protein purification from bacterial hosts. However, the current state-of-the-art methods for protein secretion in bacteria are still hindered by low yields relative to traditional protein purification strategies. Engineers are now seeking strategies to enhance protein secretion titers from bacterial hosts, often through genetic manipulations. In this study, we demonstrate that protein engineering strategies focused on altering the secretion apparatus can be a fruitful avenue toward this goal. Specifically, this study focuses on how changes to the PrgI needle protein from the type 3 secretion system from Salmonella enterica can impact secretion titer. We demonstrate that this complex is amenable to comprehensive mutagenesis studies and that this can yield both PrgI variants with increased secretory capabilities and insight into the normal functioning of the type 3 secretion system.
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Affiliation(s)
- Lisa Ann Burdette
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Samuel Alexander Leach
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Nolan Kennedy
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Bon C Ikwuagwu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Jordan S Summers
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
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214
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Manville RW, Yoshimura RF, Yeromin AV, Hogenkamp D, van der Horst J, Zavala A, Chinedu S, Arena G, Lasky E, Fisher M, Tracy CR, Othy S, Jepps TA, Cahalan MD, Abbott GW. Polymodal K + channel modulation contributes to dual analgesic and anti-inflammatory actions of traditional botanical medicines. Commun Biol 2024; 7:1059. [PMID: 39198706 PMCID: PMC11358443 DOI: 10.1038/s42003-024-06752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Pain and inflammation contribute immeasurably to reduced quality of life, yet modern analgesic and anti-inflammatory therapeutics can cause dependence and side effects. Here, we screened 1444 plant extracts, prepared primarily from native species in California and the United States Virgin Islands, against two voltage-gated K+ channels - T-cell expressed Kv1.3 and nociceptive-neuron expressed Kv7.2/7.3. A subset of extracts both inhibits Kv1.3 and activates Kv7.2/7.3 at hyperpolarized potentials, effects predicted to be anti-inflammatory and analgesic, respectively. Among the top dual hits are witch hazel and fireweed; polymodal modulation of multiple K+ channel types by hydrolysable tannins contributes to their dual anti-inflammatory, analgesic actions. In silico docking and mutagenesis data suggest pore-proximal extracellular linker sequence divergence underlies opposite effects of hydrolysable tannins on different Kv1 isoforms. The findings provide molecular insights into the enduring, widespread medicinal use of witch hazel and fireweed and demonstrate a screening strategy for discovering dual anti-inflammatory, analgesic small molecules.
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Affiliation(s)
- Rían W Manville
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Ryan F Yoshimura
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Andriy V Yeromin
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Derk Hogenkamp
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Jennifer van der Horst
- Department of Biomedical Sciences, Vascular Biology Group, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Angel Zavala
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Sonia Chinedu
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Grey Arena
- Redwood Creek Vegetation Team, National Park Service, Sausalito, CA, USA
| | - Emma Lasky
- Redwood Creek Vegetation Team, National Park Service, Sausalito, CA, USA
| | - Mark Fisher
- Philip L. Boyd Deep Canyon Desert Research Center, University of California Natural Reserve System, Indian Wells, CA, USA
| | - Christopher R Tracy
- Philip L. Boyd Deep Canyon Desert Research Center, University of California Natural Reserve System, Indian Wells, CA, USA
| | - Shivashankar Othy
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Thomas A Jepps
- Department of Biomedical Sciences, Vascular Biology Group, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Cahalan
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA.
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215
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Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB. Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex. Mol Cell 2024:S1097-2765(24)00669-5. [PMID: 39226902 DOI: 10.1016/j.molcel.2024.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/17/2024] [Accepted: 08/09/2024] [Indexed: 09/05/2024]
Abstract
The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome intermediate in the reaction pathway of histone exchange, in which an H2A/H2B dimer has been extracted from a nucleosome prior to the insertion of a dimer comprising Htz1/H2B. The structure reveals a key role for the Swc5 subunit in stabilizing the unwrapping of DNA from the histone core of the hexasome. By engineering a crosslink between an Htz1/H2B dimer and its chaperone protein Chz1, we show that this blocks histone exchange by SWR1 but allows the incoming chaperone-dimer complex to insert into the hexasome. We use this reagent to trap an SWR1/hexasome complex with an incoming Htz1/H2B dimer that shows how the reaction progresses to the next step. Taken together the structures reveal insights into the mechanism of histone exchange by SWR1 complex.
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Affiliation(s)
- Adam S B Jalal
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Paul Girvan
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; Single Molecule Imaging Group, MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0HS, UK
| | - Eugene Y D Chua
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Lexin Liu
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Shijie Wang
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Elizabeth A McCormack
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Michael T Skehan
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Carol L Knight
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - David S Rueda
- Single Molecule Imaging Group, MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0HS, UK; Section of Virology, Department Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0HS, UK
| | - Dale B Wigley
- Section of Structural Biology, Department Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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216
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Ferreira JC, Fadl S, Cardoso THS, Andrade BS, Melo TS, Silva EMDA, Agarwal A, Turville SJ, Saksena NK, Rabeh WM. Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro. Biosci Rep 2024; 44:BSR20240617. [PMID: 39045772 PMCID: PMC11327220 DOI: 10.1042/bsr20240617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- G42 Healthcare Omics Excellence Center, Masdar City, Abu Dhabi, United Arabes Emirates
| | - Bruno Silva Andrade
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | - Tarcisio S Melo
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | | | | | | | - Nitin K Saksena
- Victoria University, Footscray Park Campus, Melbourne, VIC, 3134, Australia
- Aegros Therapeutics Pty Ltd, 5-6 Eden Park Drive, Macquarie Park, NSW 2113, Australia
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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217
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Ryu JK, Yan Z, Montano M, Sozmen EG, Dixit K, Suryawanshi RK, Matsui Y, Helmy E, Kaushal P, Makanani SK, Deerinck TJ, Meyer-Franke A, Rios Coronado PE, Trevino TN, Shin MG, Tognatta R, Liu Y, Schuck R, Le L, Miyajima H, Mendiola AS, Arun N, Guo B, Taha TY, Agrawal A, MacDonald E, Aries O, Yan A, Weaver O, Petersen MA, Meza Acevedo R, Alzamora MDPS, Thomas R, Traglia M, Kouznetsova VL, Tsigelny IF, Pico AR, Red-Horse K, Ellisman MH, Krogan NJ, Bouhaddou M, Ott M, Greene WC, Akassoglou K. Fibrin drives thromboinflammation and neuropathology in COVID-19. Nature 2024:10.1038/s41586-024-07873-4. [PMID: 39198643 DOI: 10.1038/s41586-024-07873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/24/2024] [Indexed: 09/01/2024]
Abstract
Life-threatening thrombotic events and neurological symptoms are prevalent in COVID-19 and are persistent in patients with long COVID experiencing post-acute sequelae of SARS-CoV-2 infection1-4. Despite the clinical evidence1,5-7, the underlying mechanisms of coagulopathy in COVID-19 and its consequences in inflammation and neuropathology remain poorly understood and treatment options are insufficient. Fibrinogen, the central structural component of blood clots, is abundantly deposited in the lungs and brains of patients with COVID-19, correlates with disease severity and is a predictive biomarker for post-COVID-19 cognitive deficits1,5,8-10. Here we show that fibrin binds to the SARS-CoV-2 spike protein, forming proinflammatory blood clots that drive systemic thromboinflammation and neuropathology in COVID-19. Fibrin, acting through its inflammatory domain, is required for oxidative stress and macrophage activation in the lungs, whereas it suppresses natural killer cells, after SARS-CoV-2 infection. Fibrin promotes neuroinflammation and neuronal loss after infection, as well as innate immune activation in the brain and lungs independently of active infection. A monoclonal antibody targeting the inflammatory fibrin domain provides protection from microglial activation and neuronal injury, as well as from thromboinflammation in the lung after infection. Thus, fibrin drives inflammation and neuropathology in SARS-CoV-2 infection, and fibrin-targeting immunotherapy may represent a therapeutic intervention for patients with acute COVID-19 and long COVID.
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Affiliation(s)
- Jae Kyu Ryu
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Zhaoqi Yan
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Mauricio Montano
- Gladstone Institute of Virology, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
| | - Elif G Sozmen
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Karuna Dixit
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | | | - Yusuke Matsui
- Gladstone Institute of Virology, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
| | - Ekram Helmy
- Gladstone Institute of Virology, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
| | - Prashant Kaushal
- Department of Microbiology, Immunology and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles, CA, USA
| | - Sara K Makanani
- Department of Microbiology, Immunology and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles, CA, USA
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California San Diego, La Jolla, CA, USA
| | | | | | - Troy N Trevino
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Min-Gyoung Shin
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Reshmi Tognatta
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Yixin Liu
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Renaud Schuck
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Lucas Le
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Hisao Miyajima
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Andrew S Mendiola
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Nikhita Arun
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Brandon Guo
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Taha Y Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
| | - Ayushi Agrawal
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Eilidh MacDonald
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Oliver Aries
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Aaron Yan
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Olivia Weaver
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Mark A Petersen
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Rosa Meza Acevedo
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Maria Del Pilar S Alzamora
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | - Reuben Thomas
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Michela Traglia
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
- CureScience Institute, San Diego, CA, USA
| | - Igor F Tsigelny
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
- CureScience Institute, San Diego, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Alexander R Pico
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Kristy Red-Horse
- Department of Biology, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- Department of Microbiology, Immunology and Molecular Genetics (MIMG), University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences (QCBio), University of California Los Angeles, Los Angeles, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA, USA
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA
- COVID-19 Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Warner C Greene
- Gladstone Institute of Virology, San Francisco, CA, USA.
- Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
| | - Katerina Akassoglou
- Center for Neurovascular Brain Immunology at Gladstone and UCSF, San Francisco, CA, USA.
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
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218
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Li C, Xu Y, Su W, He X, Li J, Li X, Xu HE, Yin W. Structural insights into ligand recognition, selectivity, and activation of bombesin receptor subtype-3. Cell Rep 2024; 43:114511. [PMID: 39024101 DOI: 10.1016/j.celrep.2024.114511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/16/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024] Open
Abstract
Bombesin receptor subtype-3 (BRS3) is an important orphan G protein-coupled receptor that regulates energy homeostasis and insulin secretion. As a member of the bombesin receptor (BnR) family, the lack of known endogenous ligands and high-resolution structure has hindered the understanding of BRS3 signaling and function. We present two cryogenic electron microscopy (cryo-EM) structures of BRS3 in complex with the heterotrimeric Gq protein in its active states: one bound to the pan-BnR agonist BA1 and the other bound to the synthetic BRS3-specific agonist MK-5046. These structures reveal the architecture of the orthosteric ligand pocket underpinning molecular recognition and provide insights into the structural basis for BRS3's selectivity and low affinity for bombesin peptides. Examination of conserved micro-switches suggests a shared activation mechanism among BnRs. Our findings shed light on BRS3's ligand selectivity and signaling mechanisms, paving the way for exploring its therapeutic potential for diabetes, obesity, and related metabolic disorders.
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Affiliation(s)
- Changyao Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Lingang Laboratory, Shanghai 200031, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenxin Su
- Guangzhou University of Chinese Medicine, Zhongshan Institute for Drug Discovery, Guangdong 510000, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong 528400, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingru Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xinzhu Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Lingang Laboratory, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Wanchao Yin
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong 528400, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Guangzhou University of Chinese Medicine, Zhongshan Institute for Drug Discovery, Guangdong 510000, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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219
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Liu K, Tao Y, Zhao Q, Xia W, Li X, Zhang S, Yao Y, Xiang H, Han C, Tan L, Sun B, Li D, Li A, Liu C. Binding adaptability of chemical ligands to polymorphic α-synuclein amyloid fibrils. Proc Natl Acad Sci U S A 2024; 121:e2321633121. [PMID: 39172784 PMCID: PMC11363296 DOI: 10.1073/pnas.2321633121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 07/17/2024] [Indexed: 08/24/2024] Open
Abstract
α-synuclein (α-syn) assembles into structurally distinct fibril polymorphs seen in different synucleinopathies, such as Parkinson's disease and multiple system atrophy. Targeting these unique fibril structures using chemical ligands holds diagnostic significance for different disease subtypes. However, the molecular mechanisms governing small molecules interacting with different fibril polymorphs remain unclear. Here, we investigated the interactions of small molecules belonging to four distinct scaffolds, with different α-syn fibril polymorphs. Using cryo-electron microscopy, we determined the structures of these molecules when bound to the fibrils formed by E46K mutant α-syn and compared them to those bound with wild-type α-syn fibrils. Notably, we observed that these ligands exhibit remarkable binding adaptability, as they engage distinct binding sites across different fibril polymorphs. While the molecular scaffold primarily steered the binding locations and geometries on specific sites, the conjugated functional groups further refined this adaptable binding by fine-tuning the geometries and binding sites. Overall, our finding elucidates the adaptability of small molecules binding to different fibril structures, which sheds light on the diagnostic tracer and drug developments tailored to specific pathological fibril polymorphs.
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Affiliation(s)
- Kaien Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai200240, China
| | - Qinyue Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai200240, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Xiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai200240, China
| | - Shenqing Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yuxuan Yao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai200240, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Chao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai200240, China
| | - Ang Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
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220
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Ali M, Zhang Z, Ibrahim MAA, Soliman MES. Heat shock protein (Hsp27)-ceramide synthase (Cers1) protein-protein interactions provide a new avenue for unexplored anti-cancer mechanism and therapy. J Recept Signal Transduct Res 2024:1-13. [PMID: 39189140 DOI: 10.1080/10799893.2024.2392711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024]
Abstract
Hsp27 is a member of the small heat-shock proteins (sHSPs) - the known cellular line of defence against abnormal protein folding behaviors. Nevertheless, its upregulation is linked to a variety of pathological disorders, including several types of cancers. The ceramide synthases (CerS) mediate the synthesis of ceramide, a critical structural and signaling lipid. Functionally, downstream ceramide metabolites are implicated in the apoptosis process and their abnormal functionality has been linked to anticancer resistance. Studies showed that CerS1 are possibly inhibited by Hsp27 leading to biochemical anticancer effects in vitro. Nevertheless, the nature of such protein-protein interaction (PPI) has not been considerably investigated in molecular terms, hence, we present the first description of the dynamics CerS1-Hsp27 interaction landscapes using molecular dynamics simulations. Time-scale molecular dynamics simulation analysis indicated a system-wide conformational events of decreased stability, increased flexibility, reduced compactness, and decreased folding of CerS1. Analysis of binding energy showed a favorable interaction entailing 56 residues at the interface and a total stabilizing energy of -158 KJ/mol. The CerS1 catalytic domain experienced an opposite trend compared to the protein backbone. Yet, these residues adopted a highly compact conformation as per DCCM and DSSP analysis. Furthermore, conserved residues (SER 212, ASP 213, ALA 240, GLY 243, ASP 319) comprising the substrate shuttling machinery showed notable rigidity implying a restrained ceramide precursor access and assembly; hence, a possible inhibitory mechanism. Findings from this report would streamline a better molecular understanding of CerS1-Hsp27 interactions and decipher its potential avenue toward unexplored anti-cancer mechanisms and therapy.
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Affiliation(s)
- Musab Ali
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Zhichao Zhang
- School of Chemistry, Dalian University of Technology, Dalian, Liaoning, China
| | - Mahmoud A A Ibrahim
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa
- Computational Chemistry Laboratory, Chemistry Department, Minia University, Minia, Egypt
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Research Group, School of Health Sciences, University of KwaZulu Natal, Durban, South Africa
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221
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Niu Z, Gui X, Feng S, Reif B. Aggregation Mechanisms and Molecular Structures of Amyloid-β in Alzheimer's Disease. Chemistry 2024; 30:e202400277. [PMID: 38888453 DOI: 10.1002/chem.202400277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/20/2024]
Abstract
Amyloid plaques are a major pathological hallmark involved in Alzheimer's disease and consist of deposits of the amyloid-β peptide (Aβ). The aggregation process of Aβ is highly complex, which leads to polymorphous aggregates with different structures. In addition to aberrant aggregation, Aβ oligomers can undergo liquid-liquid phase separation (LLPS) and form dynamic condensates. It has been hypothesized that these amyloid liquid droplets affect and modulate amyloid fibril formation. In this review, we briefly introduce the relationship between stress granules and amyloid protein aggregation that is associated with neurodegenerative diseases. Then we highlight the regulatory role of LLPS in Aβ aggregation and discuss the potential relationship between Aβ phase transition and aggregation. Furthermore, we summarize the current structures of Aβ oligomers and amyloid fibrils, which have been determined using nuclear magnetic resonance (NMR) and cryo-electron microscopy (cryo-EM). The structural variations of Aβ aggregates provide an explanation for the different levels of toxicity, shed light on the aggregation mechanism and may pave the way towards structure-based drug design for both clinical diagnosis and treatment.
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Affiliation(s)
- Zheng Niu
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Xinrui Gui
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shuang Feng
- School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China
| | - Bernd Reif
- Bavarian NMR Center (B NMRZ), Department of Bioscience, TUM School of Natural Sciences, Technische Universität München (TUM), Garching, 85747, Germany
- Institute of Structural Biology (STB), Helmholtz-Zentrum, München (HMGU), Neuherberg, 85764, Germany
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222
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Delyea CJ, Forster MD, Luo S, Dubrule BE, Julien O, Bhavsar AP. The Salmonella Effector SspH2 Facilitates Spatially Selective Ubiquitination of NOD1 to Enhance Inflammatory Signaling. Biochemistry 2024. [PMID: 39189508 DOI: 10.1021/acs.biochem.4c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
As part of its pathogenesis, Salmonella enterica serovar Typhimurium delivers effector proteins into host cells. One effector is SspH2, a member of the so-called novel E3 ubiquitin ligase family, that interacts with and enhances, NOD1 pro-inflammatory signaling, though the underlying mechanisms are unclear. Here, we report that SspH2 interacts with multiple members of the NLRC family to enhance pro-inflammatory signaling by targeted ubiquitination. We show that SspH2 modulates host innate immunity by interacting with both NOD1 and NOD2 in mammalian epithelial cell culture via the NF-κB pathway. Moreover, purified SspH2 and NOD1 directly interact, where NOD1 potentiates SspH2 E3 ubiquitin ligase activity. Mass spectrometry and mutational analyses identified four key lysine residues in NOD1 that are required for its enhanced activation by SspH2, but not its basal activity. These critical lysine residues are positioned in the same region of NOD1 and define a surface on the receptor that appears to be targeted by SspH2. Overall, this work provides evidence for post-translational modification of NOD1 by ubiquitin and uncovers a unique mechanism of spatially selective ubiquitination to enhance the activation of an archetypal NLR.
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Affiliation(s)
- Cole J Delyea
- Department of Medical Microbiology and Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Malcolm D Forster
- Department of Medical Microbiology and Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Shu Luo
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Bradley E Dubrule
- Department of Medical Microbiology and Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Amit P Bhavsar
- Department of Medical Microbiology and Immunology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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223
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Ngo QB, Juffer AH. Theoretical Investigations of a point mutation affecting H5 Hemagglutinin's receptor binding preference. Comput Biol Chem 2024; 113:108189. [PMID: 39216409 DOI: 10.1016/j.compbiolchem.2024.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/20/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
The avian influenza A H5N1 virus is a subtype of influenza A virus (IAV) that causes a highly infectious and severe respiratory illness in birds and poses significant economic losses in poultry farming. To infect host cell, the virus uses its surface glycoprotein named Hemagglutinin (HA) to recognize and to interact with the host cell receptor containing either α2,6- (SAα2,6 Gal) or α2,3-linked Sialic Acid (SAα2,3 Gal). The H5N1 virus has not yet acquired the capability for efficient human-to-human transmission. However, studies have demonstrated that even a single amino acid substitution in the HA can switch its glycan receptor preference from the avian-type SAα2,3 Gal to the human-type SAα2,6 Gal. The present study aims to explain the underlying mechanism of a mutation (D94N) on the H5 HA that causes the protein to change its glycan receptor-binding preference using molecular dynamics (MD) simulations. Our results reveal that the mutation alters the electrostatic interactions pattern near the HA receptor binding pocket, leading to a reduced stability for the HA-avian-type SAα2,3 Gal complex. On the other hand, the detrimental effect of the mutation D94N is not observed in the HA-human-type SAα2,6 Gal complex due to the glycan's capability to switch its topology.
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Affiliation(s)
- Quoc Bao Ngo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu 90014, Finland
| | - André H Juffer
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu 90014, Finland.
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224
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Cordery C, Craddock J, Malý M, Basavaraja K, Webb JS, Walsh MA, Tews I. Control of phosphodiesterase activity in the regulator of biofilm dispersal RbdA from Pseudomonas aeruginosa. RSC Chem Biol 2024:d4cb00113c. [PMID: 39247681 PMCID: PMC11372557 DOI: 10.1039/d4cb00113c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/26/2024] [Indexed: 09/10/2024] Open
Abstract
The switch between planktonic and biofilm lifestyle correlates with intracellular concentration of the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). While bacteria possess cyclase and phosphodiesterase enzymes to catalyse formation or hydrolysis of c-di-GMP, both enzymatic domains often occur in a single protein. It is tacitly assumed that one of the two enzymatic activities is dominant, and that additional domains and protein interactions enable responses to environmental conditions and control activity. Here we report the structure of the phosphodiesterase domain of the membrane protein RbdA (regulator of biofilm dispersal) in a dimeric, activated state and show that phosphodiesterase activity is controlled by the linked cyclase. The phosphodiesterase region around helices α5/α6 forms the dimer interface, providing a rationale for activation, as this region was seen in contact with the cyclase domain in an auto-inhibited structure previously described. Kinetic analysis supports this model, as the activity of the phosphodiesterase alone is lower when linked to the cyclase. Analysis of a computed model of the RbdA periplasmatic domain reveals an all-helical architecture with a large binding pocket that could accommodate putative ligands. Unravelling the regulatory circuits in multi-domain phosphodiesterases like RbdA is important to develop strategies to manipulate or disperse bacterial biofilms.
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Affiliation(s)
- Charlotte Cordery
- Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK
- National Biofilms Innovation Centre, University of Southampton Southampton SO17 1BJ UK
- Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0FA UK
| | - Jack Craddock
- Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK
- National Biofilms Innovation Centre, University of Southampton Southampton SO17 1BJ UK
| | - Martin Malý
- Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK
| | - Kieran Basavaraja
- Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK
- National Biofilms Innovation Centre, University of Southampton Southampton SO17 1BJ UK
- Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0FA UK
| | - Jeremy S Webb
- Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK
- National Biofilms Innovation Centre, University of Southampton Southampton SO17 1BJ UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0FA UK
| | - Ivo Tews
- Biological Sciences, Institute for Life Sciences, University of Southampton Southampton SO17 1BJ UK
- National Biofilms Innovation Centre, University of Southampton Southampton SO17 1BJ UK
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225
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Leitl KD, Sperl LE, Hagn F. Preferred inhibition of pro-apoptotic Bak by BclxL via a two-step mechanism. Cell Rep 2024; 43:114526. [PMID: 39046879 DOI: 10.1016/j.celrep.2024.114526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Bak is a pore-forming Bcl2 protein that induces apoptosis at the outer mitochondrial membrane, which can either proceed via Bak oligomerization or be inhibited by anti-apoptotic Bcl2 proteins, such as BclxL. BclxL is very efficient in inhibiting Bak pore formation, but the mechanistic basis of this preferred interaction has remained enigmatic. Here, we identify Bakα1 as a second binding site for BclxL and show that it specifically interacts with the Bcl2-homology (BH)3 binding groove of BclxL. The affinity between BclxL and Bakα1 is weaker than with Bak-BH3, suggesting that Bakα1, being exposed early in the pore-forming trajectory, transiently captures BclxL, which subsequently transitions to the proximal BH3 site. Bak variants where the initial transient interaction with BclxL is modulated show a markedly altered response to BclxL inhibition. This work contributes to a better mechanistic understanding of the fine-tuned interactions between different players of the Bcl2 protein family.
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Affiliation(s)
- Kira D Leitl
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany; Molecular Targets and Therapeutics Center (MTTC), Institute of Structural Biology, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Laura E Sperl
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany; Molecular Targets and Therapeutics Center (MTTC), Institute of Structural Biology, Helmholtz Munich, 85764 Neuherberg, Germany.
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226
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Zhang P, Gorman J, Tsybovsky Y, Lu M, Liu Q, Gopan V, Singh M, Lin Y, Miao H, Seo Y, Kwon A, Olia AS, Chuang GY, Geng H, Lai YT, Zhou T, Mascola JR, Mothes W, Kwong PD, Lusso P. Design of soluble HIV-1 envelope trimers free of covalent gp120-gp41 bonds with prevalent native-like conformation. Cell Rep 2024; 43:114518. [PMID: 39028623 DOI: 10.1016/j.celrep.2024.114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
Soluble HIV-1 envelope (Env) trimers may serve as effective vaccine immunogens. The widely utilized SOSIP trimers have been paramount for structural studies, but the disulfide bond they feature between gp120 and gp41 constrains intersubunit mobility and may alter antigenicity. Here, we report an alternative strategy to generate stabilized soluble Env trimers free of covalent gp120-gp41 bonds. Stabilization was achieved by introducing an intrasubunit disulfide bond between the inner and outer domains of gp120, defined as interdomain lock (IDL). Correctly folded IDL trimers displaying a native-like antigenic profile were produced for HIV-1 Envs of different clades. Importantly, the IDL design abrogated CD4 binding while not affecting recognition by potent neutralizing antibodies to the CD4-binding site. By cryoelectron microscopy, IDL trimers were shown to adopt a closed prefusion configuration, while single-molecule fluorescence resonance energy transfer documented a high prevalence of native-like conformation. Thus, IDL trimers may be promising candidates as vaccine immunogens.
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Affiliation(s)
- Peng Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Qingbo Liu
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Vinay Gopan
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mamta Singh
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yin Lin
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huiyi Miao
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuna Seo
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alice Kwon
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yen-Ting Lai
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; ModeX Therapeutics, 20 Riverside Road, Weston, MA 02493, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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227
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Yang Y, Rocamonde-Lago I, Shen B, Berzina I, Zipf J, Högberg B. Re-engineered guide RNA enables DNA loops and contacts modulating repression in E. coli. Nucleic Acids Res 2024; 52:9328-9339. [PMID: 39011887 PMCID: PMC11347156 DOI: 10.1093/nar/gkae591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/17/2024] Open
Abstract
RNA serves as information media as well as molecular scaffold in nature and synthetic systems. The single guide RNA (sgRNA) widely applied in CRISPR techniques exemplifies both functions, with a guide region bearing DNA base-pairing information, and a structural motif for Cas9 protein scaffolding. The scaffold region has been modified by fusing RNA aptamers to the tetra-stem loop. The guide region is typically not regarded as a pluggable module as it encodes the essential function of DNA sequence recognition. Here, we investigate a chimera of two sgRNAs, with distinct guide sequences joined by an RNA linker (dgRNA), regarding its DNA binding function and loop induction capability. First, we studied the sequence bi-specificity of the dgRNA and discovered that the RNA linker allows distal parts of double-stranded DNA to be brought into proximity. To test the activity of the dgRNA in organisms, we used the LacZ gene as a reporter and recapitulated the loop-mediated gene inhibition by LacI in E. coli. We found that the dgRNA can be applied to target distal genomic regions with comparable levels of inhibition. The capability of dgRNA to induce DNA contacts solely requires dCas9 and RNA, making it a minimal system to remodel chromosomal conformation in various organisms.
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Affiliation(s)
- Yunshi Yang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden
| | - Iris Rocamonde-Lago
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden
| | - Boxuan Shen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Ieva Berzina
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden
| | - Johanna Zipf
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm 17177, Sweden
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228
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He J, Liu G, Kong F, Tan Q, Wang Z, Yang M, He Y, Jia X, Yan C, Wang C, Qian H. Structural basis for the transport and substrate selection of human urate transporter 1. Cell Rep 2024; 43:114628. [PMID: 39146184 DOI: 10.1016/j.celrep.2024.114628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/17/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024] Open
Abstract
High serum urate levels are the major risk factor for gout. URAT1, the primary transporter for urate absorption in the kidneys, is well known as an anti-hyperuricemia drug target. However, the clinical application of URAT1-targeted drugs is limited because of their low specificity and severe side effects. The lack of structural information impedes elucidation of the transport mechanism and the development of new drugs. Here, we present the cryoelectron microscopy (cryo-EM) structures of human URAT1(R477S), its complex with urate, and its closely related homolog OAT4. URAT1(R477S) and OAT4 exhibit major facilitator superfamily (MFS) folds with outward- and inward-open conformations, respectively. Structural comparison reveals a 30° rotation between the N-terminal and C-terminal domains, supporting an alternating access mechanism. A conserved arginine (OAT4-Arg473/URAT1-Arg477) is found to be essential for chloride-mediated inhibition. The URAT1(R477S)-urate complex reveals the specificity of urate recognition. Taken together, our study promotes our understanding of the transport mechanism and substrate selection of URAT1.
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Affiliation(s)
- Jingjing He
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Guoyun Liu
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Fang Kong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiulong Tan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Zhenzhou Wang
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Meng Yang
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yonglin He
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaoxiao Jia
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chao Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Hongwu Qian
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
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229
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Nuqui X, Casalino L, Zhou L, Shehata M, Wang A, Tse AL, Ojha AA, Kearns FL, Rosenfeld MA, Miller EH, Acreman CM, Ahn SH, Chandran K, McLellan JS, Amaro RE. Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nat Commun 2024; 15:7370. [PMID: 39191724 PMCID: PMC11350062 DOI: 10.1038/s41467-024-50976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, S2's usage as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design S2-only immunogens stabilized in a closed prefusion conformation. Molecular simulations provide a mechanistic characterization of the S2 trimer's opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Structural characterization via cryo-EM shows the molecular basis of S2 stabilization in the closed prefusion conformation. Informed by molecular simulations and corroborated by experiments, we report an engineered S2 immunogen that exhibits increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.
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Affiliation(s)
- Xandra Nuqui
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Lorenzo Casalino
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Mohamed Shehata
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anupam A Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Fiona L Kearns
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cory M Acreman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California Davis, Davis, CA, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
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230
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Banerjee A, Ataman M, Smialek MJ, Mookherjee D, Rabl J, Mironov A, Mues L, Enkler L, Coto-Llerena M, Schmidt A, Boehringer D, Piscuoglio S, Spang A, Mittal N, Zavolan M. Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains. Nucleic Acids Res 2024; 52:9028-9048. [PMID: 39041433 PMCID: PMC11347166 DOI: 10.1093/nar/gkae630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we revealed the expression of RPL39L protein beyond mouse germ cells, in human pluripotent cells, cancer cell lines and tissue samples. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread autophagy. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.
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Affiliation(s)
| | - Meric Ataman
- Biozentrum, University of Basel, Basel, Switzerland
| | - Maciej Jerzy Smialek
- Biozentrum, University of Basel, Basel, Switzerland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Julius Rabl
- Cryo-EM Knowledge Hub (CEMK), ETH Zürich, Switzerland
| | | | - Lea Mues
- Biozentrum, University of Basel, Basel, Switzerland
| | - Ludovic Enkler
- Biozentrum, University of Basel, Basel, Switzerland
- University of Strasbourg, UMR7156 GMGM, Strasbourg, France
| | - Mairene Coto-Llerena
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | | | | | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
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231
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Liang K, Zhan X, Li Y, Yang Y, Xie Y, Jin Z, Xu X, Zhang W, Lu Y, Zhang S, Zou Y, Feng S, Wu J, Yan Z. Conservation and specialization of the Ycf2-FtsHi chloroplast protein import motor in green algae. Cell 2024:S0092-8674(24)00893-6. [PMID: 39197449 DOI: 10.1016/j.cell.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/31/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024]
Abstract
The protein import motor in chloroplasts plays a pivotal role in their biogenesis and homeostasis by driving the translocation of preproteins into chloroplasts. While the Ycf2-FtsHi complex serves as the import motor in land plants, its evolutionary conservation, specialization, and mechanisms across photosynthetic organisms are largely unexplored. Here, we isolated and determined the cryogenic electron microscopy (cryo-EM) structures of the native Ycf2-FtsHi complex from Chlamydomonas reinhardtii, uncovering a complex composed of up to 19 subunits, including multiple green-algae-specific components. The heterohexameric AAA+ ATPase motor module is tilted, potentially facilitating preprotein handover from the translocon at the inner chloroplast membrane (TIC) complex. Preprotein interacts with Ycf2-FtsHi and enhances its ATPase activity in vitro. Integrating Ycf2-FtsHi and translocon at the outer chloroplast membrane (TOC)-TIC supercomplex structures reveals insights into their physical and functional interplay during preprotein translocation. By comparing these findings with those from land plants, our study establishes a structural foundation for understanding the assembly, function, evolutionary conservation, and diversity of chloroplast protein import motors.
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Affiliation(s)
- Ke Liang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Xiechao Zhan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yuxin Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yi Yang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yanqiu Xie
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Zeyu Jin
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Xiaoyan Xu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Wenwen Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Yang Lu
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Research Center for the Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Sheng Zhang
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Research Center for the Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yilong Zou
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Research Center for the Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Jianping Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Zhen Yan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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232
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Almeida GDO, Cintra ACO, Silva TA, de Oliveira IS, Correia LIV, Torquato RJS, Ferreira Junior RS, Arantes EC, Sampaio SV. Moojecin: The first disintegrin from Bothrops moojeni venom and its antitumor activity in acute myeloid leukemia. Int J Biol Macromol 2024; 279:135066. [PMID: 39197621 DOI: 10.1016/j.ijbiomac.2024.135066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/01/2024]
Abstract
Disintegrins are a class of peptides found in snake venom that inhibit the activity of integrins, which are essential cell adhesion receptors in tumor progression and development. In this work, moojecin, a RGD disintegrin, was isolated from Bothrops moojeni snake venom, and its antitumor potential in acute myeloid leukemia (AML) HL-60 and THP-1 cells was characterized. The isolation was performed using a C18 reverse-phase column in two chromatographic steps, and its molecular mass is 7417.84 Da. N-terminal and de novo sequencing was performed to identify moojecin. Moojecin did not show cytotoxic or antiproliferative activity in THP-1 and HL-60 at tested concentrations, but it exhibited significant antimigratory activity in both cell lines, as well as inhibition of angiogenesis in the tube formation assay on Matrigel in a dose-dependent manner. A stronger interaction with integrin αVβ3 was shown in integrin interaction assays compared to α5β1, and the platelet aggregation assay indicated an IC50 of 5.039 μg/mL. Preliminary evaluation of disintegrin toxicity revealed no incidence of hemolysis or cytotoxic effects on peripheral blood mononuclear cells (PBMCs) across the tested concentrations. Thus, this is the first study to report the isolation, functional and structural characterization of a disintegrin from B. moojeni venom and bring a new perspective to assist in AML treatment.
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Affiliation(s)
- Gabriela de Oliveira Almeida
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Adélia Cristina Oliveira Cintra
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Thiago Abrahão Silva
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Isadora Sousa de Oliveira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | | | - Rui Seabra Ferreira Junior
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Eliane Candiani Arantes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Suely Vilela Sampaio
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
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233
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Takenoya M, Hiratsuka Y, Shimamura K, Ito S, Sasaki Y, Yajima S. Characterizing an amidase and its operon from actinomycete bacteria responsible for paraben catabolism. Biosci Biotechnol Biochem 2024; 88:1047-1054. [PMID: 38886122 DOI: 10.1093/bbb/zbae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
Hydrazidase from Microbacterium hydrocarbonoxydans was revealed to catalyze synthetic hydrazide compounds, enabling the bacteria to grow with them as a sole carbon source, but natural substrates have remained unknown. In this study, kinetic analyses of hydrazidase with parabens showed that the compounds can be substrates. Then, methylparaben induced gene expressions of the operon containing hydrazidase and ABC transporter, and the compound as a sole carbon source was able to grow the bacteria. Furthermore, homology search was carried out revealing that several actinomycetes possess hydrazidase homologs in the operon. Among those bacteria, an amidase from Pseudonocardia acaciae was subjected to a kinetic analysis and a structure determination revealing similar but not identical to those of hydrazidase. Since parabens are reported to exist in plants and soil, and several actinomycetes code the homologous operon, the enzymes with those operons may play a physiologically important role for bacterial survival with use of parabens.
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Affiliation(s)
- Mihoko Takenoya
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yoshiaki Hiratsuka
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Kaho Shimamura
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Shinsaku Ito
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yasuyuki Sasaki
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
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234
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Shankar S, Pan J, Yang P, Bian Y, Oroszlán G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J. Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance. Cell 2024:S0092-8674(24)00842-0. [PMID: 39197451 DOI: 10.1016/j.cell.2024.07.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/27/2024] [Accepted: 07/26/2024] [Indexed: 09/01/2024]
Abstract
DNA polymerases are important drug targets, and many structural studies have captured them in distinct conformations. However, a detailed understanding of the impact of polymerase conformational dynamics on drug resistance is lacking. We determined cryoelectron microscopy (cryo-EM) structures of DNA-bound herpes simplex virus polymerase holoenzyme in multiple conformations and interacting with antivirals in clinical use. These structures reveal how the catalytic subunit Pol and the processivity factor UL42 bind DNA to promote processive DNA synthesis. Unexpectedly, in the absence of an incoming nucleotide, we observed Pol in multiple conformations with the closed state sampled by the fingers domain. Drug-bound structures reveal how antivirals may selectively bind enzymes that more readily adopt the closed conformation. Molecular dynamics simulations and the cryo-EM structure of a drug-resistant mutant indicate that some resistance mutations modulate conformational dynamics rather than directly impacting drug binding, thus clarifying mechanisms that drive drug selectivity.
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Affiliation(s)
- Sundaresh Shankar
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Junhua Pan
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Biomedical Research Institute and School of Life and Health Sciences, Hubei University of Technology, Wuhan, Hubei, China
| | - Pan Yang
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yuemin Bian
- School of Medicine, Shanghai University, Shanghai, China; Center for the Development of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gábor Oroszlán
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zishuo Yu
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Purba Mukherjee
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - David J Filman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - James M Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mrinal Shekhar
- Center for the Development of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Donald M Coen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Integrated Solutions in Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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235
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Lynch EM, Hansen H, Salay L, Cooper M, Timr S, Kollman JM, Webb BA. Structural basis for allosteric regulation of human phosphofructokinase-1. Nat Commun 2024; 15:7323. [PMID: 39183237 PMCID: PMC11345425 DOI: 10.1038/s41467-024-51808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024] Open
Abstract
Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively. Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.
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Affiliation(s)
- Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Heather Hansen
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Lauren Salay
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison Cooper
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Stepan Timr
- Department of Computational Chemistry, J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Bradley A Webb
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, USA.
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236
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Tymecka D, Redkiewicz P, Lipiński PFJ, Misicka A. Peptidomimetic inhibitors of the VEGF-A 165/NRP-1 complex obtained by modification of the C-terminal arginine. Amino Acids 2024; 56:49. [PMID: 39181965 PMCID: PMC11344719 DOI: 10.1007/s00726-024-03411-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Inhibitors of the interaction between Neuropilin-1 (NRP-1) and Vascular Endothelial Growth Factor-A165 (VEGF-A165) hold significant promise as therapeutic and diagnostic agents directed against cancers overexpressing NRP-1. In our efforts in this field, a few series of strong and fairly stable peptide-like inhibitors of the general formula Lys(Har)1-Xaa2-Xaa3-Arg4 have been previously discovered. In the current work, we focused on Lys(Har)-Dap/Dab-Pro-Arg sequence. The aim was to examine whether replacing C-terminal Arg with its homologs and mimetics would yield more stable yet still potent inhibitors. Upon considering the results of modelling and other factors, ten novel analogues with Xaa4 = homoarginine (Har), 2-amino-4-guanidino-butyric acid (Agb), 2-amino-3-guanidino-propionic acid (Agp), citrulline (Cit), 4-aminomethyl-phenylalanine [Phe(4-CH2-NH2)] were designed, synthesized and evaluated. Two of the proposed modifications resulted in inhibitors with activity slightly lower [e.g. IC50 = 14.3 μM for Lys(Har)-Dab-Pro-Har and IC50 = 19.8 μM for Lys(Har)-Dab-Pro-Phe(4-CH2-NH2)] than the parent compounds [e.g. IC50 = 4.7 μM for Lys(Har)-Dab-Pro-Arg]. What was a surprise to us, the proteolytic stability depended more on position two of the sequence than on position four. The Dab2-analogues exhibited half-life times beyond 60 h. Our results build up the knowledge on the structural requirements that effective VEGF-A165/NRP-1 inhibitors should fulfil.
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Affiliation(s)
- Dagmara Tymecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
| | - Patrycja Redkiewicz
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
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Zheng L, Xu J, Wang W, Gao X, Zhao C, Guo W, Sun L, Cheng H, Meng F, Chen B, Sun W, Jia X, Zhou X, Wu K, Liu Z, Ding F, Liu N, Wang HW, Peng H. Self-assembled superstructure alleviates air-water interface effect in cryo-EM. Nat Commun 2024; 15:7300. [PMID: 39181869 PMCID: PMC11344764 DOI: 10.1038/s41467-024-51696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air-water interface during standard cryo-EM specimen preparation. The interaction of proteins with air-water interface will significantly impede the success of reconstruction and achievable resolution. Here, we highlight the critical role of impenetrable surfactant monolayers in passivating the air-water interface problems, and develop a robust effective method for high-resolution cryo-EM analysis, by using the superstructure GSAMs which comprises surfactant self-assembled monolayers (SAMs) and graphene membrane. The GSAMs works well in enriching the orientations and improving particle utilization ratio of multiple proteins, facilitating the 3.3-Å resolution reconstruction of a 100-kDa protein complex (ACE2-RBD), which shows strong preferential orientation using traditional specimen preparation protocol. Additionally, we demonstrate that GSAMs enables the successful determinations of small proteins (<100 kDa) at near-atomic resolution. This study expands the understanding of SAMs and provides a key to better control the interaction of protein with air-water interface.
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Affiliation(s)
- Liming Zheng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jie Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Weihua Wang
- China Academy of Aerospace Science and Innovation, Beijing, 100088, China
| | - Xiaoyin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Chao Zhao
- Faculty of Materials Science and Energy Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518055, China.
- Shenzhen Institute of Advanced Electronic Materials, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518103, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Weijun Guo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Luzhao Sun
- Beijing Graphene Institute (BGI), Beijing, 100095, China
| | - Hang Cheng
- Shuimu BioSciences Ltd, Beijing, 100089, China
| | - Fanhao Meng
- Shuimu BioSciences Ltd, Beijing, 100089, China
| | - Buhang Chen
- Beijing Graphene Institute (BGI), Beijing, 100095, China
| | - Weiyu Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Xia Jia
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiong Zhou
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Kai Wu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhongfan Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Beijing Graphene Institute (BGI), Beijing, 100095, China
| | - Feng Ding
- Faculty of Materials Science and Energy Engineering, Shenzhen University of Advanced Technology, Shenzhen, 518055, China
- Shenzhen Institute of Advanced Electronic Materials, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518103, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Biological Sciences, The University of Hong Kong, Hong Kong, 999077, China.
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Hailin Peng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Beijing Graphene Institute (BGI), Beijing, 100095, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
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238
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Margelevičius M. GTalign: spatial index-driven protein structure alignment, superposition, and search. Nat Commun 2024; 15:7305. [PMID: 39181863 PMCID: PMC11344802 DOI: 10.1038/s41467-024-51669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024] Open
Abstract
With protein databases growing rapidly due to advances in structural and computational biology, the ability to accurately align and rapidly search protein structures has become essential for biological research. In response to the challenge posed by vast protein structure repositories, GTalign offers an innovative solution to protein structure alignment and search-an algorithm that achieves optimal superposition at high speeds. Through the design and implementation of spatial structure indexing, GTalign parallelizes all stages of superposition search across residues and protein structure pairs, yielding rapid identification of optimal superpositions. Rigorous evaluation across diverse datasets reveals GTalign as the most accurate among structure aligners while presenting orders of magnitude in speedup at state-of-the-art accuracy. GTalign's high speed and accuracy make it useful for numerous applications, including functional inference, evolutionary analyses, protein design, and drug discovery, contributing to advancing understanding of protein structure and function.
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239
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Galvão GDF, Trefilio LM, Salvio AL, da Silva EV, Alves-Leon SV, Fontes-Dantas FL, de Souza JM. Comprehensive analysis of Novel mutations in CCM1/KRIT1 and CCM2/MGC4607 and their clinical implications in Cerebral Cavernous malformations. J Stroke Cerebrovasc Dis 2024; 33:107947. [PMID: 39181174 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Cerebral Cavernous Malformations (CCM) is a genetic disease characterized by vascular abnormalities in the brain and spinal cord, affecting 0.4-0.5 % of the population. We identified two novel pathogenic mutations, CCM1/KRIT1 c.811delT (p.Trp271GlyfsTer5) and CCM2/MGC4607 c.613_614insGG p.Glu205GlyfsTer31), which disrupt crucial protein domains and potentially alter disease progression. OBJECTIVE The study aims to comprehensively analyze a Brazilian cohort of CCM patients, integrating genetic, clinical, and structural aspects. Specifically, we sought to identify novel mutations within the CCM complex, and explore their potential impact on disease progression. METHODS We conducted a detailed examination of neuroradiological and clinical features in both symptomatic and asymptomatic CCM patients, performing genetic analyses through sequencing of the CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10 genes In silico structural predictions were carried out using PolyPhen-2, SIFT, and Human Genomics Community tools. Protein-protein interactions and docking analyses were explored using the STRING database. RESULTS Genetic analysis identifies 6 pathogenic mutations, 4 likely pathogenic, 1 variants of uncertain significance, and 7 unclassified mutations, including the novel mutations in CCM1 c.811delT and CCM2 c.613_614insGG. In silico structural analysis revealed significant alterations in protein structure, supporting their pathogenicity. Protein-protein interaction analysis indicated nuanced impacts on cellular processes. Clinically, we observed a broad spectrum of symptoms, including seizures and focal neurological deficits. However, no statistically significant differences were found in lesion burden, age of first symptom onset, or sex between the identified CCM1/KRIT1 and CCM2/MGC4607 mutations among all patients studied. CONCLUSION This study enhances the understanding of CCM by linking clinical variability, genetic mutations, and structural effects. The identification of these novel mutations opens new avenues for research and potential therapeutic strategies.
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Affiliation(s)
- Gustavo da Fontoura Galvão
- Universidade Federal do Estado do Rio de Janeiro, Laboratório de Neurociências Translacional, Programa de Pós-Graduação em Neurologia, Rio de Janeiro RJ, Brasil; Universidade Federal do Rio de Janeiro, Hospital Universitário Clementino Fraga Filho, Departamento de Neurocirurgia, Rio de Janeiro RJ, Brasil
| | - Luisa Menezes Trefilio
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brasil; Universidade Federal do Estado do Rio de Janeiro, Instituto Biomédico, Rio de Janeiro RJ, Brasil
| | - Andreza Lemos Salvio
- Universidade Federal do Estado do Rio de Janeiro, Laboratório de Neurociências Translacional, Programa de Pós-Graduação em Neurologia, Rio de Janeiro RJ, Brasil
| | - Elielson Veloso da Silva
- Universidade Federal do Estado do Rio de Janeiro, Laboratório de Neurociências Translacional, Programa de Pós-Graduação em Neurologia, Rio de Janeiro RJ, Brasil
| | - Soniza Vieira Alves-Leon
- Universidade Federal do Estado do Rio de Janeiro, Laboratório de Neurociências Translacional, Programa de Pós-Graduação em Neurologia, Rio de Janeiro RJ, Brasil; Universidade Federal do Rio de Janeiro, Hospital Universitário Clementino Fraga Filho, Departamento de Neurologia, Rio de Janeiro RJ, Brasil
| | - Fabrícia Lima Fontes-Dantas
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brasil.
| | - Jorge Marcondes de Souza
- Universidade Federal do Rio de Janeiro, Hospital Universitário Clementino Fraga Filho, Departamento de Neurocirurgia, Rio de Janeiro RJ, Brasil
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240
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Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C. Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer. SCIENCE ADVANCES 2024; 10:eadl1150. [PMID: 39167653 PMCID: PMC11338233 DOI: 10.1126/sciadv.adl1150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/15/2024] [Indexed: 08/23/2024]
Abstract
An outbreak of mpox virus in May 2022 has spread over 110 nonpandemic regions in the world, posing a great threat to global health. Mpox virus E5, a helicase-primase, plays an essential role in DNA replication, but the molecular mechanisms are elusive. Here, we report seven structures of mpox virus E5 in a double hexamer (DH) and six in single hexamer in different conformations, indicating a rotation mechanism for helicase and a coupling action for primase. The DH is formed through the interface of zinc-binding domains, and the central channel density indicates potential double-stranded DNA (dsDNA), which helps to identify dsDNA binding residues Arg249, Lys286, Lys315, and Lys317. Our work is important not only for understanding poxviral DNA replication but also for the development of novel therapeutics for serious poxviral infections including smallpox virus and mpox virus.
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Affiliation(s)
- Yunxia Xu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yaqi Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yuanyuan Zhang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Kaiting Gao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiaoying Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yaxue Yang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Danyang Li
- The Cryo-EM Center, Core facility of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Biao Yang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhengyu Zhang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Changjiang Dong
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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241
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Tan J, Zhang L, Zhou X, Han S, Zhou Y, Zhu Y. Structural basis of the bacterial flagellar motor rotational switching. Cell Res 2024:10.1038/s41422-024-01017-z. [PMID: 39179739 DOI: 10.1038/s41422-024-01017-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024] Open
Abstract
The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the switch complex for the rotational direction switching from counterclockwise to clockwise. However, the structural basis of the rotational switching and how the C ring is assembled have long remained elusive. Here, we present two high-resolution cryo-electron microscopy structures of the C ring-containing flagellar basal body-hook complex from Salmonella Typhimurium, which are in the default counterclockwise state and in a constitutively active CheY mutant-induced clockwise state, respectively. In both complexes, the C ring consists of four subrings, but is in two different conformations. The CheY proteins are bound into an open groove between two adjacent protomers on the surface of the middle subring of the C ring and interact with the FliG and FliM subunits. The binding of the CheY protein induces a significant upward shift of the C ring towards the MS ring and inward movements of its protomers towards the motor center, which eventually remodels the structures of the FliG subunits and reverses the orientations and surface electrostatic potential of the αtorque helices to trigger the counterclockwise-to-clockwise rotational switching. The conformational changes of the FliG subunits reveal that the stator units on the motor require a relocation process in the inner membrane during the rotational switching. This study provides unprecedented molecular insights into the rotational switching mechanism and a detailed overall structural view of the bacterial flagellar motors.
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Affiliation(s)
- Jiaxing Tan
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ling Zhang
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xingtong Zhou
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Siyu Han
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Yongqun Zhu
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Center for Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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242
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Ebrahim S, Ballesteros A, Zheng WS, Mukherjee S, Hu G, Weng WH, Montgomery JS, Agyemang Y, Cui R, Sun W, Krystofiak E, Foster MP, Sotomayor M, Kachar B. Transmembrane channel-like 4 and 5 proteins at microvillar tips are potential ion channels and lipid scramblases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609173. [PMID: 39229161 PMCID: PMC11370596 DOI: 10.1101/2024.08.22.609173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Microvilli-membrane bound actin protrusions on the surface of epithelial cells-are sites of critical processes including absorption, secretion, and adhesion. Increasing evidence suggests microvilli are mechanosensitive, but underlying molecules and mechanisms remain unknown. Here, we localize transmembrane channel-like proteins 4 and 5 (TMC4 and 5) and calcium and integrin binding protein 3 (CIB3) to microvillar tips in intestinal epithelial cells, near glycocalyx insertion sites. We find that TMC5 colocalizes with CIB3 in cultured cells and that a TMC5 fragment forms a complex with CIB3 in vitro. Homology and AlphaFold2 models reveal a putative ion permeation pathway in TMC4 and 5, and molecular dynamics simulations predict both proteins can conduct ions and perform lipid scrambling. These findings raise the possibility that TMC4 and 5 interact with CIB3 at microvillar tips to form a mechanosensitive complex, akin to TMC1 and 2, and CIB2 and 3, within the mechanotransduction channel complex at the tips of inner ear stereocilia.
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Affiliation(s)
- Seham Ebrahim
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Angela Ballesteros
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - W Sharon Zheng
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Shounak Mukherjee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Gaizun Hu
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Wei-Hsiang Weng
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yaw Agyemang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Runjia Cui
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Willy Sun
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
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243
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Wang X, Nyenhuis SB, Bernstein HD. The translocation assembly module (TAM) catalyzes the assembly of bacterial outer membrane proteins in vitro. Nat Commun 2024; 15:7246. [PMID: 39174534 PMCID: PMC11341756 DOI: 10.1038/s41467-024-51628-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
The translocation and assembly module (TAM) has been proposed to play a crucial role in the assembly of a small subset of outer membrane proteins (OMPs) in Proteobacteria based on experiments conducted in vivo using tamA and tamB mutant strains and in vitro using biophysical methods. TAM consists of an OMP (TamA) and a periplasmic protein that is anchored to the inner membrane by a single α helix (TamB). Here we examine the function of the purified E. coli complex in vitro after reconstituting it into proteoliposomes. We find that TAM catalyzes the assembly of four model OMPs nearly as well as the β-barrel assembly machine (BAM), a universal heterooligomer that contains a TamA homolog (BamA) and that catalyzes the assembly of almost all E. coli OMPs. Consistent with previous results, both TamA and TamB are required for significant TAM activity. Our study provides direct evidence that TAM can function as an independent OMP insertase and describes a new method to gain insights into TAM function.
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Affiliation(s)
- Xu Wang
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah B Nyenhuis
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harris D Bernstein
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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244
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Jungholm O, Trkulja C, Moche M, Srinivasa SP, Christakopoulou MN, Davidson M, Reymer A, Jardemark K, Fogaça RL, Ashok A, Jeffries G, Ampah-Korsah H, Strandback E, Andréll J, Nyman T, Nouairia G, Orwar O. Novel druggable space in human KRAS G13D discovered using structural bioinformatics and a P-loop targeting monoclonal antibody. Sci Rep 2024; 14:19656. [PMID: 39179604 PMCID: PMC11344056 DOI: 10.1038/s41598-024-70217-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
KRAS belongs to a family of small GTPases that act as binary switches upstream of several signalling cascades, controlling proliferation and survival of cells. Mutations in KRAS drive oncogenesis, especially in pancreatic, lung, and colorectal cancers (CRC). Although historic attempts at targeting mutant KRAS with small molecule inhibitors have proven challenging, there are recent successes with the G12C, and G12D mutations. However, clinically important RAS mutations such as G12V, G13D, Q61L, and A146T, remain elusive drug targets, and insights to their structural landscape is of critical importance to develop novel, and effective therapeutic concepts. We present a fully open, P-loop exposing conformer of KRAS G13D by X-ray crystallography at 1.4-2.4 Å resolution in Mg2+-free phosphate and malonate buffers. The G13D conformer has the switch-I region displaced in an upright position leaving the catalytic core fully exposed. To prove that this state is druggable, we developed a P-loop-targeting monoclonal antibody (mAb). The mAb displayed high-affinity binding to G13D and was shown using high resolution fluorescence microscopy to be spontaneously taken up by G13D-mutated HCT 116 cells (human CRC derived) by macropinocytosis. The mAb inhibited KRAS signalling in phosphoproteomic and genomic studies. Taken together, the data propose novel druggable space of G13D that is reachable in the cellular context. It is our hope that these findings will stimulate attempts to drug this fully open state G13D conformer using mAbs or other modalities.
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Affiliation(s)
- Oscar Jungholm
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Carolina Trkulja
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
- Fluicell AB, Flöjelbergsgatan 8C, 431 37, Mölndal, Sweden
| | - Martin Moche
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Sreesha P Srinivasa
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
- Manipal Center for Biotherapeutics Research, Manipal Academy of Higher Education, Manipal, India
| | | | - Max Davidson
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
| | - Anna Reymer
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Kent Jardemark
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | | | | | - Gavin Jeffries
- Fluicell AB, Flöjelbergsgatan 8C, 431 37, Mölndal, Sweden
| | - Henry Ampah-Korsah
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Emilia Strandback
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Juni Andréll
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Tomas Nyman
- Protein Science Facility, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Ghada Nouairia
- Department of Medicine Huddinge, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Owe Orwar
- Oblique Therapeutics AB, 41346, Gothenburg, Sweden.
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.
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245
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Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y. Transcription elongation of the plant RNA polymerase IV is prone to backtracking. SCIENCE ADVANCES 2024; 10:eadq3087. [PMID: 39178250 PMCID: PMC11343019 DOI: 10.1126/sciadv.adq3087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/22/2024] [Indexed: 08/25/2024]
Abstract
RNA polymerase IV (Pol IV) forms a complex with RNA-directed RNA polymerase 2 (RDR2) to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In the "backtracking-triggered RNA channeling" model, Pol IV backtracks and delivers its transcript's 3' terminus to RDR2, which synthesizes dsRNA. However, the mechanisms underlying Pol IV backtracking and RNA protection from cleavage are unclear. Here, we determined cryo-electron microscopy structures of Pol IV elongation complexes at four states of its nucleotide addition cycle (NAC): posttranslocation, guanosine triphosphate-bound, pretranslocation, and backtracked states. The structures reveal that Pol IV maintains an open DNA cleft and kinked bridge helix in all NAC states, loosely interacts with the nucleoside triphosphate substrate, and barely contacts proximal backtracked nucleotides. Biochemical data indicate that Pol IV is inefficient in forward translocation and RNA cleavage. These findings suggest that Pol IV transcription elongation is prone to backtracking and incapable of RNA hydrolysis, ensuring efficient dsRNA production by Pol IV-RDR2.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongwei Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhanxi Gu
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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246
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Gan N, Zeng W, Han Y, Chen Q, Jiang Y. Structural mechanism of proton conduction in otopetrin proton channel. Nat Commun 2024; 15:7250. [PMID: 39179582 PMCID: PMC11343839 DOI: 10.1038/s41467-024-51803-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
The otopetrin (OTOP) proteins were recently characterized as extracellular proton-activated proton channels. Several recent OTOP channel structures demonstrated that the channels form a dimer with each subunit adopting a double-barrel architecture. However, the structural mechanisms underlying some basic functional properties of the OTOP channels remain unresolved, including extracellular pH activation, proton conducting pathway, and rapid desensitization. In this study, we performed structural and functional characterization of the Caenorhabditis elegans OTOP8 (CeOTOP8) and mouse OTOP2 (mOTOP2) and illuminated a set of conformational changes related to the proton-conducting process in OTOP. The structures of CeOTOP8 reveal the conformational change at the N-terminal part of TM12 that renders the channel in a transiently proton-transferring state, elucidating an inter-barrel, Glu/His-bridged proton passage within each subunit. The structures of mOTOP2 reveal the conformational change at the N-terminal part of TM6 that exposes the central glutamate to the extracellular solution for protonation. In addition, the structural comparison between CeOTOP8 and mOTOP2, along with the structure-based mutagenesis, demonstrates that an inter-subunit movement at the OTOP channel dimer interface plays a central role in regulating channel activity. Combining the structural information from both channels, we propose a working model describing the multi-step conformational changes during the proton conducting process.
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Affiliation(s)
- Ninghai Gan
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weizhong Zeng
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qingfeng Chen
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Youxing Jiang
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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247
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Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Côté J, Nogales E. Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Science 2024; 385:eadl5816. [PMID: 39088653 DOI: 10.1126/science.adl5816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/25/2024] [Accepted: 06/25/2024] [Indexed: 08/03/2024]
Abstract
The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.
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Affiliation(s)
- Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, USA
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Arul Banerjea
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Amélie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Jean-Philippe Lambert
- Endocrinology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | | | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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248
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Shree M, Vaishnav J, Gurudayal, Ampapathi RS. In-silico assessment of novel peptidomimetics inhibitor targeting STAT3 and STAT4 N-terminal domain dimerization: A comprehensive study using molecular docking, molecular dynamics simulation, and binding free energy analysis. Biochem Biophys Res Commun 2024; 733:150584. [PMID: 39208642 DOI: 10.1016/j.bbrc.2024.150584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/04/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Dysregulation in Janus kinase-Signal Transducer and Activation of Transcription (JAK-STAT) pathway is closely linked to various cancer types. The N-terminal domain (NTD) of STAT proteins, upon dimerization, assumes a multifaceted role with remarkable adaptability in mediating interactions between proteins. Consequently, the strategic targeting of the N-terminal domain of STATs has emerged as a promising tactic for disrupting dimerization and impeding the translocation of STAT proteins. In this study, we have deployed an integrated in-silico methodology to rationally design Peptidomimetic foldamers as inhibitors of the N-terminal domains of STAT3 and STAT4, with the objective of disrupting protein dimerization. Consequently, we have judiciously designed a series of peptidomimetics that encompass β3-amino acids, bearing side chains that mimic the residues within interface II of the dimeric structures of the NTDs. Employing molecular docking techniques; we have assessed the binding affinity of these designed peptidomimetics toward both the NTDs. Furthermore, we have conducted an evaluation of the stability and conformational alterations within the docked complexes over an extensive Molecular Dynamics, subsequently computing the binding free energy utilizing MM/PBSA calculations. Our findings unequivocally demonstrate that the peptidomimetic foldamers we have devised (Peptide-A, Peptide-B, and Peptide-C) exhibit a propensity to bind to and impede the dimerization process of the NTDs of both STAT3 and STAT4. These outcomes serve to underscore the potential of these meticulously designed peptidomimetics as potential candidates meriting further exploration in the realm of cancer prevention and management.
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Affiliation(s)
- Megha Shree
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Jayanti Vaishnav
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India
| | - Gurudayal
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India
| | - Ravi Sankar Ampapathi
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
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249
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Saha S, Khanppnavar B, Maharana J, Kim H, Carino CMC, Daly C, Houston S, Sharma S, Zaidi N, Dalal A, Mishra S, Ganguly M, Tiwari D, Kumari P, Jhingan GD, Yadav PN, Plouffe B, Inoue A, Chung KY, Banerjee R, Korkhov VM, Shukla AK. Molecular mechanism of distinct chemokine engagement and functional divergence of the human Duffy antigen receptor. Cell 2024; 187:4751-4769.e25. [PMID: 39089252 DOI: 10.1016/j.cell.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 04/13/2024] [Accepted: 07/03/2024] [Indexed: 08/03/2024]
Abstract
The Duffy antigen receptor is a seven-transmembrane (7TM) protein expressed primarily at the surface of red blood cells and displays strikingly promiscuous binding to multiple inflammatory and homeostatic chemokines. It serves as the basis of the Duffy blood group system in humans and also acts as the primary attachment site for malarial parasite Plasmodium vivax and pore-forming toxins secreted by Staphylococcus aureus. Here, we comprehensively profile transducer coupling of this receptor, discover potential non-canonical signaling pathways, and determine the cryoelectron microscopy (cryo-EM) structure in complex with the chemokine CCL7. The structure reveals a distinct binding mode of chemokines, as reflected by relatively superficial binding and a partially formed orthosteric binding pocket. We also observe a dramatic shortening of TM5 and 6 on the intracellular side, which precludes the formation of the docking site for canonical signal transducers, thereby providing a possible explanation for the distinct pharmacological and functional phenotype of this receptor.
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Affiliation(s)
- Shirsha Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Basavraj Khanppnavar
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Heeryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Carlo Marion C Carino
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Carole Daly
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Shane Houston
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Saloni Sharma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nashrah Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Annu Dalal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Divyanshu Tiwari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Poonam Kumari
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | | | - Prem N Yadav
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Bianca Plouffe
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
| | - Volodymyr M Korkhov
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
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Jeong J, Park J, Young Mo G, Shin J, Cho Y. Structural Basis for the Recognition of GPRC5D by Talquetamab, a Bispecific Antibody for Multiple Myeloma. J Mol Biol 2024; 436:168748. [PMID: 39181182 DOI: 10.1016/j.jmb.2024.168748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
Multiple myeloma (MM) is a complex hematological malignancy characterized by abnormal antibody production from plasma cells. Despite advances in the treatment, many patients experience disease relapse or become refractory to treatment. G-protein-coupled receptor class C group 5 member D (GPRC5D), an orphan GPCR predominantly expressed in MM cells, is emerging as a promising target for MM immunotherapy. Talquetamab, a Food and Drug Administration-approved T-cell-directing bispecific antibody developed for treatment of MM, targets GPRC5D. Here, we elucidate the structure of GPRC5D complexed with the Fab fragment of talquetamab, using cryo-electron microscopy, providing the basis for recognition of GPRC5D by the bispecific antibody. GPRC5D forms a symmetric homodimer with the interface between transmembrane helix (TM) 4 of one protomer and TM4/5 of the other protomer. A single talquetamab Fab interacts with the GPRC5D dimer with its orientation toward the dimer interface. All six complementarity-determining regions of talquetamab engage with extracellular loops and TM3/5/7. In particular, the side-chain of an arginine residue from the antibody penetrates into a shallow pocket on the extracellular surface of GPRC5D. The structure offers insights for optimizing antibody design against GPRC5D for relapsed or refractory MM therapy.
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Affiliation(s)
- Jihong Jeong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Junhyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Geun Young Mo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Jinwoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Yunje Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea; Institute of Convergence Science, Yonsei University, Seoul 166-20, South Korea.
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