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Verzino SJ, Priyev SA, Estrada VAS, Crowley GX, Rutkowski A, Lam AC, Nazginov ES, Kotemelo P, Bacelo A, Sukhram DT, Vázquez FX, Juárez JF. Expanding salivary biomarker detection by creating a synthetic neuraminic acid sensor via chimeragenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598939. [PMID: 38915506 PMCID: PMC11195194 DOI: 10.1101/2024.06.13.598939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Accurate and timely diagnosis of oral squamous cell carcinoma (OSCC) is crucial in preventing its progression to advanced stages with a poor prognosis. As such, the construction of sensors capable of detecting previously established disease biomarkers for the early and non-invasive diagnosis of this and many other conditions has enormous therapeutic potential. In this work, we apply synthetic biology techniques for the development of a whole-cell biosensor (WCB) that leverages the physiology of engineered bacteria in vivo to promote the expression of an observable effector upon detection of a soluble molecule. To this end, we have constructed a bacterial strain expressing a novel chimeric transcription factor (Sphnx) for the detection of N-acetylneuraminic acid (Neu5Ac), a salivary biomolecule correlated with the onset of OSCC. This WCB serves as the proof-of-concept of a platform that can eventually be applied to clinical screening panels for a multitude of oral and systemic medical conditions whose biomarkers are present in saliva.
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2
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Dinic J, Tirrell MV. Effects of Charge Sequence Pattern and Lysine-to-Arginine Substitution on the Structural Stability of Bioinspired Polyampholytes. Biomacromolecules 2024; 25:2838-2851. [PMID: 38567844 PMCID: PMC11094733 DOI: 10.1021/acs.biomac.4c00002] [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: 01/01/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 05/14/2024]
Abstract
A comprehensive study focusing on the combined influence of the charge sequence pattern and the type of positively charged amino acids on the formation of secondary structures in sequence-specific polyampholytes is presented. The sequences of interest consisting exclusively of ionizable amino acids (lysine, K; arginine, R; and glutamic acid, E) are (EKEK)5, (EKKE)5, (ERER)5, (ERRE)5, and (EKER)5. The stability of the secondary structure was examined at three pH values in the presence of urea and NaCl. The results presented here underscore the combined prominent effects of the charge sequence pattern and the type of positively charged monomers on secondary structure formation. Additionally, (ERRE)5 readily aggregated across a wide range of pH. In contrast, sequences with the same charge pattern, (EKKE)5, as well as the sequences with the equivalent amino acid content, (ERER)5, exhibited no aggregate formation under equivalent pH and concentration conditions.
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Affiliation(s)
- Jelena Dinic
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Center
for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Matthew V. Tirrell
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Center
for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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3
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Gupta MN, Uversky VN. Reexamining the diverse functions of arginine in biochemistry. Biochem Biophys Res Commun 2024; 705:149731. [PMID: 38432110 DOI: 10.1016/j.bbrc.2024.149731] [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: 12/24/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Arginine in a free-state and as part of peptides and proteins shows distinct tendency to form clusters. In free-form, it has been found useful in cryoprotection, as a drug excipient for both solid and liquid formulations, as an aggregation suppressor, and an eluent in protein chromatography. In many cases, the mechanisms by which arginine acts in all these applications is either debatable or at least continues to attract interest. It is quite possible that arginine clusters may be involved in many such applications. Furthermore, it is possible that such clusters are likely to behave as intrinsically disordered polypeptides. These considerations may help in understanding the roles of arginine in diverse applications and may even lead to better strategies for using arginine in different situations.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya Str., 7, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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4
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Curcic J, Dinic M, Novovic K, Vasiljevic Z, Kojic M, Jovcic B, Malesevic M. A novel thermostable YtnP lactonase from Stenotrophomonas maltophilia inhibits Pseudomonas aeruginosa virulence in vitro and in vivo. Int J Biol Macromol 2024; 264:130421. [PMID: 38423425 DOI: 10.1016/j.ijbiomac.2024.130421] [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: 08/25/2023] [Revised: 01/18/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Infections caused by multidrug-resistant pathogens are one of the biggest challenges facing the healthcare system today. Quorum quenching (QQ) enzymes have the potential to be used as innovative enzyme-based antivirulence therapeutics to combat infections caused by multidrug-resistant pathogens. The main objective of this research was to describe the novel YtnP lactonase derived from the clinical isolate Stenotrophomonas maltophilia and to investigate its antivirulence potential against multidrug-resistant Pseudomonas aeruginosa MMA83. YtnP lactonase, the QQ enzyme, belongs to the family of metallo-β-lactamases. The recombinant enzyme has several advantageous biotechnological properties, such as high thermostability, activity in a wide pH range, and no cytotoxic effect. High-performance liquid chromatography analysis revealed the activity of recombinant YtnP lactonase toward a wide range of N-acyl-homoserine lactones (AHLs), quorum sensing signaling molecules, with a higher preference for long-chain AHLs. Recombinant YtnP lactonase was shown to inhibit P. aeruginosa MMA83 biofilm formation, induce biofilm decomposition, and reduce extracellular virulence factors production. Moreover, the lifespan of MMA83-infected Caenorhabditis elegans was prolonged with YtnP lactonase treatment. YtnP lactonase showed synergistic inhibitory activity in combination with gentamicin and acted additively with meropenem against MMA83. The described properties make YtnP lactonase a promising therapeutic candidate for the development of next-generation antivirulence agents.
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Affiliation(s)
- Jovana Curcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Miroslav Dinic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Katarina Novovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Zorica Vasiljevic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Radoja Dakića 8, 11070 Belgrade, Serbia
| | - Milan Kojic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; Institute of Virology, Vaccines and Sera "Torlak", Vojvode Stepe 448, 11042 Belgrade, Serbia
| | - Branko Jovcic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Milka Malesevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia.
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5
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Hanif N, Sari S. Discovery of novel IDO1/TDO2 dual inhibitors: a consensus Virtual screening approach with molecular dynamics simulations, and binding free energy analysis. J Biomol Struct Dyn 2024:1-17. [PMID: 38498355 DOI: 10.1080/07391102.2024.2329302] [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: 05/30/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
The pursuit of effective cancer immunotherapy drugs remains challenging, with overexpression of indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase 2 (TDO2) allowing cancer cells to evade immune attacks. While several IDO1 inhibitors have undergone clinical testing, only three dual IDO1/TDO2 inhibitors have reached human trials. Hence, this study focuses on identifying novel IDO1/TDO2 dual inhibitors through consensus structure-based virtual screening (SBVS). ZINC15 natural products library was refined based on molecular descriptors, and the selected compounds were docked to the holo form IDO1 and TDO2 using two different software programs and ranked according to their consensus docking scores. The top-scoring compounds underwent in silico evaluations for pharmacokinetics, toxicity, CYP3A4 affinity, molecular dynamics (MD) simulations, and MM-GBSA binding free energy calculations. Five compounds (ZINC00000079405/10, ZINC00004028612/11, ZINC00013380497/12, ZINC00014613023/13, and ZINC00103579819/14) were identified as potential IDO1/TDO2 dual inhibitors due to their high consensus docking scores, key residue interactions with the enzymes, favorable pharmacokinetics, and avoidance of CYP3A4 binding. MD simulations of the top three hits with IDO1 indicated conformational changes and compactness, while MM-GBSA analysis revealed strong binding free energy for compounds 10 (ΔG: -20.13 kcal/mol) and 11 (ΔG: -16.22 kcal/mol). These virtual hits signify a promising initial step in identifying candidates as supplementary therapeutics to immune checkpoint inhibitors in cancer treatment. Their potential to deliver potent dual inhibition of IDO1/TDO2, along with safety and favorable pharmacokinetics, makes them compelling. Validation through in vitro and in vivo assays should be conducted to confirm their activity, selectivity, and preclinical potential as holo IDO1/TDO2 dual inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Naufa Hanif
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Sekip Utara II, Yogyakarta, Indonesia
| | - Suat Sari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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6
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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7
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Suhail M. Biophysical chemistry behind sickle cell anemia and the mechanism of voxelotor action. Sci Rep 2024; 14:1861. [PMID: 38253605 PMCID: PMC10803371 DOI: 10.1038/s41598-024-52476-8] [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: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024] Open
Abstract
Sickle cell anemia disease has been a great challenge to the world in the present situation. It occurs only due to the polymerization of sickle hemoglobin (HbS) having Pro-Val-Glu typed mutation, while the polymerization does not occur in normal hemoglobin (HbA) having Pro-Glu-Glu peptides. It is also well confirmed that the oxygenated HbS (OHbS) does not participate in the polymerization, while the deoxygenated HbS (dHbS) does, which causes the shape of red blood cells sickled. After polymerization, the blood has a low oxygen affinity. Keeping this fact into consideration, only those drugs are being synthesized that stabilize the OHbS structure so that the polymerization of HbS can be stopped. The literature data showed no systematic description of the changes occurring during the OHbS conversion to dHbS before polymerization. Hence, an innovative reasonable study between HbA and HbS, when they convert into their deoxygenated forms, was done computationally. In this evaluation, physiochemical parameters in HbA/HbS before and after deoxygenation were studied and compared deeply. The computationally collected data was used to understand the abnormal behaviour of dHbS arising due to the replacement of Glu6 with Val6. Consequently, during the presented computational study, the changes occurring in HbS were found opposite/abnormal as compared to HbA after the deoxygenation of both. The mechanism of Voxelotor (GBT-440) action to stop the HbS polymerization was also explained with the help of computationally collected data. Besides, a comparative study between GBT-440 and another suggested drug was also done to know their antisickling strength. Additionally, the effect of pH, CO, CO2, and 2,3-diphosphoglycerate (2,3-DPG) on HbS structure was also studied computationally.
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Affiliation(s)
- Mohd Suhail
- Department of Chemistry, Siddhartha (PG) College, Aakhlor Kheri, Deoband (Saharanpur), Uttar Pradesh, 247554, India.
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8
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Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [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: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
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Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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9
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Vásquez-Suárez A, Ortega L, González-Chavarría I, Valenzuela A, Muñoz-Flores C, Altamirano C, Acosta J, Toledo JR. Agonistic effect of peptides derived from a truncated HMGB1 acidic tail sequence in TLR5 from Salmo salar. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109219. [PMID: 37952850 DOI: 10.1016/j.fsi.2023.109219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Based on the structural knowledge of TLR5 surface and using blind docking platforms, peptides derived from a truncated HMGB1 acidic tail from Salmo salar was designed as TLR5 agonistic. Additionally, a template peptide with the native N-terminal of the acidic tail sequence as a reference was included (SsOri). Peptide binding poses complexed on TLR5 ectodomain model from each algorithm were filtrated based on docking scoring functions and predicted theoretical binding affinity of the complex. The best peptides, termed 6WK and 5LWK, were selected for chemical synthesis and experimental functional assay. The agonist activity by immunoblotting and immunocytochemistry was determined following the NF-κBp65 phosphorylation (p-NF-κBp65) and the nuclear translocation of the NF-κBp65 subunit from the cytosol, respectively. HeLa cells stably expressing a S. salar TLR5 chimeric form (TLR5c7) showed increased p-NF-κBp65 levels regarding extracts from flagellin-treated cells. No statistically significant differences (p > 0.05) were found in the detected p-NF-κBp65 levels between cellular extracts treated with peptides or flagellin by one-way ANOVA. The image analysis of NF-κBp65 immunolabeled cells obtained by confocal microscopy showed increased nuclear NF-κBp65 co-localization in cells both 5LWK and flagellin stimulated, while 6WK and SsOri showed less effect on p65 nuclear translocation (p < 0.05). Also, an increased transcript expression profile of proinflammatory cytokines such as TNFα, IL-1β, and IL-8 in HKL cells isolated from Salmo salar was evidenced in 5LWK - stimulated by RT-PCR analysis. Overall, the result indicates the usefulness of novel peptides as a potential immunostimulant in S. salar.
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Affiliation(s)
- Aleikar Vásquez-Suárez
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Leonardo Ortega
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Iván González-Chavarría
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Ariel Valenzuela
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Carolina Muñoz-Flores
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Claudia Altamirano
- Laboratorio de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, 2362803, Valparaíso, Chile
| | - Jannel Acosta
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Jorge R Toledo
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile.
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10
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Roy C, Islam RNU, Banerjee S, Bandyopadhyay AK. Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one. J Biomol Struct Dyn 2023:1-16. [PMID: 38147414 DOI: 10.1080/07391102.2023.2295972] [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: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chittran Roy
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
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11
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Yuan HK, Li B, Wu L, Wang XL, Lv ZY, Liu Z, Xu Z, Lu J, Chen CT, Yang YQ, Zhu W, Yin LM. Discovery of zolinium TSG1180 as a novel agonist of transgelin-2 for treating asthma. Biomed Pharmacother 2023; 167:115556. [PMID: 37778269 DOI: 10.1016/j.biopha.2023.115556] [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: 12/27/2022] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023] Open
Abstract
Asthma is a complex and heterogeneous respiratory disease that causes serious social and economic burdens. Current drugs such as β2-agonists cannot fully control asthma. Our previous study found that Transgelin-2 is a potential target for treating asthmatic pulmonary resistance. Herein, we discovered a zolinium compound, TSG1180, that showed a strong interaction with Transgelin-2. The equilibrium dissociation constants (KD) of TSG1180 to Transgelin-2 were determined to be 5.363 × 10-6 and 9.81 × 10-6 M by surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). Cellular thermal shift assay (CETSA) results showed that the thermal stability of Transgelin-2 increased after coincubation of TSG1180 with lysates of airway smooth muscle cells (ASMCs). Molecular docking showed that Arg39 may be the key residue for the binding. Then, the SPR result showed that the binding affinity of TSG1180 to Transgelin-2 mutant (R39E) was decreased by 1.69-fold. Real time cell analysis (RTCA) showed that TSG1180 treatment could relax ASMCs by 19 % (P < 0.05). Once Transgelin-2 was inhibited, TSG1180 cannot induce a relaxation effect, suggesting that the relaxation effect was specifically mediated by Transgelin-2. In vivo study showed TSG1180 effectively reduced pulmonary resistance by 64 % in methacholine-induced mice model (P < 0.05). Furthermore, the phosphorylation of Ezrin at T567 was increased by 8.06-fold, the phosphorylation of ROCK at Y722 was reduced by 38 % and the phosphorylation of RhoA at S188 was increased by 52 % after TSG1180 treatment. These results suggested that TSG1180 could be a Transgelin-2 agonist for further optimization and development as an anti-asthma drug.
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Affiliation(s)
- Hong-Kai Yuan
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Bo Li
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leyun Wu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue-Ling Wang
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Zhi-Ying Lv
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Zhikai Liu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Lu
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Cai-Tao Chen
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China
| | - Yong-Qing Yang
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China.
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lei-Miao Yin
- Yueyang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200030, China.
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12
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Wu Q, Xu C, Shi W, Li L, Zhang H, Liu T, Fan J, Cui L, Li J. Suitable carrier protein and linker peptide significantly increase the secretory expression of human lysozyme in Aspergillus niger. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1677-1680. [PMID: 37661695 PMCID: PMC10577450 DOI: 10.3724/abbs.2023153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/06/2023] [Indexed: 09/05/2023] Open
Affiliation(s)
- Qi Wu
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Can Xu
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Wei Shi
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Lifang Li
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Hui Zhang
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Tianqi Liu
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Junbo Fan
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Lingmeng Cui
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Jie Li
- />College of Life SciencesNortheast Agricultural UniversityHarbin150030China
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13
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Leth JM, Newcombe EA, Grønnemose AL, Jørgensen JT, Qvist K, Clausen AS, Knudsen LBS, Kjaer A, Kragelund BB, Jørgensen TJD, Ploug M. Targeted imaging of uPAR expression in vivo with cyclic AE105 variants. Sci Rep 2023; 13:17248. [PMID: 37821532 PMCID: PMC10567728 DOI: 10.1038/s41598-023-43934-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: 08/17/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
A comprehensive literature reports on the correlation between elevated levels of urokinase-type plasminogen activator receptor (uPAR) and the severity of diseases with chronic inflammation including solid cancers. Molecular imaging is widely used as a non-invasive method to locate disease dissemination via full body scans and to stratify patients for targeted treatment. To date, the only imaging probe targeting uPAR that has reached clinical phase-II testing relies on a high-affinity 9-mer peptide (AE105), and several studies by positron emission tomography (PET) scanning or near-infra red (NIR) fluorescence imaging have validated its utility and specificity in vivo. While our previous studies focused on applying various reporter groups, the current study aims to improve uPAR-targeting properties of AE105. We successfully stabilized the small uPAR-targeting core of AE105 by constraining its conformational landscape by disulfide-mediated cyclization. Importantly, this modification mitigated the penalty on uPAR-affinity typically observed after conjugation to macrocyclic chelators. Cyclization did not impair tumor targeting efficiency of AE105 in vivo as assessed by PET imaging and a trend towards increased tracer uptake was observed. In future studies, we predict that this knowledge will aid development of new fluorescent AE105 derivatives with a view to optical imaging of uPAR to assist precision guided cancer surgery.
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Affiliation(s)
- Julie Maja Leth
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Estella Anne Newcombe
- Structural Biology and NMR Laboratory, Copenhagen N, Denmark
- REPIN, Copenhagen N, Denmark
- The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anne Louise Grønnemose
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Jesper Tranekjær Jørgensen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Katrine Qvist
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Anne Skovsbo Clausen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Line Bruhn Schneider Knudsen
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology and Nuclear Medicine and Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Birthe Brandt Kragelund
- Structural Biology and NMR Laboratory, Copenhagen N, Denmark
- REPIN, Copenhagen N, Denmark
- The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Michael Ploug
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, 2200, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen N, Denmark.
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14
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Biswal S, Gupta PSS, Panda SK, Bhat HR, Rana MK. Insights into the binding mechanism of ascorbic acid and violaxanthin with violaxanthin de-epoxidase (VDE) and chlorophycean violaxanthin de-epoxidase (CVDE) enzymes. PHOTOSYNTHESIS RESEARCH 2023; 156:337-354. [PMID: 36847893 DOI: 10.1007/s11120-023-01006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/11/2023] [Indexed: 05/23/2023]
Abstract
Photosynthetic organisms have evolved to work under low and high lights in photoprotection, acting as a scavenger of reactive oxygen species. The light-dependent xanthophyll cycle involved in this process is performed by a key enzyme (present in the thylakoid lumen), Violaxanthin De-Epoxidase (VDE), in the presence of violaxanthin (Vio) and ascorbic acid substrates. Phylogenetically, VDE is found to be connected with an ancestral enzyme Chlorophycean Violaxanthin De-Epoxidase (CVDE), present in the green algae on the stromal side of the thylakoid membrane. However, the structure and functions of CVDE were not known. In search of functional similarities involving this cycle, the structure, binding conformation, stability, and interaction mechanism of CVDE are explored with the two substrates compared to VDE. The structure of CVDE was determined by homology modeling and validated. In silico docking (of first-principles optimized substrates) revealed it has a larger catalytic domain than VDE. A thorough analysis of the binding affinity and stability of four enzyme-substrate complexes is performed by computing free energies and their decomposition, the root-mean-square deviation (RMSD) and fluctuation (RMSF), the radius of gyration, salt bridge, and hydrogen bonding interactions in molecular dynamics. Based on these, violaxanthin interacts with CVDE to a similar extent as that of VDE. Hence, its role is expected to be the same for both enzymes. On the contrary, ascorbic acid has a weaker interaction with CVDE than VDE. Given these interactions drive epoxidation or de-epoxidation in the xanthophyll cycle, it immediately discerns that either ascorbic acid does not participate in de-epoxidation or a different cofactor is necessary as CVDE has a weaker interaction with ascorbic acid than VDE.
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Affiliation(s)
- Satyaranjan Biswal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, 760010, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, Maharashtra-411044, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, 760010, India
| | - Haamid Rasool Bhat
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, 760010, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, 760010, India.
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15
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Umitaibatin R, Harisna AH, Jauhar MM, Syaifie PH, Arda AG, Nugroho DW, Ramadhan D, Mardliyati E, Shalannanda W, Anshori I. Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein. Vaccines (Basel) 2023; 11:vaccines11020399. [PMID: 36851275 PMCID: PMC9964839 DOI: 10.3390/vaccines11020399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
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Affiliation(s)
- Ramadhita Umitaibatin
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Azza Hanif Harisna
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Putri Hawa Syaifie
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Dwi Wahyu Nugroho
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | - Donny Ramadhan
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Wervyan Shalannanda
- Department of Telecommunication Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
- Correspondence:
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16
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Singh NK, Agarwal M, Radhakrishna M. Understanding the helical stability of charged peptides. Proteins 2023; 91:268-276. [PMID: 36121161 DOI: 10.1002/prot.26427] [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: 07/05/2022] [Revised: 08/12/2022] [Accepted: 09/06/2022] [Indexed: 01/10/2023]
Abstract
Cationic helical peptides play a crucial role in applications such as anti-microbial and anticancer activity. The activity of these peptides directly correlates with their helicity. In this study, we have performed extensive all-atom molecular dynamics simulations of 25 Lysine-Leucine co-polypeptide sequences of varying charge density ( λ ) and patterns. Our findings showed that, an increase in the charge density on the peptide leads to a gradual decrease in the helicity up to a critical charge density λ c . Beyond λ c , a complete helix to coil transition was observed. The decrease in the helicity is correlated with the increased number of water molecules in first solvation shell, solvent-exposed surface area, and a higher value of the radius of gyration of the peptide.
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Affiliation(s)
- Nitin Kumar Singh
- Discipline of Chemical Engineering, Indian Institute of Technology (IIT), Gandhinagar, Gujarat, India
| | - Manish Agarwal
- Computer Services Centre, Indian Institute of Technology (IIT), Delhi, India
| | - Mithun Radhakrishna
- Discipline of Chemical Engineering, Indian Institute of Technology (IIT), Gandhinagar, Gujarat, India.,Center for Biomedical Engineering, Indian Institute of Technology (IIT), Gandhinagar, Gujarat, India
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17
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Galindo-Hernández O, García-Salazar LA, García-González VG, Díaz-Molina R, Vique-Sánchez JL. Potential Inhibitors of The OTUB1 Catalytic Site to Develop an Anti-Cancer Drug Using In-Silico Approaches. Rep Biochem Mol Biol 2023; 11:684-693. [PMID: 37131907 PMCID: PMC10149122 DOI: 10.52547/rbmb.11.4.684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/13/2022] [Indexed: 05/04/2023]
Abstract
Background : Cancer continues worldwide. It has been reported that OTUB1, a cysteine protease, plays a critical role in a variety of tumors and is strongly related to tumor proliferation, migration, and clinical prognosis by its functions on deubiquitination. Drug advances continue against new therapeutic targets. In this study we used OTUB1 to develop a specific pharmacological treatment to regulate deubiquitination by OTUB1. The aim of this research is to regulate OTUB1 functions. Methods By molecular docking in a specific potential OTUB1 interaction site between Asp88, Cys91, and His26 amino acids, using a chemical library of over 500,000 compounds, we selected potential inhibitors of the OTUB1 catalytic site. Results Ten compounds (OT1 - OT10) were selected by molecular docking to develop a new anti-cancer drug to decrease OTUB1 functions in cancer processes. Conclusion OT1 - OT10 compounds could be interacting in the potential site between Asp88, Cys91, and His265 amino acids in OTUB1. This site is necessary for the deubiquitinating function of OTUB1. Therefore, this study shows another way to attack cancer.
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Affiliation(s)
- Octavio Galindo-Hernández
- Autonomous University of Baja California, School of Medicine Campus Mexicali, Mexicali, BC, México.
- Corresponding author: José Luis Vique-Sánchez; Tel: +52 5549928664; E-mail: .
| | | | | | - Raúl Díaz-Molina
- Autonomous University of Baja California, School of Medicine Campus Mexicali, Mexicali, BC, México.
| | - José Luis Vique-Sánchez
- Autonomous University of Baja California, School of Medicine Campus Mexicali, Mexicali, BC, México.
- Corresponding author: José Luis Vique-Sánchez; Tel: +52 5549928664; E-mail: .
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18
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Rizuan A, Jovic N, Phan TM, Kim YC, Mittal J. Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins. J Chem Inf Model 2022; 62:4474-4485. [PMID: 36066390 PMCID: PMC10165611 DOI: 10.1021/acs.jcim.2c00450] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent advances in residue-level coarse-grained (CG) computational models have enabled molecular-level insights into biological condensates of intrinsically disordered proteins (IDPs), shedding light on the sequence determinants of their phase separation. The existing CG models that treat protein chains as flexible molecules connected via harmonic bonds cannot populate common secondary-structure elements. Here, we present a CG dihedral angle potential between four neighboring beads centered at Cα atoms to faithfully capture the transient helical structures of IDPs. In order to parameterize and validate our new model, we propose Cα-based helix assignment rules based on dihedral angles that succeed in reproducing the atomistic helicity results of a polyalanine peptide and folded proteins. We then introduce sequence-dependent dihedral angle potential parameters (εd) and use experimentally available helical propensities of naturally occurring 20 amino acids to find their optimal values. The single-chain helical propensities from the CG simulations for commonly studied prion-like IDPs are in excellent agreement with the NMR-based α-helix fraction, demonstrating that the new HPS-SS model can accurately produce structural features of IDPs. Furthermore, this model can be easily implemented for large-scale assembly simulations due to its simplicity.
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Affiliation(s)
- Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Nina Jovic
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Tien M Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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19
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Dinic J, Schnorenberg MR, Tirrell MV. Sequence-Controlled Secondary Structures and Stimuli Responsiveness of Bioinspired Polyampholytes. Biomacromolecules 2022; 23:3798-3809. [PMID: 35969881 DOI: 10.1021/acs.biomac.2c00666] [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] [Indexed: 11/28/2022]
Abstract
A comprehensive study focusing on the influence of the sequence charge pattern on the secondary structure preferences of annealed polyampholytes and their responsiveness to external stimuli is presented. Two sequences are designed composed entirely of ionizable amino acids (charge fraction, f = 1) and an equal number of positive and negative charges (f+ = f- = 0.5) with distinct charge patterns consisting of lysine and glutamic acid monomers. The study reveals that the sequence charge pattern has a significant influence on the secondary structure preferences of polyampholytes at physiological pH. Furthermore, it shows that external stimuli such as pH, ionic strength, and solvent dielectric constant can be used to modulate the secondary structure of the two studied sequences. The observed secondary structure transformations for the two sequences are also substantially different from those determined for uniformly charged homo-polypeptides under matching conditions.
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Affiliation(s)
- Jelena Dinic
- Center for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Mathew R Schnorenberg
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew V Tirrell
- Center for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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20
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Chaudhari AM, Joshi M, Kumar D, Patel A, Lokhande KB, Krishnan A, Hanack K, Filipek S, Liepmann D, Renugopalakrishnan V, Paulmurugan R, Joshi C. Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants. Comput Struct Biotechnol J 2022; 20:4501-4516. [PMID: 35965661 PMCID: PMC9359593 DOI: 10.1016/j.csbj.2022.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 12/18/2022] Open
Abstract
Emerging SARS-CoV-2 variants with higher transmissibility and immune escape remain a persistent threat across the globe. This is evident from the recent outbreaks of the Delta (B.1.617.2) and Omicron variants. These variants have originated from different continents and spread across the globe. In this study, we explored the genomic and structural basis of these variants for their lineage defining mutations of the spike protein through computational analysis, protein modeling, and molecular dynamic (MD) simulations. We further experimentally validated the importance of these deletion mutants for their immune escape using a pseudovirus-based neutralization assay, and an antibody (4A8) that binds directly to the spike protein's NTD. Delta variant with the deletion and mutations in the NTD revealed a better rigidity and reduced flexibility as compared to the wild-type spike protein (Wuhan isolate). Furthermore, computational studies of 4A8 monoclonal antibody (mAb) revealed a reduced binding of Delta variant compared to the wild-type strain. Similarly, the MD simulation data and virus neutralization assays revealed that the Omicron also exhibits immune escape, as antigenic beta-sheets appear to be disrupted. The results of the present study demonstrate the higher possibility of immune escape and thereby achieved better fitness advantages by the Delta and Omicron variants, which warrants further demonstrations through experimental evidences. Our study, based on in-silico computational modelling, simulations, and pseudovirus-based neutralization assay, highlighted and identified the probable mechanism through which the Delta and Omicron variants are more pathogenically evolved with higher transmissibility as compared to the wild-type strain.
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Affiliation(s)
- Armi M Chaudhari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Amrutlal Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Kiran Bharat Lokhande
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Anandi Krishnan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
| | - Katja Hanack
- Immunotechnology Group, Department of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Slawomir Filipek
- Faculty of Chemistry & Biological and Chemical Research, Centre, University of Warsaw, ul, Pasteura 1, 02-093 Warsaw, Poland
| | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Venkatesan Renugopalakrishnan
- Department of Chemistry, Northeastern University, Boston Children's Hospital, Harvard Medical School, Boston, MGB Center for COVID Innovation, MA 02115, United States
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
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21
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Ahn SH, Huber GA, McCammon JA. Investigating Intrinsically Disordered Proteins With Brownian Dynamics. Front Mol Biosci 2022; 9:898838. [PMID: 35755809 PMCID: PMC9213797 DOI: 10.3389/fmolb.2022.898838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) have recently become systems of great interest due to their involvement in modulating many biological processes and their aggregation being implicated in many diseases. Since IDPs do not have a stable, folded structure, however, they cannot be easily studied with experimental techniques. Hence, conducting a computational study of these systems can be helpful and be complementary with experimental work to elucidate their mechanisms. Thus, we have implemented the coarse-grained force field for proteins (COFFDROP) in Browndye 2.0 to study IDPs using Brownian dynamics (BD) simulations, which are often used to study large-scale motions with longer time scales and diffusion-limited molecular associations. Specifically, we have checked our COFFDROP implementation with eight naturally occurring IDPs and have investigated five (Glu-Lys)25 IDP sequence variants. From measuring the hydrodynamic radii of eight naturally occurring IDPs, we found the ideal scaling factor of 0.786 for non-bonded interactions. We have also measured the entanglement indices (average C α distances to the other chain) between two (Glu-Lys)25 IDP sequence variants, a property related to molecular association. We found that entanglement indices decrease for all possible pairs at excess salt concentration, which is consistent with long-range interactions of these IDP sequence variants getting weaker at increasing salt concentration.
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Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Gary A. Huber
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
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22
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On the quest of small molecules that can mimic Psalmotoxin-1, the most powerful peptidic modulator of the acid sensing channel ASIC1a. Struct Chem 2022. [DOI: 10.1007/s11224-021-01826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Sai CB, Chidambaranathan P. In-silico evolutionary analysis of plant-OBERON proteins during compatible MYMV infection in respect of improving host resistance. JOURNAL OF PLANT RESEARCH 2022; 135:405-422. [PMID: 35201523 DOI: 10.1007/s10265-022-01372-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Yellow mosaic disease (YMD) of pulses caused by mungbean yellow mosaic virus is a major threat to crop production. An infection that is compatible with regulating and interacting host proteins and the virus causes YMD. Oberon families of proteins OBE1-4 and VIN1-4 are imperative for plants, functions in meristem and vascular development, and were also regulated during compatible disease infection. Furthermore, in-silico expression results suggested the involvement of OBE1 and OBE2 proteins during virus infection of Vigna, Arabidopsis and soybean. Moreover, a common ancestor for the meristem and virus movement related Oberons was inferred through phylogenetic analysis. Protein interaction studies showed three amino acids (Aspartate, glutamate and lysine) in the plant homeodomain (PHD), involved in interaction with the N-terminal region of the virus movement protein and were also conserved in both monocot and dicots. Additionally, major differences in the nuclear localization signal (NLS) showing clade specific conservation and significant variation between dicots and monocots were ascertained in meristem and virus movement related Oberons. Consequently, a combination of PHD, CCD and their interactions with the VPg viral domain increases the susceptibility to YMD. Further, modification in the NLS regions of the viral movement clade Oberons, to knock out allele generation in the OBE1 and OBE2 homologs through genome-editing approaches could be established as alternate strategies for the improvement of host resistance and control yellow mosaic disease in plants, especially in pulse crops.
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Affiliation(s)
- Cayalvizhi B Sai
- ICAR-National Rice Research Institute (ICAR-NRRI), Cuttack, 753006, India.
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24
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McGlacken-Byrne SM, Del Valle I, Le Quesne Stabej P, Bellutti L, Garcia-Alonso L, Ocaka LA, Ishida M, Suntharalingham JP, Gagunashvili A, Ogunbiyi OK, Mistry T, Buonocore F, Crespo B, Moreno N, Niola P, Brooks T, Brain CE, Dattani MT, Kelberman D, Vento-Tormo R, Lagos CF, Livera G, Conway GS, Achermann JC. Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency. JCI Insight 2022; 7:154671. [PMID: 35138268 PMCID: PMC8983136 DOI: 10.1172/jci.insight.154671] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022] Open
Abstract
Primary ovarian insufficiency (POI) affects 1% of women and carries significant medical and psychosocial sequelae. Approximately 10% of POI has a defined genetic cause, with most implicated genes relating to biological processes involved in early fetal ovary development and function. Recently, Ythdc2, an RNA helicase and N6-methyladenosine (m6a) reader, has emerged as a novel regulator of meiosis in mice. Here, we describe homozygous pathogenic variants in YTHDC2 in three women with early-onset POI from two families: c. 2567C>G, p.P856R in the helicase-associated (HA2) domain; and c.1129G>T, p.E377*. We demonstrate that YTHDC2 is expressed in the developing human fetal ovary and is upregulated in meiotic germ cells, together with related meiosis-associated factors. The p.P856R variant results in a less flexible protein that likely disrupts downstream conformational kinetics of the HA2 domain, whereas the p.E377* variant truncates the helicase core. Taken together, our results reveal that YTHDC2 is a key new regulator of meiosis in humans and pathogenic variants within this gene are associated with POI.
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Affiliation(s)
- Sinead M McGlacken-Byrne
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ignacio Del Valle
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Laura Bellutti
- Laboratory of Development of the Gonads, UMR E008, Université de Paris, Université Paris Saclay, CEA, Fontenay aux Roses, France
| | - Luz Garcia-Alonso
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Louise A Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Miho Ishida
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jenifer P Suntharalingham
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Andrey Gagunashvili
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Olumide K Ogunbiyi
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Talisa Mistry
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Federica Buonocore
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Berta Crespo
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child health, London, United Kingdom
| | - Nadjeda Moreno
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Paola Niola
- UCL Genomics, Zayed Centre for Research, London, United Kingdom
| | - Tony Brooks
- UCL Genomics, Zayed Centre for Research, London, United Kingdom
| | - Caroline E Brain
- Department of Paediatric Endocrinology, Great Ormond Street Hospital, London, United Kingdom
| | - Mehul T Dattani
- Genetics and Genomics Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Daniel Kelberman
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Carlos F Lagos
- Chemical Biology & Drug Discovery Lab, Escuela de Química y Farmacia, Universidad San Sebastián, Santiago, Chile
| | - Gabriel Livera
- Laboratory of Development of the Gonads, UMR E008, Université de Paris, Université Paris Saclay, CEA, Fontenay aux Roses, France
| | - Gerard S Conway
- Institute for Women's Health, University College London, London, United Kingdom
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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25
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Richaud AD, Zhao G, Hobloss S, Roche SP. Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops. J Org Chem 2021; 86:13535-13547. [PMID: 34499510 PMCID: PMC8576641 DOI: 10.1021/acs.joc.1c01442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Samir Hobloss
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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26
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Greene D, Barton M, Luchko T, Shiferaw Y. Computational Analysis of Binding Interactions between the Ryanodine Receptor Type 2 and Calmodulin. J Phys Chem B 2021; 125:10720-10735. [PMID: 34533024 DOI: 10.1021/acs.jpcb.1c03896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to a variety of cardiac arrhythmias, such as catecholaminergic polymorphic ventricular tachycardia (CPVT). RyR2 is regulated by calmodulin (CaM), and mutations that disrupt their interaction can cause aberrant calcium release, leading to an arrhythmia. It was recently shown that increasing the RyR2-CaM binding affinity could rescue a defective CPVT-related RyR2 channel to near wild-type behavior. However, the interactions that determine the binding affinity at the RyR2-CaM binding interface are not well understood. In this study, we identify the key domains and interactions, including several new interactions, involved in the binding of CaM to RyR2. Also, our comparison between the wild-type and V3599K mutant suggests how the RyR2-CaM binding affinity can be increased via a change in the central and N-terminal lobe binding contacts for CaM. This computational approach provides new insights into the effect of a mutation at the RyR2-CaM binding interface, and it may find utility in drug design for the future treatment of cardiac arrhythmias.
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Affiliation(s)
- D'Artagnan Greene
- Department of Physics, California State University, Northridge, California 91330, United States
| | - Michael Barton
- Department of Physics, California State University, Northridge, California 91330, United States
| | - Tyler Luchko
- Department of Physics, California State University, Northridge, California 91330, United States
| | - Yohannes Shiferaw
- Department of Physics, California State University, Northridge, California 91330, United States
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27
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Bhat R, Foster LL, Rani G, Vemparala S, Kuroda K. The function of peptide-mimetic anionic groups and salt bridges in the antimicrobial activity and conformation of cationic amphiphilic copolymers. RSC Adv 2021; 11:22044-22056. [PMID: 35480841 PMCID: PMC9034112 DOI: 10.1039/d1ra02730a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
Herein we report the synthesis of ternary statistical methacrylate copolymers comprising cationic ammonium (amino-ethyl methacrylate: AEMA), carboxylic acid (propanoic acid methacrylate: PAMA) and hydrophobic (ethyl methacrylate: EMA) side chain monomers, to study the functional role of anionic groups on their antimicrobial and hemolytic activities as well as the conformation of polymer chains. The hydrophobic monomer EMA was maintained at 40 mol% in all the polymers, with different percentages of cationic ammonium (AEMA) and anionic carboxylate (PAMA) side chains, resulting in different total net charge for the polymers. The antimicrobial and hemolytic activities of the copolymer were determined by the net charge of +3 or larger, suggesting that there was no distinct effect of the anionic carboxylate groups on the antimicrobial and hemolytic activities of the copolymers. However, the pH titration and atomic molecular dynamics simulations suggest that anionic groups may play a strong role in controlling the polymer conformation. This was achieved via formation of salt bridges between cationic and anionic groups, transiently crosslinking the polymer chain allowing dynamic switching between compact and extended conformations. These results suggest that inclusion of functional groups in general, other than the canonical hydrophobic and cationic groups in antimicrobial agents, may have broader implications in acquiring functional structures required for adequate antimicrobial activity. In order to explain the implications, we propose a molecular model in which formation of intra-chain, transient salt bridges, due to the presence of both anionic and cationic groups along the polymer, may function as "adhesives" which facilitate compact packing of the polymer chain to enable functional group interaction but without rigidly locking down the overall polymer structure, which may adversely affect their functional roles.
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Affiliation(s)
- Rajani Bhat
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry, University of Michigan Ann Arbor Michigan 48109 USA
| | - Leanna L Foster
- Macromolecular Science and Engineering Center, University of Michigan Ann Arbor Michigan 48109 USA
| | - Garima Rani
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad 500046 India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C. I. T. Campus Taramani Chennai 600113 India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry, University of Michigan Ann Arbor Michigan 48109 USA
- Macromolecular Science and Engineering Center, University of Michigan Ann Arbor Michigan 48109 USA
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28
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Yu L, Deng Z, Zhang W, Liu S, Zhang F, Zhou J, Ma C, Wang C. Opposite Regulatory Effects of Immobilized Cations on the Folding Vs. Assembly of Melittin. Front Chem 2021; 9:685947. [PMID: 34178946 PMCID: PMC8225954 DOI: 10.3389/fchem.2021.685947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Ions are crucial in modulating the protein structure. For the free ions in bulk solution, ammonium is kosmotropic (structure forming) and guanidinium is chaotropic (structure breaking) to the protein structure within the Hofmeister series. However, the effect of immobilized ions on a protein surface is less explored. Herein, we explored the influence of two immobilized cations (ammonium in the side chain of lysine and guanidinium in the side chain of arginine) on the folding and assembly of melittin. Melittin adopts an α-helix structure and is driven by hydrophobic interactions to associate into a helical bundle. To test the influence of immobilized cations on the peptide structure, we designed the homozygous mutants exclusively containing ammonium (melittin-K) or guanidinium (melittin-R) and compared the differences of melittin-K vs. melittin-R in their folding, assembly, and molecular functions. The side chains of lysine and arginine differ in their influences on the folding and assembly of melittin. Specifically, the side chain of R increases the α-helical propensity of melittin relative to that of K, following an inverse Hofmeister series. In contrast, the side chain of K favors the assembly of melittin relative to the side chain of R in line with a direct Hofmeister series. The opposite regulatory effects of immobilized cations on the folding and assembly of melittin highlight the complexity of the noncovalent interactions that govern protein intermolecular architecture.
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Affiliation(s)
- Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Zhun Deng
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
| | - Shuli Liu
- Department of Clinical Laboratory, Peking University Civil Aviation School of Clinical Medicine, Beijing, China
| | - Feiyi Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, China
| | | | | | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Basic Medical Sciences, Beijing, China
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29
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Banerjee S, Gupta PSS, Islam RNU, Bandyopadhyay AK. Intrinsic basis of thermostability of prolyl oligopeptidase from Pyrococcus furiosus. Sci Rep 2021; 11:11553. [PMID: 34078944 PMCID: PMC8172842 DOI: 10.1038/s41598-021-90723-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/13/2021] [Indexed: 12/04/2022] Open
Abstract
Salt-bridges play a key role in the thermostability of proteins adapted in stress environments whose intrinsic basis remains to be understood. We find that the higher hydrophilicity of PfP than that of HuP is due to the charged but not the polar residues. The primary role of these residues is to enhance the salt-bridges and their ME. Unlike HuP, PfP has made many changes in its intrinsic property to strengthen the salt-bridge. First, the desolvation energy is reduced by directing the salt-bridge towards the surface. Second, it has made bridge-energy more favorable by recruiting energetically advantageous partners with high helix-propensity among the six possible salt-bridge pairs. Third, ME-residues that perform intricate interactions have increased their energy contribution by making major changes in their binary properties. The use of salt-bridge partners as ME-residues, and ME-residues' overlapping usage, predominant in helices, and energetically favorable substitution are some of the favorable features of PfP compared to HuP. These changes in PfP reduce the unfavorable, increase the favorable ME-energy. Thus, the per salt-bridge stability of PfP is greater than that of HuP. Further, unfavorable target ME-residues can be identified whose mutation can increase the stability of salt-bridge. The study applies to other similar systems.
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Affiliation(s)
- Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
| | - Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur , Orissa, India
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30
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Computational Study on Temperature Driven Structure-Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme. Polymers (Basel) 2021; 13:polym13111771. [PMID: 34071348 PMCID: PMC8198650 DOI: 10.3390/polym13111771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
Glycosyltransferase (GTs) is a wide class of enzymes that transfer sugar moiety, playing a key role in the synthesis of bacterial exopolysaccharide (EPS) biopolymer. In recent years, increased demand for bacterial EPSs has been observed in pharmaceutical, food, and other industries. The application of the EPSs largely depends upon their thermal stability, as any industrial application is mainly reliant on slow thermal degradation. Keeping this in context, EPS producing GT enzymes from three different bacterial sources based on growth temperature (mesophile, thermophile, and hyperthermophile) are considered for in silico analysis of the structural–functional relationship. From the present study, it was observed that the structural integrity of GT increases significantly from mesophile to thermophile to hyperthermophile. In contrast, the structural plasticity runs in an opposite direction towards mesophile. This interesting temperature-dependent structural property has directed the GT–UDP-glucose interactions in a way that thermophile has finally demonstrated better binding affinity (−5.57 to −10.70) with an increased number of hydrogen bonds (355) and stabilizing amino acids (Phe, Ala, Glu, Tyr, and Ser). The results from this study may direct utilization of thermophile-origin GT as best for industrial-level bacterial polysaccharide production.
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31
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Jiang V, Khare SD, Banta S. Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans. Protein Sci 2021; 30:1640-1652. [PMID: 33969560 DOI: 10.1002/pro.4106] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Cyc2 is the key protein in the outer membrane of Acidithiobacillus ferrooxidans that mediates electron transfer between extracellular inorganic iron and the intracellular central metabolism. This cytochrome c is specific for iron and interacts with periplasmic proteins to complete a reversible electron transport chain. A structure of Cyc2 has not yet been characterized experimentally. Here we describe a structural model of Cyc2, and associated proteins, to highlight a plausible mechanism for the ferrous iron electron transfer chain. A comparative modeling protocol specific for trans membrane beta barrel (TMBB) proteins in acidophilic conditions (pH ~ 2) was applied to the primary sequence of Cyc2. The proposed structure has three main regimes: Extracellular loops exposed to low-pH conditions, a TMBB, and an N-terminal cytochrome-like region within the periplasmic space. The Cyc2 model was further refined by identifying likely iron and heme docking sites. This represents the first computational model of Cyc2 that accounts for the membrane microenvironment and the acidity in the extracellular matrix. This approach can be used to model other TMBBs which can be critical for chemolithotrophic microbial growth.
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Affiliation(s)
- Virginia Jiang
- Department of Chemical Engineering, Columbia University in the City of New York, New York, New York, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University in the City of New York, New York, New York, USA
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32
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Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021; 60:11448-11456. [PMID: 33687787 PMCID: PMC8252522 DOI: 10.1002/anie.202101642] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 11/06/2022]
Abstract
Biocatalysis for the synthesis of fine chemicals is highly attractive but usually requires organic (co-)solvents (OSs). However, native enzymes often have low activity and resistance in OSs and at elevated temperatures. Herein, we report a smart salt bridge design strategy for simultaneously improving OS resistance and thermostability of the model enzyme, Bacillus subtilits Lipase A (BSLA). We combined comprehensive experimental studies of 3450 BSLA variants and molecular dynamics simulations of 36 systems. Iterative recombination of four beneficial substitutions yielded superior resistant variants with up to 7.6-fold (D64K/D144K) improved resistance toward three OSs while exhibiting significant thermostability (thermal resistance up to 137-fold, and half-life up to 3.3-fold). Molecular dynamics simulations revealed that locally refined flexibility and strengthened hydration jointly govern the highly increased resistance in OSs and at 50-100 °C. The salt bridge redesign provides protein engineers with a powerful and likely general approach to design OSs- and/or thermal-resistant lipases and other α/β-hydrolases.
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Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| | - Lobna Eltoukhy
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Lingling Zhang
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th Avenue 32, Tianjin Airport Economic Area300308TianjinChina
| | - Ulrich Markel
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfWilhelm Johnen Strasse52426JülichGermany
- Institute of Bio-and Geosciences IBG 1: BiotechnologyForschungszentrum Jülich GmbHWilhelm Johnen Strasse52426JülichGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
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33
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Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | - Lobna Eltoukhy
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Lingling Zhang
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue 32, Tianjin Airport Economic Area 300308 Tianjin China
| | - Ulrich Markel
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf Wilhelm Johnen Strasse 52426 Jülich Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology Forschungszentrum Jülich GmbH Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Mehdi D. Davari
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
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34
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Tiwari MK, Murarka RK. Interaction strength of osmolytes with the anion of a salt-bridge determines its stability. Phys Chem Chem Phys 2021; 23:5527-5539. [PMID: 33651069 DOI: 10.1039/d0cp05378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.
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Affiliation(s)
- Mrityunjay K Tiwari
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| | - Rajesh K Murarka
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
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35
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Dicarbonyl stress, protein glycation and the unfolded protein response. Glycoconj J 2021; 38:331-340. [PMID: 33644826 PMCID: PMC8116241 DOI: 10.1007/s10719-021-09980-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 01/26/2021] [Accepted: 02/10/2021] [Indexed: 12/22/2022]
Abstract
The reactive dicarbonyl metabolite, methylglyoxal (MG), is increased in obesity and diabetes and is implicated in the development of insulin resistance, type 2 diabetes mellitus and vascular complications of diabetes. Dicarbonyl stress is the metabolic state of abnormal high MG concentration. MG is an arginine-directed glycating agent and precursor of the major advanced glycation endproduct, arginine-derived hydroimidazolone MG-H1. MG-H1 is often formed on protein surfaces and an uncharged hydrophobic residue, inducing protein structural distortion and misfolding. Recent studies indicate that dicarbonyl stress in human endothelial cells and fibroblasts in vitro induced a proteomic response consistent with activation of the unfolded protein response (UPR). The response included: increased abundance of heat shock proteins and ubiquitin ligases catalysing the removal of proteins with unshielded surface hydrophobic patches and formation of polyubiquitinated chains to encapsulate misfolded proteins; and increased low grade inflammation. Activation of the UPR is implicated in insulin resistance. An effective strategy to counter increased MG is inducing increased expression of glyoxalase-1 (Glo1). An optimized inducer of Glo1 expression, trans-resveratrol and hesperetin combination, normalized increased MG concentration, corrected insulin resistance and decreased low grade inflammation in overweight and obese subjects. We propose that dicarbonyl stress, through increased formation of MG-glycated proteins, may be an important physiological stimulus of the UPR and Glo1 inducers may provide a route to effective suppression and therapy. With further investigation and validation, this may provide key new insight into physiological activators of the UPR and association with dicarbonyl stress.
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36
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Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nat Commun 2021; 12:407. [PMID: 33462223 PMCID: PMC7814010 DOI: 10.1038/s41467-020-20689-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Charles Modlin
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Puneet Juneja
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA. .,The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.
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Gräwe A, Stein V. Linker Engineering in the Context of Synthetic Protein Switches and Sensors. Trends Biotechnol 2020; 39:731-744. [PMID: 33293101 DOI: 10.1016/j.tibtech.2020.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022]
Abstract
Linkers play critical roles in the construction of synthetic protein switches and sensors as they functionally couple a receptor with an actuator. With an increasing number of molecular toolboxes and experimental strategies becoming available that can be applied to engineer protein switches and sensors with tailored response functions, optimising the connecting linkers remains an idiosyncratic and empiric process. This review aims to provide an in-depth analysis of linker motifs, the biophysical properties they confer, and how they impact the performance of synthetic protein switches and sensors while identifying trends, mechanisms, and strategies that underlie the most potent switches and sensors.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.
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38
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Jayaraman M, Ramadas K. An integrated computational investigation to unveil the structural impacts of mutation on the InhA structural gene of Mycobacterium tuberculosis. J Mol Graph Model 2020; 101:107768. [DOI: 10.1016/j.jmgm.2020.107768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 10/23/2022]
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39
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Li Y, Tahlan K, Bignell DR. Functional Cross-Talk of MbtH-Like Proteins During Thaxtomin Biosynthesis in the Potato Common Scab Pathogen Streptomyces scabiei. Front Microbiol 2020; 11:585456. [PMID: 33178168 PMCID: PMC7593251 DOI: 10.3389/fmicb.2020.585456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Thaxtomin A is a potent phytotoxin that serves as the principle pathogenicity determinant of the common scab pathogen, Streptomyces scabiei, and is also a promising natural herbicide for agricultural applications. The biosynthesis of thaxtomin A involves the non-ribosomal peptide synthetases (NRPSs) TxtA and TxtB, and an MbtH-like protein (MLP), TxtH, which may function as a chaperone by promoting the proper folding of the two NRPS enzymes in S. scabiei. MLPs are required for the proper function of many NRPS enzymes in bacteria, and they are often capable of interacting with NRPSs from different biosynthetic pathways, though the mechanism by which this occurs is still poorly understood. To gain additional insights into MLP functional cross-talk, we conducted a broad survey of MLPs from diverse phylogenetic lineages to determine if they could functionally replace TxtH. The MLPs were assessed using a protein solubility assay to determine whether they could promote the soluble expression of the TxtA and TxtB adenylation domains. In addition, the MLPs were tested for their ability to restore thaxtomin production in a S. scabiei mutant that lacked TxtH and other endogenous MLPs. Our results showed that the MLPs investigated vary in their ability to exhibit functional cross-talk with TxtH, with two of the MLPs being unable to compensate for the loss of TxtH in the assays performed. The ability of an MLP to serve as a functional partner for the thaxtomin NRPS was not correlated with its overall amino acid similarity with TxtH, but instead with the presence of highly conserved residues. In silico structural analysis of TxtH in association with the TxtA and TxtB adenylation domains revealed that several such residues are situated at the predicted interaction interface, suggesting that they might be critical for promoting functional interactions between MLPs and the thaxtomin NRPS enzymes. Overall, our study provides additional insights into the mechanism of MLP cross-talk, and it enhances our understanding of the thaxtomin biosynthetic machinery. It is anticipated that our findings will have useful applications for both the control of common scab disease and the commercial production of thaxtomin A for agricultural use.
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40
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Ghosh G, Fernández G. pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide. Beilstein J Org Chem 2020; 16:2017-2025. [PMID: 32874348 PMCID: PMC7445398 DOI: 10.3762/bjoc.16.168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
Peptide-based biopolymers represent highly promising biocompatible materials with multiple applications, such as tailored drug delivery, tissue engineering and regeneration, and as stimuli-responsive materials. Herein, we report the pH- and concentration-dependent self-assembly and conformational transformation of the newly synthesized octapeptide PEP-1. At pH 7.4, PEP-1 forms β-sheet-rich secondary structures into fractal-like morphologies, as verified by circular dichroism (CD), Fourier-transform infrared (FTIR) spectroscopy, thioflavin T (ThT) fluorescence spectroscopy assay, and atomic force microscopy (AFM). Upon changing the pH value (using pH 5.5 and 13.0), PEP-1 forms different types of secondary structures and resulting morphologies due to electrostatic repulsion between charged amino acids. PEP-1 can also form helical or random-coil secondary structures at a relatively low concentration. The obtained pH-sensitive self-assembly behavior of the target octapeptide is expected to contribute to the development of novel drug nanocarrier assemblies.
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Affiliation(s)
- Goutam Ghosh
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Correnstraße 40, 48149 Münster, Germany
| | - Gustavo Fernández
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Correnstraße 40, 48149 Münster, Germany
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41
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Szigyártó IC, Mihály J, Wacha A, Bogdán D, Juhász T, Kohut G, Schlosser G, Zsila F, Urlacher V, Varga Z, Fülöp F, Bóta A, Mándity I, Beke-Somfai T. Membrane active Janus-oligomers of β 3-peptides. Chem Sci 2020; 11:6868-6881. [PMID: 33042513 PMCID: PMC7504880 DOI: 10.1039/d0sc01344g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/12/2020] [Indexed: 11/21/2022] Open
Abstract
Self-assembly of an acyclic β3-hexapeptide with alternating side chain chirality, into nanometer size oligomeric bundles showing membrane activity and hosting capacity for hydrophobic small molecules.
Self-assembling peptides offer a versatile set of tools for bottom-up construction of supramolecular biomaterials. Among these compounds, non-natural peptidic foldamers experience increased focus due to their structural variability and lower sensitivity to enzymatic degradation. However, very little is known about their membrane properties and complex oligomeric assemblies – key areas for biomedical and technological applications. Here we designed short, acyclic β3-peptide sequences with alternating amino acid stereoisomers to obtain non-helical molecules having hydrophilic charged residues on one side, and hydrophobic residues on the other side, with the N-terminus preventing formation of infinite fibrils. Our results indicate that these β-peptides form small oligomers both in water and in lipid bilayers and are stabilized by intermolecular hydrogen bonds. In the presence of model membranes, they either prefer the headgroup regions or they insert between the lipid chains. Molecular dynamics (MD) simulations suggest the formation of two-layered bundles with their side chains facing opposite directions when compared in water and in model membranes. Analysis of the MD calculations showed hydrogen bonds inside each layer, however, not between the layers, indicating a dynamic assembly. Moreover, the aqueous form of these oligomers can host fluorescent probes as well as a hydrophobic molecule similarly to e.g. lipid transfer proteins. For the tested, peptides the mixed chirality pattern resulted in similar assemblies despite sequential differences. Based on this, it is hoped that the presented molecular framework will inspire similar oligomers with diverse functionality.
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Affiliation(s)
- Imola Cs Szigyártó
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Judith Mihály
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - András Wacha
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Dóra Bogdán
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Department of Organic Chemistry , Faculty of Pharmacy , Semmelweis University , H-1092 Budapest , Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Gergely Kohut
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Institute of Chemistry , Eötvös Loránd University , H-1117 Budapest , Hungary
| | - Gitta Schlosser
- Institute of Chemistry , Eötvös Loránd University , H-1117 Budapest , Hungary
| | - Ferenc Zsila
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Vlada Urlacher
- Institute of Biochemistry , Heinrich-Heine University , 40225 Düsseldorf , Germany
| | - Zoltán Varga
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Ferenc Fülöp
- MTA-SZTE Stereochemistry Research Group , Institute of Pharmaceutical Chemistry , University of Szeged , H-6720 Szeged , Hungary
| | - Attila Bóta
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - István Mándity
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Department of Organic Chemistry , Faculty of Pharmacy , Semmelweis University , H-1092 Budapest , Hungary
| | - Tamás Beke-Somfai
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Department of Chemistry and Chemical Engineering , Physical Chemistry , Chalmers University of Technology , SE-41296 Göteborg , Sweden
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42
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Tolmachev D, Lukasheva N, Mamistvalov G, Karttunen M. Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length. Polymers (Basel) 2020; 12:E1279. [PMID: 32503199 PMCID: PMC7362111 DOI: 10.3390/polym12061279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 11/21/2022] Open
Abstract
Investigation of the effect of CaCl2 salt on conformations of two anionic poly(amino acids) with different side chain lengths, poly-(α-l glutamic acid) (PGA) and poly-(α-l aspartic acid) (PASA), was performed by atomistic molecular dynamics (MD) simulations. The simulations were performed using both unbiased MD and the Hamiltonian replica exchange (HRE) method. The results show that at low CaCl2 concentration adsorption of Ca2+ ions lead to a significant chain size reduction for both PGA and PASA. With the increase in concentration, the chains sizes partially recover due to electrostatic repulsion between the adsorbed Ca2+ ions. Here, the side chain length becomes important. Due to the longer side chain and its ability to distance the charged groups with adsorbed ions from both each other and the backbone, PGA remains longer in the collapsed state as the CaCl2 concentration is increased. The analysis of the distribution of the mineral ions suggests that both poly(amino acids) should induce the formation of mineral with the same structure of the crystal cell.
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Affiliation(s)
- Dmitry Tolmachev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia;
| | - Natalia Lukasheva
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia;
| | - George Mamistvalov
- Faculty of Physics, St. Petersburg State University, Petrodvorets, 198504 St. Petersburg, Russia;
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy pr. 31, 199004 St. Petersburg, Russia;
- Department of Chemistry, the University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Applied Mathematics, the University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, the University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
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43
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Melien R, Garidel P, Hinderberger D, Blech M. Thermodynamic Unfolding and Aggregation Fingerprints of Monoclonal Antibodies Using Thermal Profiling. Pharm Res 2020; 37:78. [DOI: 10.1007/s11095-020-02792-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023]
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44
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Zakeri-Milani P, Shirani A, Nokhodchi A, Mussa Farkhani S, Mohammadi S, Shahbazi Mojarrad J, Mahmoudian M, Gholikhani T, Farshbaf M, Valizadeh H. Self-assembled peptide nanoparticles for efficient delivery of methotrexate into cancer cells. Drug Dev Ind Pharm 2020; 46:521-530. [PMID: 32116040 DOI: 10.1080/03639045.2020.1734017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The low cellular uptake of Methotrexate (MTX), a commonly used anticancer drug, is a big challenge for efficient cancer therapy. Self-assembled peptide nanoparticles (SAPNs) are one of the major classes of peptide vectors that have gained much attention toward novel drug delivery systems. In the present study, different sequences of cell-penetrating peptides including R2W4R2 and W3R4W3 and their SAPNs (R2W4R2-E12 and W3R4W3-E12) were designed for efficient delivery of MTX into MCF7 breast cancer cells. Based on electron microscopy results, the obtained SAPNs were in nano scale with spherical shape. There was a positive relationship between the free energy of water to octanol transferring and cellular penetration of designed nanostructures. The R2W4R2 possessed proper free energy and ability to form a spherical structure and hydrophobic-hydrophobic interactions, therefore, exhibited more cellular penetration than W3R4W3. The cellular uptake of obtained nanoparticles was examined by flow cytometry and fluorescence microscopy, in which, R2W4R2 and R2W4R2-E12 showed more appropriate penetration into MCF7 cells than W3R4W3 and W3R4W3-E12. The cytotoxicity of MTX-loaded peptides and SAPNs was examined by MTT assay. As a result, at higher concentrations, the R2W4R2 and R2W4R2-E12 showed higher cytotoxic behavior than their counterparts. Despite their enhanced cellular internalization, the cytotoxic behavior of MTX-loaded SAPNs at lower concentrations was relatively less than free MTX, which could be ascribed to the gradual nature of drug detachment from these conjugates. Therefore, R2W4R2 could be considered as an efficient choice to enhance the therapeutic efficiency of MTX in cancer treatments.
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Affiliation(s)
- Parvin Zakeri-Milani
- Liver and Gastrointestinal Diseases Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shirani
- Student Research Committee, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Nokhodchi
- Pharmaceutics Research Laboratory, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Samad Mussa Farkhani
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Samaneh Mohammadi
- Student Research Committee, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Shahbazi Mojarrad
- Biotechnology Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Mahmoudian
- Drug Applied Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tooba Gholikhani
- Biotechnology Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Farshbaf
- Student Research Committee, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Valizadeh
- Drug Applied Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Ramanayake Mudiyanselage TM, Michigami M, Ye Z, Uyeda A, Inoue N, Sugiura K, Fujii I, Fujiwara D. An Immune-Stimulatory Helix-Loop-Helix Peptide: Selective Inhibition of CTLA-4-B7 Interaction. ACS Chem Biol 2020; 15:360-368. [PMID: 31841301 DOI: 10.1021/acschembio.9b00743] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular-targeting peptides and mini-proteins are promising alternatives to antibodies in a wide range of applications in bioscience and medicine. We have developed a helix-loop-helix (HLH) peptide as an alternative to antibodies to inhibit specific protein interactions. Cytotoxic T lymphocyte antigen-4 (CTLA-4) downregulates immune responses of cytotoxic T-cells by interaction with B7-1, a co-stimulatory molecule expressed on antigen presenting cells (APCs). To induce immune stimulatory activity, we used directed evolution methods to generate a HLH peptide that binds to CTLA-4, inhibiting the CTLA-4-B7-1 interaction and inducing immune stimulatory activity. Yeast-displayed libraries of HLH peptides were constructed and screened against CTLA-4 and identified the binding peptide Y-2, which exhibits a moderate affinity. The affinity of Y-2 was improved by in vitro affinity maturation to afford a stronger binder, ERY2-4. Peptide ERY2-4 specifically bound to CTLA-4 with a KD of 196.8 ± 2.3 nM, comparable to the affinity of the CTLA-4-B7-1 interaction. Furthermore, ERY2-4 inhibited the CTLA-4-B7-1 interaction with an IC50 of 1.1 ± 0.03 μM and blocked the interaction between CTLA-4 and dendritic cells (DCs) presenting B7 on their surface. Importantly, ERY2-4 showed no cross-reactivity against CD28, suggesting it does not suppress T-cell activation. Finally, in a mixed lymphocyte reaction assay with DCs and T cells, ERY2-4 enhanced an allogeneic lymphocyte response. Since CTLA-4 is a critical immune checkpoint for restricting the cancer immune response, this inhibitory HLH peptide represents a new class of drug candidates for immunotherapy.
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Affiliation(s)
- Tharanga M.R. Ramanayake Mudiyanselage
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Zhengmao Ye
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norimitsu Inoue
- Department of Tumor Immunology, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka-shi, Osaka 541-8567, Japan
| | - Kikuya Sugiura
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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46
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Biok NA, Passow AD, Wang C, Bingman CA, Abbott NL, Gellman SH. Retention of Coiled-Coil Dimer Formation in the Absence of Ion Pairing at Positions Flanking the Hydrophobic Core. Biochemistry 2019; 58:4821-4826. [DOI: 10.1021/acs.biochem.9b00668] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Naomi A. Biok
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Alexander D. Passow
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chenxuan Wang
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca, New York 14853, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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47
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Zhang D, Lazim R, Yip YM. Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides. Biophys J 2019; 117:2079-2086. [PMID: 31685242 DOI: 10.1016/j.bpj.2019.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022] Open
Abstract
Reliability of force fields is an essential aspect of protein-folding simulation. In this work, we introduced a newly developed on-the-fly charge-updating scheme called the polarized structure-specific backbone charge (PSBC) model. The PSBC model was designed with the purpose of building the polarizability of backbone hydrogen bonds into the force field by updating the partial charges of backbone hydrogen-bond donor and acceptor atoms during folding simulation. This implementation was intended to mimic the heterogeneity of the protein surrounding during folding. Multiple single-trajectory molecular dynamics simulations were performed to fold a polyalanine peptide, namely ER (Ac-A(EAAAR)3A-NH2), using both polarizable (PSBC) and nonpolarizable (Amber03) force fields. Through the PSBC model, ER was folded into a helical peptide with helix content that agrees well with experiments. Comparison between simulations performed using the aforementioned force fields demonstrably showed the importance of electrostatic polarization effect in the folding of the short α-helical peptide. The PSBC model was further validated by folding two other short peptides with different helicities.
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Affiliation(s)
- Dawei Zhang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang, P. R. China; Henan Key Laboratory of Photoelectric Energy Storage Materials and Applications, Henan University of Science and Technology, Luoyang, P. R. China.
| | - Raudah Lazim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Yew Mun Yip
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
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48
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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49
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Pham LTM, Seo H, Kim KJ, Kim YH. In silico-designed lignin peroxidase from Phanerochaete chrysosporium shows enhanced acid stability for depolymerization of lignin. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:325. [PMID: 30555531 PMCID: PMC6287364 DOI: 10.1186/s13068-018-1324-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/29/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND The lignin peroxidase isozyme H8 from the white-rot fungus Phanerochaete chrysosporium (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lignin. However, native LiPH8 is unstable under acidic pH conditions. This characteristic is a barrier to lignin depolymerization, as repolymerization of phenolic products occurs simultaneously at neutral pH. Because repolymerization of phenolics is repressed at acidic pH, a highly acid-stable LiPH8 could accelerate the selective depolymerization of recalcitrant lignin. RESULTS The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from Phanerochaete chrysosporium and acid-stable manganese peroxidase isozyme 6 (MnP6) from Ceriporiopsis subvermispora. Effective salt bridges were probed by molecular dynamics simulation and changes to Gibbs free energy following mutagenesis were predicted, suggesting promising variants with higher stability under extremely acidic conditions. The rationally designed variant, A55R/N156E-H239E, demonstrated a 12.5-fold increased half-life under extremely acidic conditions, 9.9-fold increased catalytic efficiency toward veratryl alcohol, and a 7.8-fold enhanced lignin model dimer conversion efficiency compared to those of native LiPH8. Furthermore, the two constructed salt bridges in the variant A55R/N156E-H239E were experimentally confirmed to be identical to the intentionally designed LiPH8 variant using X-ray crystallography (PDB ID: 6A6Q). CONCLUSION Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin.
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Affiliation(s)
- Le Thanh Mai Pham
- School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea
| | - Hogyun Seo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea
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You X, Qin Z, Li YX, Yan QJ, Li B, Jiang ZQ. Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 β-mannanase. Biochim Biophys Acta Gen Subj 2018; 1862:1376-1388. [DOI: 10.1016/j.bbagen.2018.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 12/11/2022]
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