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Rooney J, Rivera-de-Torre E, Li R, Mclean K, Price DR, Nisbet AJ, Laustsen AH, Jenkins TP, Hofmann A, Bakshi S, Zarkan A, Cantacessi C. Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions. Comput Struct Biotechnol J 2024; 23:1522-1533. [PMID: 38633385 PMCID: PMC11021794 DOI: 10.1016/j.csbj.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.
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Affiliation(s)
- James Rooney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ruizhe Li
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Kevin Mclean
- Moredun Research Institute, Penicuik Midlothian, United Kingdom
| | | | | | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Hofmann
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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2
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Wang J, Hu J, Pu W, Chen X, Ma C, Jiang Y, Wang T, Chen T, Shaw C, Zhou M, Wang L. Discovery, development and optimisation of a novel frog antimicrobial peptide with combined mode of action against drug-resistant bacteria. Comput Struct Biotechnol J 2024; 23:3391-3406. [PMID: 39345903 PMCID: PMC11437748 DOI: 10.1016/j.csbj.2024.09.006] [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: 06/28/2024] [Revised: 09/12/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024] Open
Abstract
Antimicrobial peptides (AMP) have emerged as promising candidates for addressing the clinical challenges posed by the rapid evolution of antibiotic-resistant microorganisms. Brevinins, a representative frog-derived AMP family, exhibited broad-spectrum antimicrobial activities, attacking great attentions in previous studies. However, their strong haemolytic activity and cytotoxicity, greatly limit their further development. In this work, we identified and characterised a novel brevinin-1 peptide, brevinin-1pl, from the skin secretions of the northern leopard frog, Rana pipiens. Like many brevinins, brevinin-1pl also displayed strong haemolytic activity, resulting in a lower therapeutic index. We employed several bioinformatics tools to analyse the structure and potential membrane interactions of brevinin-1pl, leading to a series of modifications. Among these analogues, des-Ala16-[Lys4]brevinin-1pl exhibited great enhanced therapeutic efficacy in both in vitro and in vivo tests, particularly against some antibiotics-resistant Escherichia coli strains. Mechanistic studies suggest that des-Ala16-[Lys4]brevinin-1pl may exert bactericidal effects through multiple mechanisms, including membrane disruption and DNA binding. Consequently, des-Ala16-[Lys4]brevinin-1pl holds promise as a candidate for the treatment of drug-resistant Escherichia coli infections.
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Affiliation(s)
- Jingkai Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Jibo Hu
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
- China Medical University-The Queen's University of Belfast Joint College, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, PR China
| | - Wenyuan Pu
- College of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, PR China
| | - Xiaoling Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Yangyang Jiang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Tao Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
- China Medical University-The Queen's University of Belfast Joint College, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, PR China
| | - Chris Shaw
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
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3
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Elbahnsi A, Dudas B, Cisternino S, Declèves X, Miteva MA. Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations. Comput Struct Biotechnol J 2024; 23:2548-2564. [PMID: 38989058 PMCID: PMC11233806 DOI: 10.1016/j.csbj.2024.06.010] [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: 05/02/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
P-glycoprotein (P-gp) plays a crucial role in cellular detoxification and drug efflux processes, transitioning between inward-facing (IF) open, occluded, and outward-facing (OF) states to facilitate substrate transport. Its role is critical in cancer therapy, where P-gp contributes to the multidrug resistance phenotype. In our study, classical and enhanced molecular dynamics (MD) simulations were conducted to dissect the structural and functional features of the P-gp conformational states. Our advanced MD simulations, including kinetically excited targeted MD (ketMD) and adiabatic biasing MD (ABMD), provided deeper insights into state transition and translocation mechanisms. Our findings suggest that the unkinking of TM4 and TM10 helices is a prerequisite for correctly achieving the outward conformation. Simulations of the IF-occluded conformations, characterized by kinked TM4 and TM10 helices, consistently demonstrated altered communication between the transmembrane domains (TMDs) and nucleotide binding domain 2 (NBD2), suggesting the implication of this interface in inhibiting P-gp's efflux function. A particular emphasis was placed on the unstructured linker segment connecting the NBD1 to TMD2 and its role in the transporter's dynamics. With the linker present, we specifically noticed a potential entrance of cholesterol (CHOL) through the TM4-TM6 portal, shedding light on crucial residues involved in accommodating CHOL. We therefore suggest that this entry mechanism could be employed for some P-gp substrates or inhibitors. Our results provide critical data for understanding P-gp functioning and developing new P-gp inhibitors for establishing more effective strategies against multidrug resistance.
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Affiliation(s)
- Ahmad Elbahnsi
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Salvatore Cisternino
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Xavier Declèves
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Maria A. Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
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Anandhan Sujatha V, Gopalakrishnan C, Anbarasu A, Ponnusamy CS, Choudhary R, Saravanan Geetha SA, Ramalingam R. Beyond the venom: Exploring the antimicrobial peptides from Androctonus species of scorpion. J Pept Sci 2024; 30:e3613. [PMID: 38749486 DOI: 10.1002/psc.3613] [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: 01/04/2024] [Revised: 04/12/2024] [Accepted: 05/01/2024] [Indexed: 10/08/2024]
Abstract
Prevalent worldwide, the Androctonus scorpion genus contributes a vital role in scorpion envenoming. While diverse scorpionisms are observed because of several different species, their secretions to protect themselves have been identified as a potent source of antimicrobial peptide (AMP)-like compounds. Distinctly, the venom of these species contains around 24 different AMPs, with definite molecules studied for their therapeutic potential as antimicrobial, antifungal, antiproliferative and antiangiogenic agents. Our review focuses on the therapeutic potential of native and synthetic AMPs identified so far in the Androctonus scorpion genus, identifying research gaps in peptide therapeutics and guiding further investigations. Certain AMPs have demonstrated remarkable compatibility to be prescribed as anticancer drug to reduce cancer cell proliferation and serve as a potent antibiotic alternative. Besides, analyses were performed to explore the characteristics and affinities of peptides for membranes. Overall, the study of AMPs derived from the Androctonus scorpion genus provides valuable insights into their potential applications in medicine and drug development.
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Affiliation(s)
- Vinutha Anandhan Sujatha
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - Chandrasekhar Gopalakrishnan
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - Amarnath Anbarasu
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - Chandra Sekar Ponnusamy
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - Rajkumar Choudhary
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - Sree Agash Saravanan Geetha
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
| | - Rajasekaran Ramalingam
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, India
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5
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Pipatpadungsin N, Chao K, Rouse SL. Coarse-Grained Simulations of Adeno-Associated Virus and Its Receptor Reveal Influences on Membrane Lipid Organization and Curvature. J Phys Chem B 2024; 128:10139-10153. [PMID: 39356546 DOI: 10.1021/acs.jpcb.4c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Adeno-associated virus (AAV) is a well-known gene delivery tool with a wide range of applications, including as a vector for gene therapies. However, the molecular mechanism of its cell entry remains unknown. Here, we performed coarse-grained molecular dynamics simulations of the AAV serotype 2 (AAV2) capsid and the universal AAV receptor (AAVR) in a model plasma membrane environment. Our simulations show that binding of the AAV2 capsid to the membrane induces membrane curvature, along with the recruitment and clustering of GM3 lipids around the AAV2 capsid. We also found that the AAVR binds to the AAV2 capsid at the VR-I loops using its PKD2 and PKD3 domains, whose binding poses differs from previous structural studies. These first molecular-level insights into AAV2 membrane interactions suggest a complex process during the initial phase of AAV2 capsid internalization.
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Affiliation(s)
- Nichakorn Pipatpadungsin
- Department of Life Sciences, South Kensington Campus, Imperial College London, London SW7 5NH, U.K
| | - Kin Chao
- Department of Chemistry, Imperial College London, London W12 7TA, U.K
| | - Sarah L Rouse
- Department of Life Sciences, South Kensington Campus, Imperial College London, London SW7 5NH, U.K
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Hardy BJ, Ford HC, Rudin M, Anderson JLR, Curnow P. Polymer nanodiscs support the functional extraction of an artificial transmembrane cytochrome. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1867:184392. [PMID: 39414100 DOI: 10.1016/j.bbamem.2024.184392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 09/25/2024] [Accepted: 10/11/2024] [Indexed: 10/18/2024]
Abstract
Polymer nanodiscs are an attractive alternative to surfactants for studying integral membrane proteins within their native lipid environment. Here, we investigate the use of such polymers to isolate a computationally-designed de novo membrane cytochrome named CytbX. We show that the block copolymers known as CyclAPols can efficiently extract CytbX directly from biomembranes and are compatible with the downstream purification and biophysical characterisation of this artificial protein. CyclAPol-solubilised CytbX is well-folded and highly robust with properties that are essentially identical to those observed for the same protein in a detergent micelle. However, electron transfer to CytbX from a diffusive flavoprotein is substantially faster in micelles than in the nanodisc system. Our results confirm that polymer nanodiscs will be a useful tool for the ongoing study and application of de novo membrane proteins.
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Affiliation(s)
| | - Holly C Ford
- School of Biochemistry, University of Bristol, UK
| | - May Rudin
- School of Biochemistry, University of Bristol, UK
| | | | - Paul Curnow
- School of Biochemistry, University of Bristol, UK.
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7
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Nordquist EB, Zhao M, Kumar A, MacKerell AD. Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots. J Chem Inf Model 2024; 64:7743-7757. [PMID: 39283165 PMCID: PMC11473228 DOI: 10.1021/acs.jcim.4c01189] [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: 10/15/2024]
Abstract
Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Competitive Saturation (SILCS) method accounts for the flexibility of the target protein using all-atom molecular simulations that include various small molecule solutes in aqueous solution. During the simulations, the combination of protein flexibility and comprehensive sampling of the water and solute spatial distributions can identify buried binding pockets absent in experimentally determined structures. Previously, we reported a method for leveraging the information in the SILCS sampling to identify binding sites (termed Hotspots) of small mono- or bicyclic compounds, a subset of which coincide with known binding sites of drug-like molecules. Here, we build on that physics-based approach and present a ML model for ranking the Hotspots according to the likelihood they can accommodate drug-like molecules (e.g., molecular weight >200 Da). In the independent validation set, which includes various enzymes and receptors, our model recalls 67% and 89% of experimentally validated ligand binding sites in the top 10 and 20 ranked Hotspots, respectively. Furthermore, we show that the model's output Decision Function is a useful metric to predict binding sites and their potential druggability in new targets. Given the utility the SILCS method for ligand discovery and optimization, the tools presented represent an important advancement in the identification of orthosteric and allosteric binding sites and the discovery of drug-like molecules targeting those sites.
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Affiliation(s)
- Erik B. Nordquist
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Mingtian Zhao
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Anmol Kumar
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
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8
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Salsabila SD, Kim J. Structural insights into phosphatidylethanolamine N-methyltransferase PmtA mediating bacterial phosphatidylcholine synthesis. SCIENCE ADVANCES 2024; 10:eadr0122. [PMID: 39356767 PMCID: PMC11446283 DOI: 10.1126/sciadv.adr0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024]
Abstract
Phosphatidylethanolamine N-methyltransferase (PmtA) catalyzes the biosynthesis of phosphatidylcholine (PC) from phosphatidylethanolamine (PE). Although PC is one of the major phospholipids constituting bilayer membranes in eukaryotes, certain bacterial species encode PmtA, a membrane-associated methyltransferase, to produce PC, which is correlated with cellular stress responses, adaptability to environmental changes, and symbiosis or virulence with eukaryotic hosts. Depending on the organism, multiple PmtAs may be required for producing monomethyl- and dimethyl-PE derivatives along with PC, whereas in organisms such as Rubellimicrobium thermophilum, a single enzyme is sufficient to direct all three methylation steps. In this study, we present the x-ray crystal structures of PmtA from R. thermophilum in complex with dimethyl-PE and S-adenosyl-l-homocysteine, as well as in its lipid-free form. Moreover, we demonstrate that the enzyme associates with the cellular membrane via electrostatic interactions facilitated by a group of critical basic residues and can successively methylate PE and its methylated derivatives, culminating in the production of PC.
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Affiliation(s)
- Salma D Salsabila
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
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9
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Beauchet A, Bollier N, Grison M, Rofidal V, Gévaudant F, Bayer E, Gonzalez N, Chevalier C. The CELL NUMBER REGULATOR FW2.2 protein regulates cell-to-cell communication in tomato by modulating callose deposition at plasmodesmata. PLANT PHYSIOLOGY 2024; 196:883-901. [PMID: 38588030 PMCID: PMC11444278 DOI: 10.1093/plphys/kiae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
FW2.2 (standing for FRUIT WEIGHT 2.2), the founding member of the CELL NUMBER REGULATOR (CNR) gene family, was the first cloned gene underlying a quantitative trait locus (QTL) governing fruit size and weight in tomato (Solanum lycopersicum). However, despite this discovery over 20 yr ago, the molecular mechanisms by which FW2.2 negatively regulates cell division during fruit growth remain undeciphered. In the present study, we confirmed that FW2.2 is a membrane-anchored protein whose N- and C-terminal ends face the apoplast. We unexpectedly found that FW2.2 is located at plasmodesmata (PD). FW2.2 participates in the spatiotemporal regulation of callose deposition at PD and belongs to a protein complex which encompasses callose synthases. These results suggest that FW2.2 has a regulatory role in cell-to-cell communication by modulating PD transport capacity and trafficking of signaling molecules during fruit development.
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Affiliation(s)
- Arthur Beauchet
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Norbert Bollier
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Magali Grison
- CNRS, UMR5200 Laboratoire de Biogenèse Membranaire, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Valérie Rofidal
- IPSiM, CNRS, INRAE, Institut Sup Agro, Université Montpellier, Montpellier F-34060, France
| | - Frédéric Gévaudant
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Emmanuelle Bayer
- CNRS, UMR5200 Laboratoire de Biogenèse Membranaire, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Nathalie Gonzalez
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
| | - Christian Chevalier
- INRAE, UMR1332 Biologie du Fruit et Pathologie, Université Bordeaux, Villenave d'Ornon F-33140, France
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10
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Yalçınkaya B, Sağlam KA, Terali K, Tekin E, Taslak H, Türkyılmaz A. Biallelic Deletion of PEX26 Exon 4 in a Boy with Phenotypic Features of both Zellweger Syndrome and Infantile Refsum Disease. Mol Syndromol 2024; 15:380-388. [PMID: 39359950 PMCID: PMC11444700 DOI: 10.1159/000538676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/02/2024] [Indexed: 10/04/2024] Open
Abstract
Introduction Peroxisome biogenesis disorders (PBDs) encompass a group of diseases marked by clinical and genetic heterogeneity. Phenotypes linked to PBDs include Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum disease (IRD), rhizomelic chondrodysplasia punctata type 1, and Heimler syndrome. PBD phenotypes manifest through hypotonia, developmental delay, facial dysmorphism, seizures, liver dysfunction, sensorineural hearing loss, and retinal dystrophy. Methods The proband underwent comprehensive clinical evaluation, followed by whole-exome sequencing (WES) coupled with copy number analysis (CNV), aimed at identifying potential disease-causing variants aligning with the observed phenotype. Results Our findings detail an individual exhibiting developmental delay, hearing loss, visual impairment, hepatomegaly, and splenomegaly, attributed to a biallelic deletion of exon 4 in the PEX26 gene. The WES analysis of the index case did not uncover any pathogenic/likely pathogenic single-nucleotide variations that could account for the observed clinical findings. However, the CNV data derived from WES revealed a homozygous deletion in exon 4 of the PEX26 gene (NM_001127649.3), providing a plausible explanation for the patient's clinical features. The exon 4 region of PEX26 encodes the transmembrane domain of the protein. The transmembrane domain plays a crucial role in anchoring the protein within lipid bilayers, and its absence can disrupt proper localization and functioning. As a result, this structural alteration may impact the protein's ability to facilitate essential cellular processes related to peroxisome biogenesis and function. Conclusion The index patient, which presented with hearing loss, retinal involvement and hepatic dysfunction in adolescence age, has atypical clinical course that can be considered unusual for Zellweger syndrome (ZS) and IRD phenotypes, and its rare genotypic data (in-frame single exon deletion) expands the PBD disease spectrum. This study revealed for the first time that PEX26 protein transmembrane domain loss exhibits an unusual course with clinical findings of IRD and ZS phenotypes. WES studies, incorporating CNV analyses, empower the identification of novel genetic alterations in genes seldom associated with gross deletion/duplication variations, such as those in the PEX26 gene. This not only enhances diagnostic rates in rare diseases but also contributes to broadening the spectrum of causal mutations.
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Affiliation(s)
| | - Kübra Adanur Sağlam
- Department of Medical Genetics, Karadeniz Technical University, Faculty of Medicine, Trabzon, Turkey
| | - Kerem Terali
- Department of Medical Biochemistry, Cyprus International University Faculty of Medicine, Nicosia, Cyprus
| | - Emine Tekin
- Department of Pediatric Neurology, Giresun University, Faculty of Medicine, Giresun, Turkey
| | - Hava Taslak
- TUBITAK National Metrology Institute (TUBITAK UME), Gebze-Kocaeli, Turkey
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Ayberk Türkyılmaz
- Department of Medical Genetics, Karadeniz Technical University, Faculty of Medicine, Trabzon, Turkey
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11
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Yun Y, Jeong H, Laboute T, Martemyanov KA, Lee HH. Cryo-EM structure of human class C orphan GPCR GPR179 involved in visual processing. Nat Commun 2024; 15:8299. [PMID: 39333506 PMCID: PMC11437087 DOI: 10.1038/s41467-024-52584-z] [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: 11/18/2023] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
GPR179, an orphan class C GPCR, is expressed at the dendritic tips of ON-bipolar cells in the retina. It plays a pivotal role in the initial synaptic transmission of visual signals from photoreceptors, and its deficiency is known to be the cause of complete congenital stationary night blindness. Here, we present the cryo-electron microscopy structure of human GPR179. Notably, the transmembrane domain (TMD) of GPR179 forms a homodimer through the TM1/7 interface with a single inter-protomer disulfide bond, adopting a noncanonical dimerization mode. Furthermore, the TMD dimer exhibits architecture well-suited for the highly curved membrane of the dendritic tip and distinct from the flat membrane arrangement observed in other class C GPCR dimers. Our structure reveals unique structural features of GPR179 TMD, setting it apart from other class C GPCRs. These findings provide a foundation for understanding signal transduction through GPR179 in visual processing and offers insights into the underlying causes of ocular diseases.
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Affiliation(s)
- Yaejin Yun
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute, Chungcheongbuk-do, 28119, Republic of Korea
| | - Thibaut Laboute
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, 33458, USA
- Université de Tours, INSERM, Imaging Brain & Neuropsychiatry iBraiN U1253, 37032, Tours, France
| | - Kirill A Martemyanov
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, 33458, USA.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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12
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Rathnayake SS, Erramilli SK, Kossiakoff AA, Vecchio AJ. Cryo-EM structures of Clostridium perfringens enterotoxin bound to its human receptor, claudin-4. Structure 2024:S0969-2126(24)00384-8. [PMID: 39383874 DOI: 10.1016/j.str.2024.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/09/2024] [Accepted: 09/12/2024] [Indexed: 10/11/2024]
Abstract
Clostridium perfringens enterotoxin (CpE) causes prevalent and deadly gastrointestinal disorders. CpE binds to receptors called claudins on the apical surfaces of small intestinal epithelium. Claudins normally regulate paracellular transport but are hijacked from doing so by CpE and are instead led to form claudin/CpE complexes. Claudin/CpE complexes are the building blocks of oligomeric β-barrel pores that penetrate the plasma membrane and induce gut cytotoxicity. Here, we present the structures of CpE in complex with its native claudin receptor in humans, claudin-4, using cryogenic electron microscopy. The structures reveal the architecture of the claudin/CpE complex, the residues used in binding, the orientation of CpE relative to the membrane, and CpE-induced changes to claudin-4. Further, structures and modeling allude to the biophysical procession from claudin/CpE complexes to cytotoxic β-barrel pores during pathogenesis. In full, this work proposes a model of claudin/CpE assembly and provides strategies to obstruct its formation to treat CpE diseases.
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Affiliation(s)
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alex J Vecchio
- Department of Structural Biology, University at Buffalo, Buffalo, NY 14203, USA.
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13
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Saha S, Mandal A, Ranjan A, Ghosh DK. Membrane tension sensing formin-binding protein 1 is a neuronal nutrient stress-responsive Golgiphagy receptor. Metabolism 2024:156040. [PMID: 39341273 DOI: 10.1016/j.metabol.2024.156040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024]
Abstract
BACKGROUND Nutrient stress-responsive neuronal homeostasis relies on intricate autophagic mechanisms that modulate various organelle integrity and function. The selective autophagy of the Golgi, known as Golgiphagy, regulates secretory processes by modulating vesicle trafficking during nutrient starvation. RESULTS In this study, we explored a genetic screen of BAR-domain-containing proteins to elucidate the role of formin-binding protein 1 (FNBP1) as a Golgiphagy receptor in modulating Golgi dynamics in response to varying nutrient availability in neurons. Mapping the systems network of FNBP1 and its interacting proteins reveals the putative involvement of FNBP1 in autophagy and Golgi-associated processes. While nutrient depletion causes Golgi fragmentation, FNBP1 preferentially localizes to the fragmented Golgi membrane through its 284FEDYTQ289 motif during nutrient stress. Simultaneously, FNBP1 engages in molecular interactions with LC3B through a conserved 131WKQL134 LC3 interacting region, thereby sequestering the fragmented Golgi membrane in neuronal autophagosomes. Increased aggregation of GM130, abnormal clumping of RAB11-positive secretory granules, and enhanced senescent death of FNBP1-depleted starved neurons indicate disruptions of neuronal homeostasis under metabolic stress. CONCLUSION The identification of FNBP1 as a nutrient stress-responsive Golgiphagy receptor expands our insights into the molecular mechanisms underlying Golgiphagy, establishing the crosstalk between nutrient sensing and membrane tension-sensing regulatory autophagic processes of Golgi turnover in neurons.
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Affiliation(s)
- Smita Saha
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anirban Mandal
- Department of Microbiology, Mrinalini Datta Mahavidyapith, Kolkata, West Bengal, India
| | - Akash Ranjan
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Debasish Kumar Ghosh
- Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India.
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14
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Luo D, Zhang Y, Li Y, Liu Z, Wu H, Xue W. Structural Models of Human Norepinephrine Transporter Ensemble Reveal the Allosteric Sites and Ligand-Binding Mechanism. J Phys Chem B 2024; 128:8651-8661. [PMID: 39207306 DOI: 10.1021/acs.jpcb.4c03731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The norepinephrine transporter (NET) plays a pivotal role in recycling norepinephrine (NE) from the synaptic cleft. However, the structures referring to the conformational heterogeneity of NET during the transport cycle remain poorly understood. Here, three structural models of NE bound to the orthosteric site of NET in outward-open (OOholo), outward-occluded (OCholo), and inward-open (IOholo) conformations were first obtained using the multistate structures of serotonin transporter as templates and further characterized through Gaussian-accelerated molecular dynamics and free energy reweighting. Analysis of the structures revealed eight potential allosteric sites on the functional-specific states of NET. One of the pharmacologically relevant pockets located at the extracellular vestibule was further verified by simulating the binding behaviors of a clinical trial drug χ-MrIA that is allosterically regulating NET. These structural and energetic insights into NET advanced our understanding of NE reuptake and paved the way for discovering novel molecules targeting the allosteric sites.
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Affiliation(s)
- Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yang Zhang
- School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, China
| | - Yinghong Li
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical Co., Ltd., Luzhou 646000, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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15
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Neubergerová M, Pleskot R. Plant protein-lipid interfaces studied by molecular dynamics simulations. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5237-5250. [PMID: 38761107 DOI: 10.1093/jxb/erae228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
Abstract
The delineation of protein-lipid interfaces is essential for understanding the mechanisms of various membrane-associated processes crucial to plant development and growth, including signalling, trafficking, and membrane transport. Due to their highly dynamic nature, the precise characterization of lipid-protein interactions by experimental techniques is challenging. Molecular dynamics simulations provide a powerful computational alternative with a spatial-temporal resolution allowing the atomistic-level description. In this review, we aim to introduce plant scientists to molecular dynamics simulations. We describe different steps of performing molecular dynamics simulations and provide a broad survey of molecular dynamics studies investigating plant protein-lipid interfaces. Our aim is also to illustrate that combining molecular dynamics simulations with artificial intelligence-based protein structure determination opens up unprecedented possibilities for future investigations of dynamic plant protein-lipid interfaces.
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Affiliation(s)
- Michaela Neubergerová
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Roman Pleskot
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
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16
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Adhikary K, Poget SF. Expanding the insect defensin landscape. Structure 2024; 32:1294-1296. [PMID: 39241760 DOI: 10.1016/j.str.2024.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/09/2024]
Abstract
In this issue of Structure, Walker et al.1 determined the NMR structure of a recently discovered defensin, Pp19, from the venom of an assassin bug. This peptide adopts an α-defensin-like structure, which had not been observed in insects before. Unlike mammalian α-defensins, which are generally antimicrobial, Pp19 has insecticidal activity.
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Affiliation(s)
- Krishnakoli Adhikary
- Department of Chemistry, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY 10314, USA; PhD Program in Chemistry, The Graduate Center, CUNY, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sébastien F Poget
- Department of Chemistry, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY 10314, USA; PhD Program in Chemistry, The Graduate Center, CUNY, 365 Fifth Avenue, New York, NY 10016, USA; PhD Program in Biochemistry, The Graduate Center, CUNY, 365 Fifth Avenue, New York, NY 10016, USA.
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17
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Doktorova M, Daum S, Ebenhan J, Neudorf S, Han B, Sharma S, Kasson P, Levental KR, Bacia K, Kenworthy AK, Levental I. Caveolin assemblies displace one bilayer leaflet to organize and bend membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610209. [PMID: 39257813 PMCID: PMC11383982 DOI: 10.1101/2024.08.28.610209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this 'leaflet replacement' model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40-70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Sebastian Daum
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Jan Ebenhan
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Sarah Neudorf
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Bing Han
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
| | - Satyan Sharma
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Peter Kasson
- Department of Cell and Molecular Biology, Uppsala University, Sweden
- Departments of Chemistry and Biochemistry and Biomedical Engineering, Georgia Institute of Technology, USA
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
| | - Kirsten Bacia
- Department of Physical Chemistry, Martin Luther University Halle-Wittenberg, Germany
| | - Anne K Kenworthy
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia, USA
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18
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Elmore G, Ahern BM, McVay NM, Barker KW, Lohano SS, Ali N, Sebastian A, Andres DA, Satin J, Levitan BM. The C-terminus of Rad is required for membrane localization and L-type calcium channel regulation. J Gen Physiol 2024; 156:e202313518. [PMID: 38990175 PMCID: PMC11244639 DOI: 10.1085/jgp.202313518] [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: 12/05/2023] [Revised: 05/17/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
L-type CaV1.2 current (ICa,L) links electrical excitation to contraction in cardiac myocytes. ICa,L is tightly regulated to control cardiac output. Rad is a Ras-related, monomeric protein that binds to L-type calcium channel β subunits (CaVβ) to promote inhibition of ICa,L. In addition to CaVβ interaction conferred by the Rad core motif, the highly conserved Rad C-terminus can direct membrane association in vitro and inhibition of ICa,L in immortalized cell lines. In this work, we test the hypothesis that in cardiomyocytes the polybasic C-terminus of Rad confers t-tubular localization, and that membrane targeting is required for Rad-dependent ICa,L regulation. We introduced a 3xFlag epitope to the N-terminus of the endogenous mouse Rrad gene to facilitate analysis of subcellular localization. Full-length 3xFlag-Rad (Flag-Rad) mice were compared with a second transgenic mouse model, in which the extended polybasic C-termini of 3xFlag-Rad was truncated at alanine 277 (Flag-RadΔCT). Ventricular cardiomyocytes were isolated for anti-Flag-Rad immunocytochemistry and ex vivo electrophysiology. Full-length Flag-Rad showed a repeating t-tubular pattern whereas Flag-RadΔCT failed to display membrane association. ICa,L in Flag-RadΔCT cardiomyocytes showed a hyperpolarized activation midpoint and an increase in maximal conductance. Additionally, current decay was faster in Flag-RadΔCT cells. Myocardial ICa,L in a Rad C-terminal deletion model phenocopies ICa,L modulated in response to β-AR stimulation. Mechanistically, the polybasic Rad C-terminus confers CaV1.2 regulation via membrane association. Interfering with Rad membrane association constitutes a specific target for boosting heart function as a treatment for heart failure with reduced ejection fraction.
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Affiliation(s)
- Garrett Elmore
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Brooke M Ahern
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Nicholas M McVay
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Kyle W Barker
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Sarisha S Lohano
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Nemat Ali
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Andrea Sebastian
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Douglas A Andres
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Jonathan Satin
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Bryana M Levitan
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Gill Heart and Vascular Institute , Lexington, KY, USA
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19
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Rao RM, El Dhaybi I, Cadet F, Etchebest C, Diharce J. The mutual and dynamic role of TSPO and ligands in their binding process: An example with PK-11195. Biochimie 2024; 224:29-40. [PMID: 38494108 DOI: 10.1016/j.biochi.2024.03.009] [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: 10/30/2023] [Revised: 02/12/2024] [Accepted: 03/15/2024] [Indexed: 03/19/2024]
Abstract
Translocator protein (TSPO) is an 18 kDa transmembrane protein, localized primarily on the outer mitochondrial membrane. It has been found to be involved in various physiological processes and pathophysiological conditions. Though studies on its structure have been performed only recently, there is little information on the nature of dynamics and doubts about some structures referenced in the literature, especially the NMR structure of mouse TSPO. In the present work, we thoroughly study the dynamics of mouse TSPO protein by means of atomistic molecular dynamics simulations, in presence as well as in absence of the diagnostic ligand PKA. We considered two starting structures: the NMR structure and a homology model (HM) generated on the basis of X-ray structures from bacterial TSPO. We examine the conformational landscape in both the modes for both starting points, in presence and absence of the ligand, in order to measure its impact for both structures. The analysis highlights high flexibility of the protein globally, but NMR simulations show a surprisingly flexibility even in the presence of the ligand. Interestingly, this is not the case for HM calculations, to the point that the ligand seems not so stable as in the NMR system and an unbinding event process is partially sampled. All those results tend to show that the NMR structure of mTSPO seems not deficient but is just in another portion of the global conformation space of TSPO.
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Affiliation(s)
- Rajas M Rao
- Data Analytics, Bioinformatics and Structural Biology Division, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India; Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France
| | - Ibaa El Dhaybi
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France; Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715, Saint Denis Messag, France; PEACCEL, Artificial Intelligence Department, Paris, 75013 France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB UMR_S1134, F-74014, Paris, France; Laboratory of Excellence GR-Ex, Paris, France.
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20
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Mobilia M, Karakashian A, Neupane KR, Hage O, Whitus C, Carter A, Voy C, Johnson LA, Graf GA, Gordon SM. Enhancement of high-density lipoprotein-associated protease inhibitor activity prevents atherosclerosis progression. Atherosclerosis 2024; 396:118544. [PMID: 39126769 PMCID: PMC11404725 DOI: 10.1016/j.atherosclerosis.2024.118544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/28/2024] [Accepted: 07/11/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND AND AIMS Inflammatory cells within atherosclerotic lesions secrete proteolytic enzymes that contribute to lesion progression and destabilization, increasing the risk for an acute cardiovascular event. Elastase is a serine protease, secreted by macrophages and neutrophils, that may contribute to the development of unstable plaque. We previously reported interaction of endogenous protease-inhibitor proteins with high-density lipoprotein (HDL), including alpha-1-antitrypsin, an inhibitor of elastase. These findings support a potential role for HDL as a modulator of protease activity. In this study, we test the hypothesis that enhancement of HDL-associated elastase inhibitor activity is protective against atherosclerotic lesion progression. METHODS We designed an HDL-targeting protease inhibitor (HTPI) that binds to HDL and confers elastase inhibitor activity. Lipoprotein binding and the impact of HTPI on atherosclerosis were examined using mouse models. Histology and immunofluorescence staining of aortic root sections were used to examine the impact of HTPI on lesion morphology and inflammatory features. RESULTS HTPI is a small (1.6 kDa) peptide with an elastase inhibitor domain, a soluble linker, and an HDL-targeting domain. When incubated with human plasma ex vivo, HTPI predominantly binds to HDL. Intravenous administration of HTPI to mice resulted in its binding to plasma HDL and increased elastase inhibitor activity on isolated HDL. Accumulation of HTPI within plaque was observed after administration to Apoe-/- mice. To examine the effect of HTPI treatment on atherosclerosis, prevention and progression studies were performed using Ldlr-/- mice fed Western diet. In both study designs, HTPI-treated mice had reduced lipid deposition in plaque. CONCLUSIONS These data support the hypothesis that HDL-associated anti-elastase activity can improve the atheroprotective potential of HDL and highlight the potential utility of HDL enrichment with anti-protease activity as an approach for stabilization of atherosclerotic lesions.
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Affiliation(s)
- Maura Mobilia
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | | | - Khaga R Neupane
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Olivia Hage
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Callie Whitus
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Abigail Carter
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Clairity Voy
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Lance A Johnson
- Department of Physiology, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Gregory A Graf
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA; Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Scott M Gordon
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA; Department of Physiology, University of Kentucky, Lexington, KY, USA.
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21
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Markwardt F, Schön EC, Raycheva M, Malisetty A, Hawro Yakoob S, Berthold M, Schmalzing G. Two serial filters control P2X7 cation selectivity, Ser342 in the central pore and lateral acidic residues at the cytoplasmic interface. PNAS NEXUS 2024; 3:pgae349. [PMID: 39262850 PMCID: PMC11388005 DOI: 10.1093/pnasnexus/pgae349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 07/31/2024] [Indexed: 09/13/2024]
Abstract
The human P2X7 receptor (hP2X7R) is a homotrimeric cell surface receptor gated by extracellular ATP4- with two transmembrane helices per subunit, TM1 and TM2. A ring of three S342 residues, one from each pore-forming TM2 helix, located halfway across the membrane bilayer, functions to close and open the gate in the apo and ATP4--bound open states, respectively. The hP2X7R is selective for small inorganic cations, but can also conduct larger organic cations such as Tris+. Here, we show by voltage-clamp electrophysiology in Xenopus laevis oocytes that mutation of S342 residues to positively charged lysines decreases the selectivity for Na+ over Tris+, but maintains cation selectivity. Deep in the membrane, laterally below the S342 ring are nine acidic residues arranged as an isosceles triangle consisting of residues E14, D352, and D356 on each side, which do not move significantly during gating. When the E14K mutation is combined with lysine substitutions of D352 and/or D356, cation selectivity is lost and permeation of the small anion Cl- is allowed. Lysine substitutions of S342 together with D352 or E14 plus D356 in the acidic triangle convert the hP2X7R mutant to a fully Cl--selective ATP4--gated receptor. We conclude that the ion selectivity of wild-type hP2X7R is determined by two sequential filters in one single pathway: (i) a primary size filter, S342, in the membrane center and (ii) three cation filters lateral to the channel axis, one per subunit interface, consisting of a total of nine acidic residues at the cytoplasmic interface.
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Affiliation(s)
- Fritz Markwardt
- Julius-Bernstein-Institute of Physiology, Martin-Luther-University, Magdeburger Straße 6, D-06097 Halle/Saale, Germany
| | - Eike Christian Schön
- Julius-Bernstein-Institute of Physiology, Martin-Luther-University, Magdeburger Straße 6, D-06097 Halle/Saale, Germany
| | - Michaela Raycheva
- Institute of Clinical Pharmacology, RWTH Aachen University, Wendlingweg 2, D-52074 Aachen, Germany
| | - Aparna Malisetty
- Institute of Clinical Pharmacology, RWTH Aachen University, Wendlingweg 2, D-52074 Aachen, Germany
| | - Sanaria Hawro Yakoob
- Institute of Clinical Pharmacology, RWTH Aachen University, Wendlingweg 2, D-52074 Aachen, Germany
| | - Malte Berthold
- Julius-Bernstein-Institute of Physiology, Martin-Luther-University, Magdeburger Straße 6, D-06097 Halle/Saale, Germany
| | - Günther Schmalzing
- Institute of Clinical Pharmacology, RWTH Aachen University, Wendlingweg 2, D-52074 Aachen, Germany
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22
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Kantarcioglu I, Gaszek IK, Guclu TF, Yildiz MS, Atilgan AR, Toprak E, Atilgan C. Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance. Commun Biol 2024; 7:1051. [PMID: 39187619 PMCID: PMC11347637 DOI: 10.1038/s42003-024-06750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024] Open
Abstract
Efflux-mediated β-lactam resistance is a major public health concern, reducing the effectiveness of β-lactam antibiotics against many bacteria. Structural analyses show the efflux protein TolC in Gram-negative bacteria acts as a channel for antibiotics, impacting bacterial susceptibility and virulence. This study examines β-lactam drug efflux mediated by TolC using experimental and computational methods. Molecular dynamics simulations of drug-free TolC reveal essential movements and key residues involved in TolC opening. A whole-gene-saturation mutagenesis assay, mutating each TolC residue and measuring fitness effects under β-lactam selection, is performed. Here we show the TolC-mediated efflux of three antibiotics: oxacillin, piperacillin, and carbenicillin. Steered molecular dynamics simulations identify general and drug-specific efflux mechanisms, revealing key positions at TolC's periplasmic entry affecting efflux motions. Our findings provide insights into TolC's structural dynamics, aiding the design of new antibiotics to overcome bacterial efflux mechanisms.
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Affiliation(s)
- Isik Kantarcioglu
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ilona K Gaszek
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tandac F Guclu
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey
| | - M Sadik Yildiz
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ali Rana Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey
| | - Erdal Toprak
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, Istanbul, Turkey.
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23
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Peñaflor-Téllez Y, Escobar-Almazan JA, Pérez-Ibáñez C, Miguel-Rodríguez CE, Gómez de la Madrid J, Monge-Celestino EI, Talamás-Rohana P, Gutiérrez-Escolano AL. The Feline calicivirus Leader of the Capsid (LC) Protein Contains a Putative Transmembrane Domain, Binds to the Cytoplasmic Membrane, and Exogenously Permeates Cells. Viruses 2024; 16:1319. [PMID: 39205293 PMCID: PMC11359386 DOI: 10.3390/v16081319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Feline calicivirus (FCV), an important model for studying the biology of the Caliciviridae family, encodes the leader of the capsid (LC) protein, a viral factor known to induce apoptosis when expressed in a virus-free system. Our research has shown that the FCV LC protein forms disulfide bond-dependent homo-oligomers and exhibits intrinsic toxicity; however, it lacked a polybasic region and a transmembrane domain (TMD); thus, it was initially classified as a non-classical viroporin. The unique nature of the FCV LC protein, with no similarity to other proteins beyond the Vesivirus genus, has posed challenges for bioinformatic analysis reliant on sequence similarity. In this study, we continued characterizing the LC protein using the AlphaFold 2 and the recently released AlphaFold 3 artificial intelligence tools to predict the LC protein tertiary structure. We compared it to other molecular modeling algorithms, such as I-Tasser's QUARK, offering new insights into its putative TMD. Through exogenous interaction, we found that the recombinant LC protein associates with the CrFK plasmatic membrane and can permeate cell membranes in a disulfide bond-independent manner, suggesting that this interaction might occur through a TMD. Additionally, we examined its potential to activate the intrinsic apoptosis pathway in murine and human ovarian cancer cell lines, overexpressing survivin, an anti-apoptotic protein. All these results enhance our understanding of the LC protein's mechanism of action and suggest its role as a class-I viroporin.
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Affiliation(s)
| | | | | | | | | | | | | | - Ana Lorena Gutiérrez-Escolano
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, Col. San Pedro Zacatenco, Mexico City 07360, Mexico; (Y.P.-T.); (J.A.E.-A.); (C.P.-I.); (C.E.M.-R.); (J.G.d.l.M.); (E.I.M.-C.); (P.T.-R.)
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24
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Hardy BJ, Dubiel P, Bungay EL, Rudin M, Williams C, Arthur CJ, Guberman‐Pfeffer MJ, Sofia Oliveira A, Curnow P, Anderson JLR. Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design. Protein Sci 2024; 33:e5113. [PMID: 38980168 PMCID: PMC11232281 DOI: 10.1002/pro.5113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.
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Affiliation(s)
| | | | | | - May Rudin
- School of BiochemistryUniversity of BristolBristolUK
| | | | | | | | | | - Paul Curnow
- School of BiochemistryUniversity of BristolBristolUK
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25
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Unneberg P, Larsson M, Olsson A, Wallerman O, Petri A, Bunikis I, Vinnere Pettersson O, Papetti C, Gislason A, Glenner H, Cartes JE, Blanco-Bercial L, Eriksen E, Meyer B, Wallberg A. Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins. Nat Commun 2024; 15:6297. [PMID: 39090106 PMCID: PMC11294593 DOI: 10.1038/s41467-024-50239-7] [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: 12/06/2023] [Accepted: 05/15/2024] [Indexed: 08/04/2024] Open
Abstract
Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.
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Affiliation(s)
- Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Anna Petri
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, Department of Immunology, Genetics and Pathology, Uppsala University, National Genomics Infrastructure hosted by SciLifeLab, Uppsala, Sweden
| | | | - Astthor Gislason
- Marine and Freshwater Research Institute, Pelagic Division, Reykjavik, Iceland
| | - Henrik Glenner
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Center for Macroecology, Evolution and Climate Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joan E Cartes
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
| | | | | | - Bettina Meyer
- Section Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carlvon Ossietzky University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden.
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26
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Pradhan B, Pavan M, Fisher CL, Salmaso V, Wan TC, Keyes RF, Rollison N, Suresh RR, Kumar TS, Gao ZG, Smith BC, Auchampach JA, Jacobson KA. Lipid Trolling to Optimize A 3 Adenosine Receptor-Positive Allosteric Modulators (PAMs). J Med Chem 2024; 67:12221-12247. [PMID: 38959401 DOI: 10.1021/acs.jmedchem.4c00944] [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: 07/05/2024]
Abstract
A3 adenosine receptor (A3AR) positive allosteric modulators (PAMs) (2,4-disubstituted-1H-imidazo[4,5-c]quinolin-4-amines) allosterically increase the Emax of A3AR agonists, but not potency, due to concurrent orthosteric antagonism. Following mutagenesis/homology modeling of the proposed lipid-exposed allosteric binding site on the cytosolic side, we functionalized the scaffold, including heteroatom substitutions and exocyclic phenylamine extensions, to increase allosteric binding. Strategically appended linear alkyl-alkynyl chains with terminal amino/guanidino groups improved allosteric effects at both human and mouse A3ARs. The chain length, functionality, and attachment position were varied to modulate A3AR PAM activity. For example, 26 (MRS8247, p-alkyne-linked 8 methylenes) and homologues increased agonist Cl-IB-MECA's Emax and potency ([35S]GTPγS binding). The putative mechanism involves a flexible, terminally cationic chain penetrating the lipid environment for stable electrostatic anchoring to cytosolic phospholipid head groups, suggesting "lipid trolling", supported by molecular dynamic simulation of the active-state model. Thus, we have improved A3AR PAM activity through rational design based on an extrahelical, lipidic binding site.
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Affiliation(s)
- Balaram Pradhan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Matteo Pavan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Courtney L Fisher
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy
| | - Tina C Wan
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Robert F Keyes
- Department of Biochemistry and the Program in Chemical Biology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Noah Rollison
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - T Santhosh Kumar
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Brian C Smith
- Department of Biochemistry and the Program in Chemical Biology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - John A Auchampach
- Department of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
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27
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Tosh D, Pavan M, Cronin C, Pottie E, Wan TC, Chen E, Lewicki SA, Campbell RG, Gao ZG, Auchampach JA, Stove CP, Liang BT, Jacobson KA. 2-Substituted (N)-Methanocarba A 3 Adenosine Receptor Agonists: In Silico, In Vitro, and In Vivo Characterization. ACS Pharmacol Transl Sci 2024; 7:2154-2173. [PMID: 39022354 PMCID: PMC11249627 DOI: 10.1021/acsptsci.4c00223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
2-Arylethynyl (N)-methanocarba adenosine 5'-methylamides are selective A3 adenosine receptor (AR) agonists containing a preestablished receptor-preferred pseudoribose conformation. Here, we compare analogues having bulky 2-substitution, either containing or lacking an ethynyl spacer between adenine and a cyclic group. 2-Aryl compounds 9-11, 13, 14, 19, 22, 23, 27, 29, 31, and 34, lacking a spacer, had human (h) A3AR K i values of 2-30 nM, and others displayed lower affinity. Mouse (m) A3AR affinity varied, with 2-arylethynyl having a higher affinity than 2-aryl analogues (7, 8 > 3c, 3d > 3b). However, 2-aryl-4'-truncated derivatives had greatly reduced hA3AR affinity, even containing affinity-enhancing N 6-dopamine-derived substituents. Molecular modeling, including molecular dynamics simulation, predicted stable poses in the canonical A3AR agonist binding site, but 2-aryl (ECL2 interactions) and 2-arylethynyl (TM2 interactions) substituents have different conformations and environments. In a hA3AR miniGαi recruitment assay, 31 (MRS8062) was (slightly) more potent compared to a β-arrestin2 recruitment assay, both in engineered HEK293T cells, and its maximal efficacy (E max) was much higher (165%) than reference agonist NECA's. Thus, in the 2-aryl series, A3AR affinity and selectivity were variable and generally reduced compared to the 2-arylethynyl series, with a greater dependence on the specific aryl group present. Selected compounds were studied in vivo in an ischemic model of peripheral artery disease (PAD). Rigidified 2-arylethynyl analogues 3a-3c were protective in this model of skeletal muscle ischemia-reperfusion injury/claudication, as previously shown only for moderately A3AR-selective ribosides or (N)-methanocarba derivatives. Thus, we have expanded the A3AR agonist SAR for (N)-methanocarba adenosines.
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Affiliation(s)
- Dilip
K. Tosh
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Matteo Pavan
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Chunxia Cronin
- Pat
and Jim Calhoun Cardiology Center, University
of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Eline Pottie
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg
460, B-9000 Ghent, Belgium
| | - Tina C. Wan
- Department
of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Eric Chen
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Sarah A. Lewicki
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Ryan G. Campbell
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - John A. Auchampach
- Department
of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Christophe P. Stove
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg
460, B-9000 Ghent, Belgium
| | - Bruce T. Liang
- Pat
and Jim Calhoun Cardiology Center, University
of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
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28
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Cino EA, Tieleman DP. Curvature Footprints of Transmembrane Proteins in Simulations with the Martini Force Field. J Phys Chem B 2024; 128:5987-5994. [PMID: 38860934 PMCID: PMC11216194 DOI: 10.1021/acs.jpcb.4c01385] [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: 03/02/2024] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024]
Abstract
Membranes play essential roles in biological systems and are tremendously diverse in the topologies and chemical and elastic properties that define their functions. In many cases, a given membrane may display considerable heterogeneity, with localized clusters of lipids and proteins exhibiting distinct characteristics compared to adjoining regions. These lipid-protein assemblies can span nanometers to micrometers and are associated with cellular processes such as transport and signaling. While lipid-protein assemblages are dynamic, they can be stabilized by coupling between local membrane composition and shape. Due to the inherent difficulty in resolving atomistic details of membrane proteins in their native lipid environments, these complexes are notoriously challenging to study experimentally; however, molecular dynamics (MD) simulations might be a viable alternative. Here, we aim to assess the utility of coarse-grained (CG) MD simulations with the Martini force field for studying membrane curvature induced by transmembrane (TM) proteins that are reported to generate local curvature. The direction and magnitude of curvature induced by five different TM proteins, as well as certain lipid-protein and protein-protein interactions, were found to be in good agreement with available reference data.
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Affiliation(s)
- Elio A. Cino
- Centre for Molecular Simulation
and Department of Biological Sciences, University
of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - D. Peter Tieleman
- Centre for Molecular Simulation
and Department of Biological Sciences, University
of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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29
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Kunzmann P, Krumbach JH, Saponaro A, Moroni A, Thiel G, Hamacher K. Anisotropic Network Analysis of Open/Closed HCN4 Channel Advocates Asymmetric Subunit Cooperativity in cAMP Modulation of Gating. J Chem Inf Model 2024; 64:4727-4738. [PMID: 38830626 PMCID: PMC11203669 DOI: 10.1021/acs.jcim.4c00360] [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: 03/01/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024]
Abstract
Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels are opened in an allosteric manner by membrane hyperpolarization and cyclic nucleotides such as cAMP. Because of conflicting reports from experimental studies on whether cAMP binding to the four available binding sites in the channel tetramer operates cooperatively in gating, we employ here a computational approach as a promising route to examine ligand-induced conformational changes after binding to individual sites. By combining an elastic network model (ENM) with linear response theory (LRT) for modeling the apo-holo transition of the cyclic nucleotide-binding domain (CNBD) in HCN channels, we observe a distinct pattern of cooperativity matching the "positive-negative-positive" cooperativity reported from functional studies. This cooperativity pattern is highly conserved among HCN subtypes (HCN4, HCN1), but only to a lesser extent visible in structurally related channels, which are only gated by voltage (KAT1) or cyclic nucleotides (TAX4). This suggests an inherent cooperativity between subunits in HCN channels as part of a ligand-triggered gating mechanism in these channels.
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Affiliation(s)
- Patrick Kunzmann
- Department
of Biology, Computational Biology & Simulation, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Jan H. Krumbach
- Department
of Biology, Computational Biology & Simulation, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Andrea Saponaro
- Department
of Pharmacology and Biomolecular Sciences, University of Milano, via Balzaretti 9, 20133 Milano, Italy
| | - Anna Moroni
- Department
of Biosciences, Ion Channel Biophysics, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Gerhard Thiel
- Department
of Biology, Membrane Biophysics, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre
for Synthetic Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Kay Hamacher
- Department
of Biology, Computational Biology & Simulation, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre
for Synthetic Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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30
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Kang Y, Lehmann KS, Vanegas J, Long H, Jefferson A, Freeman M, Clark S. Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600134. [PMID: 38948693 PMCID: PMC11213131 DOI: 10.1101/2024.06.21.600134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle 1 . Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic C. elegans . LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named "Intake" and "Spigot", both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 Å along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.
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31
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Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [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: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
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Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
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32
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Solano YJ, Everett MP, Dang KS, Abueg J, Kiser PD. Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore. Nat Chem Biol 2024; 20:779-788. [PMID: 38355721 PMCID: PMC11142922 DOI: 10.1038/s41589-024-01554-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans-cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65-an evolutionary convergence that deepens our understanding of visual system diversity.
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Affiliation(s)
- Yasmeen J Solano
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Michael P Everett
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA
| | - Kelly S Dang
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Jude Abueg
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Philip D Kiser
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA.
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA.
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine School of Medicine, Irvine, CA, USA.
- Department of Clinical Pharmacy Practice, University of California Irvine School of Pharmacy and Pharmaceutical Sciences, Irvine, CA, USA.
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33
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Yee SW, Ferrández-Peral L, Alentorn-Moron P, Fontsere C, Ceylan M, Koleske ML, Handin N, Artegoitia VM, Lara G, Chien HC, Zhou X, Dainat J, Zalevsky A, Sali A, Brand CM, Wolfreys FD, Yang J, Gestwicki JE, Capra JA, Artursson P, Newman JW, Marquès-Bonet T, Giacomini KM. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nat Commun 2024; 15:4380. [PMID: 38782905 PMCID: PMC11116522 DOI: 10.1038/s41467-024-48569-7] [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: 08/14/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane. Cells expressing great ape SLC22A10 orthologs exhibit significant accumulation of estradiol-17β-glucuronide, unlike those expressing human SLC22A10. Sequence alignments reveal a proline at position 220 in humans, which is a leucine in great apes. Replacing proline with leucine in SLC22A10-P220L restores plasma membrane localization and uptake function. Neanderthal and Denisovan genomes show proline at position 220, akin to modern humans, indicating functional loss during hominin evolution. Human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220, while in great apes, its orthologs transport sex steroid conjugates. Characterizing SLC22A10 across species sheds light on its biological role, influencing organism development and steroid homeostasis.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Luis Ferrández-Peral
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pol Alentorn-Moron
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352, Copenhagen, Denmark
| | - Merve Ceylan
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Virginia M Artegoitia
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA, 95616, USA
| | - Giovanni Lara
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Jacques Dainat
- Joint Research Unit for Infectious Diseases and Vectors Ecology Genetics Evolution and Control (MIVEGEC), University of Montpellier, French National Center for Scientific Research (CNRS 5290), French National Research Institute for Sustainable Development (IRD 224), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, US
| | - Colin M Brand
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Finn D Wolfreys
- Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - John A Capra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - John W Newman
- United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA, 95616, USA
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG, Centro Nacional de Analisis Genomico, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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34
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Upton C, Healey J, Rothnie AJ, Goddard AD. Insights into membrane interactions and their therapeutic potential. Arch Biochem Biophys 2024; 755:109939. [PMID: 38387829 DOI: 10.1016/j.abb.2024.109939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Recent research into membrane interactions has uncovered a diverse range of therapeutic opportunities through the bioengineering of human and non-human macromolecules. Although the majority of this research is focussed on fundamental developments, emerging studies are showcasing promising new technologies to combat conditions such as cancer, Alzheimer's and inflammatory and immune-based disease, utilising the alteration of bacteriophage, adenovirus, bacterial toxins, type 6 secretion systems, annexins, mitochondrial antiviral signalling proteins and bacterial nano-syringes. To advance the field further, each of these opportunities need to be better understood, and the therapeutic models need to be further optimised. Here, we summarise the knowledge and insights into several membrane interactions and detail their current and potential uses therapeutically.
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Affiliation(s)
- Calum Upton
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK
| | - Joseph Healey
- Nanosyrinx, The Venture Centre, University of Warwick Science Park, Coventry, CV4 7EZ, UK
| | - Alice J Rothnie
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK
| | - Alan D Goddard
- School of Biosciences, Health & Life Science, Aston University, Birmingham, B4 7ET, UK.
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35
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Ye J, Chen H, Wang K, Wang Y, Ammerman A, Awasthi S, Xu J, Liu B, Li W. Structural insights into vesicular monoamine storage and drug interactions. Nature 2024; 629:235-243. [PMID: 38499039 PMCID: PMC11070986 DOI: 10.1038/s41586-024-07290-7] [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: 08/02/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
Biogenic monoamines-vital transmitters orchestrating neurological, endocrinal and immunological functions1-5-are stored in secretory vesicles by vesicular monoamine transporters (VMATs) for controlled quantal release6,7. Harnessing proton antiport, VMATs enrich monoamines around 10,000-fold and sequester neurotoxicants to protect neurons8-10. VMATs are targeted by an arsenal of therapeutic drugs and imaging agents to treat and monitor neurodegenerative disorders, hypertension and drug addiction1,8,11-16. However, the structural mechanisms underlying these actions remain unclear. Here we report eight cryo-electron microscopy structures of human VMAT1 in unbound form and in complex with four monoamines (dopamine, noradrenaline, serotonin and histamine), the Parkinsonism-inducing MPP+, the psychostimulant amphetamine and the antihypertensive drug reserpine. Reserpine binding captures a cytoplasmic-open conformation, whereas the other structures show a lumenal-open conformation stabilized by extensive gating interactions. The favoured transition to this lumenal-open state contributes to monoamine accumulation, while protonation facilitates the cytoplasmic-open transition and concurrently prevents monoamine binding to avoid unintended depletion. Monoamines and neurotoxicants share a binding pocket that possesses polar sites for specificity and a wrist-and-fist shape for versatility. Variations in this pocket explain substrate preferences across the SLC18 family. Overall, these structural insights and supporting functional studies elucidate the mechanism of vesicular monoamine transport and provide the basis to develop therapeutics for neurodegenerative diseases and substance abuse.
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Affiliation(s)
- Jin Ye
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Huaping Chen
- Department of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Kaituo Wang
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yi Wang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Aaron Ammerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Samjhana Awasthi
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Jinbin Xu
- Department of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Liu
- The Hormel Institute, University of Minnesota, Austin, MN, USA.
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
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36
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Hu W, Song A, Zheng H. Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2. Nat Commun 2024; 15:3616. [PMID: 38684689 PMCID: PMC11059360 DOI: 10.1038/s41467-024-48028-3] [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: 09/28/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.
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Affiliation(s)
- Wenxin Hu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Alex Song
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US.
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37
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Nussberger S, Ghosh R, Wang S. New insights into the structure and dynamics of the TOM complex in mitochondria. Biochem Soc Trans 2024; 52:911-922. [PMID: 38629718 PMCID: PMC11088910 DOI: 10.1042/bst20231236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
To date, there is no general physical model of the mechanism by which unfolded polypeptide chains with different properties are imported into the mitochondria. At the molecular level, it is still unclear how transit polypeptides approach, are captured by the protein translocation machinery in the outer mitochondrial membrane, and how they subsequently cross the entropic barrier of a protein translocation pore to enter the intermembrane space. This deficiency has been due to the lack of detailed structural and dynamic information about the membrane pores. In this review, we focus on the recently determined sub-nanometer cryo-EM structures and our current knowledge of the dynamics of the mitochondrial two-pore outer membrane protein translocation machinery (TOM core complex), which provide a starting point for addressing the above questions. Of particular interest are recent discoveries showing that the TOM core complex can act as a mechanosensor, where the pores close as a result of interaction with membrane-proximal structures. We highlight unusual and new correlations between the structural elements of the TOM complexes and their dynamic behavior in the membrane environment.
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Affiliation(s)
- Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Shuo Wang
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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38
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Yang H, Zhou D, Zhou Z, Duan M, Yu H. Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase. JACS AU 2024; 4:1422-1435. [PMID: 38665647 PMCID: PMC11040704 DOI: 10.1021/jacsau.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/28/2024]
Abstract
The essential forces stabilizing membrane proteins and governing their folding and unfolding are difficult to decipher. Single-molecule atomic force spectroscopy mechanically unfolds individual membrane proteins and quantifies their dynamics and energetics. However, it remains challenging to structurally assign unfolding intermediates precisely and to deduce dominant interactions between specific residues that facilitate either the localized stabilization of these intermediates or the global assembly of membrane proteins. Here, we performed force spectroscopy experiments and multiscale molecular dynamics simulations to study the unfolding pathway of diacylglycerol kinase (DGK), a small trimeric multispan transmembrane enzyme. The remarkable agreement between experiments and simulations allowed precise structural assignment and interaction analysis of unfolding intermediates, bypassing existing limitations on structural mapping, and thus provided mechanistic explanations for the formation of these states. DGK unfolding was found to proceed with structural segments varying in size that do not correlate with its secondary structure. We identified intermolecular side-chain packing interactions as one of the major contributions to the stability of unfolding intermediates. Mutagenesis creating packing defects induced a dramatic decrease in the mechano-stability of corresponding intermediates and also in the thermo-stability of DGK trimer, in good agreement with predictions from simulations. Hence, the molecular determinants of the mechano- and thermo-stability of a membrane protein can be identified at residue resolution. The accurate structural assignment established and microscopic mechanism revealed in this work may substantially expand the scope of single-molecule studies of membrane proteins.
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Affiliation(s)
- Huiying Yang
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Daihong Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Zhangyi Zhou
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
| | - Mojie Duan
- Innovation
Academy for Precision Measurement Science and Technology, Chinese
Academy of Sciences, Wuhan 430071, China
| | - Hao Yu
- School
of Physics, Huazhong University of Science
and Technology, Wuhan 430074, China
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39
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Giladi M, Fojtík L, Strauss T, Da'adoosh B, Hiller R, Man P, Khananshvili D. Structural dynamics of Na + and Ca 2+ interactions with full-size mammalian NCX. Commun Biol 2024; 7:463. [PMID: 38627576 PMCID: PMC11021524 DOI: 10.1038/s42003-024-06159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Cytosolic Ca2+ and Na+ allosterically regulate Na+/Ca2+ exchanger (NCX) proteins to vary the NCX-mediated Ca2+ entry/exit rates in diverse cell types. To resolve the structure-based dynamic mechanisms underlying the ion-dependent allosteric regulation in mammalian NCXs, we analyze the apo, Ca2+, and Na+-bound species of the brain NCX1.4 variant using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations. Ca2+ binding to the cytosolic regulatory domains (CBD1 and CBD2) rigidifies the intracellular regulatory loop (5L6) and promotes its interaction with the membrane domains. Either Na+ or Ca2+ stabilizes the intracellular portions of transmembrane helices TM3, TM4, TM9, TM10, and their connecting loops (3L4 and 9L10), thereby exposing previously unappreciated regulatory sites. Ca2+ or Na+ also rigidifies the palmitoylation domain (TMH2), and neighboring TM1/TM6 bundle, thereby uncovering a structural entity for modulating the ion transport rates. The present analysis provides new structure-dynamic clues underlying the regulatory diversity among tissue-specific NCX variants.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel.
- Tel-Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel.
| | - Lukáš Fojtík
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova, 595, 252 50 Vestec, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Tali Strauss
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel
| | - Benny Da'adoosh
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Reuben Hiller
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel
| | - Petr Man
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Prumyslova, 595, 252 50 Vestec, Prague, Czech Republic.
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague, Czech Republic.
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978, Israel.
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40
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Cino EA, Ramirez-Echemendia DP, Hu S, Tieleman DP. Analyzing lipid distributions and curvature in molecular dynamics simulations of complex membranes. Methods Enzymol 2024; 701:579-601. [PMID: 39025583 DOI: 10.1016/bs.mie.2024.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We describe methods to analyze lipid distributions and curvature in membranes with complex lipid mixtures and embedded membrane proteins. We discuss issues involved in these analyses, available tools to calculate curvature preferences of lipids and proteins, and focus on tools developed in our group for visual analysis of lipid-protein interactions and the analysis of membrane curvature.
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Affiliation(s)
- Elio A Cino
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Daniel P Ramirez-Echemendia
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Shangnong Hu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
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41
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Overduin M, Bhat R. Recognition and remodeling of endosomal zones by sorting nexins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184305. [PMID: 38408696 DOI: 10.1016/j.bbamem.2024.184305] [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: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Rakesh Bhat
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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42
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Bhattacharje G, Ghosh A, Das AK. Deciphering the mannose transfer mechanism of mycobacterial PimE by molecular dynamics simulations. Glycobiology 2024; 34:cwad096. [PMID: 38039077 DOI: 10.1093/glycob/cwad096] [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: 10/04/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Phosphatidyl-myo-inositol mannosides (PIMs), Lipomannan (LM), and Lipoarabinomannan (LAM) are essential components of the cell envelopes of mycobacteria. At the beginning of the biosynthesis of these compounds, phosphatidylinositol (PI) is mannosylated and acylated by various enzymes to produce Ac1/2PIM4, which is used to synthesize either Ac1/2PIM6 or LM/LAM. The protein PimE, a membrane-bound glycosyltransferase (GT-C), catalyzes the addition of a mannose group to Ac1PIM4 to produce Ac1PIM5, using polyprenolphosphate mannose (PPM) as the mannose donor. PimE-deleted Mycobacterium smegmatis (Msmeg) showed structural deformity and increased antibiotic and copper sensitivity. Despite knowing that the mutation D58A caused inactivity in Msmeg, how PimE catalyzes the transfer of mannose from PPM to Ac1/2PIM4 remains unknown. In this study, analyzing the AlphaFold structure of PimE revealed the presence of a tunnel through the D58 residue with two differently charged gates. Molecular docking suggested PPM binds to the hydrophobic tunnel gate, whereas Ac1PIM4 binds to the positively charged tunnel gate. Molecular dynamics (MD) simulations further demonstrated the critical roles of the residues N55, F87, L89, Y163, Q165, K197, L198, R251, F277, W324, H326, and I375 in binding PPM and Ac1PIM4. The mutation D58A caused a faster release of PPM from the catalytic tunnel, explaining the loss of PimE activity. Along with a hypothetical mechanism of mannose transfer by PimE, we also observe the presence of tunnels through a negatively charged aspartate or glutamate with two differently-charged gates among most GT-C enzymes. Common hydrophobic gates of GT-C enzymes probably harbor sugar donors, whereas, differently-charged tunnel gates accommodate various sugar-acceptors.
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Affiliation(s)
- Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Midnapore, WB 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Midnapore, WB 721302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Midnapore, WB 721302, India
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43
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Schleutker R, Luschnig S. Palmitoylation of proteolipid protein M6 promotes tricellular junction assembly in epithelia of Drosophila. J Cell Sci 2024; 137:jcs261916. [PMID: 38345097 DOI: 10.1242/jcs.261916] [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: 12/18/2023] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
Tricellular junctions (TCJs) seal epithelial cell vertices and are essential for tissue integrity and physiology, but how TCJs are assembled and maintained is poorly understood. In Drosophila, the transmembrane proteins Anakonda (Aka, also known as Bark), Gliotactin (Gli) and M6 organize occluding TCJs. Aka and M6 localize in an interdependent manner to vertices and act jointly to localize Gli, but how these proteins interact to assemble TCJs was not previously known. Here, we show that the proteolipid protein M6 physically interacts with Aka and with itself, and that M6 is palmitoylated on conserved juxta-membrane cysteine residues. This modification promotes vertex localization of M6 and binding to Aka, but not to itself, and becomes essential when TCJ protein levels are reduced. Abolishing M6 palmitoylation leads to delayed localization of M6 and Aka but does not affect the rate of TCJ growth or mobility of M6 or Aka. Our findings suggest that palmitoylation-dependent recruitment of Aka by M6 promotes initiation of TCJ assembly, whereas subsequent TCJ growth relies on different mechanisms that are independent of M6 palmitoylation.
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Affiliation(s)
- Raphael Schleutker
- Institute of Integrative Cell Biology and Physiology, Cells in Motion (CiM) Interfaculty Centre, University of Münster, D-48149 Münster, Germany
| | - Stefan Luschnig
- Institute of Integrative Cell Biology and Physiology, Cells in Motion (CiM) Interfaculty Centre, University of Münster, D-48149 Münster, Germany
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44
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Christoffer C, Harini K, Archit G, Kihara D. Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints. J Mol Biol 2024; 436:168486. [PMID: 38336197 PMCID: PMC10942765 DOI: 10.1016/j.jmb.2024.168486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Membrane proteins play crucial roles in various cellular processes, and their interactions with other proteins in and on the membrane are essential for their proper functioning. While an increasing number of structures of more membrane proteins are being determined, the available structure data is still sparse. To gain insights into the mechanisms of membrane protein complexes, computational docking methods are necessary due to the challenge of experimental determination. Here, we introduce Mem-LZerD, a rigid-body membrane docking algorithm designed to take advantage of modern membrane modeling and protein docking techniques to facilitate the docking of membrane protein complexes. Mem-LZerD is based on the LZerD protein docking algorithm, which has been constantly among the top servers in many rounds of CAPRI protein docking assessment. By employing a combination of geometric hashing, newly constrained by the predicted membrane height and tilt angle, and model scoring accounting for the energy of membrane insertion, we demonstrate the capability of Mem-LZerD to model diverse membrane protein-protein complexes. Mem-LZerD successfully performed unbound docking on 13 of 21 (61.9%) transmembrane complexes in an established benchmark, more than shown by previous approaches. It was additionally tested on new datasets of 44 transmembrane complexes and 92 peripheral membrane protein complexes, of which it successfully modeled 35 (79.5%) and 15 (16.3%) complexes respectively. When non-blind orientations of peripheral targets were included, the number of successes increased to 54 (58.7%). We further demonstrate that Mem-LZerD produces complex models which are suitable for molecular dynamics simulation. Mem-LZerD is made available at https://lzerd.kiharalab.org.
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Affiliation(s)
- Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Kannan Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Gupta Archit
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur 603203, India
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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45
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Woods H, Leman JK, Meiler J. Modeling membrane geometries implicitly in Rosetta. Protein Sci 2024; 33:e4908. [PMID: 38358133 PMCID: PMC10868433 DOI: 10.1002/pro.4908] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanodiscs, or liposomes. Thus, we have modified the existing membrane energy potentials within the RosettaMP framework to allow users to model MPs in different membrane geometries. We show that these modifications can be utilized in core applications within Rosetta such as structure refinement, protein-protein docking, and protein design. For MP structures found in curved membranes, refining these structures in curved, implicit membranes produces higher quality models with structures closer to experimentally determined structures. For MP systems embedded in multiple membranes, representing both membranes results in more favorable scores compared to only representing one of the membranes. Modeling MPs in geometries mimicking the membrane model system used in structure determination can improve model quality and model discrimination.
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Affiliation(s)
- Hope Woods
- Center of Structural Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Chemical and Physical Biology ProgramVanderbilt UniversityNashvilleTennesseeUSA
| | | | - Jens Meiler
- Center of Structural Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Institute for Drug Discovery, Leipzig University Medical SchoolLeipzigGermany
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46
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Tsai CT, Lin CW, Ye GL, Wu SC, Yao P, Lin CT, Wan L, Tsai HHG. Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models. ACS OMEGA 2024; 9:9357-9374. [PMID: 38434814 PMCID: PMC10905719 DOI: 10.1021/acsomega.3c08676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
Abstract
The escalating menace of multidrug-resistant (MDR) pathogens necessitates a paradigm shift from conventional antibiotics to innovative alternatives. Antimicrobial peptides (AMPs) emerge as a compelling contender in this arena. Employing in silico methodologies, we can usher in a new era of AMP discovery, streamlining the identification process from vast candidate sequences, thereby optimizing laboratory screening expenditures. Here, we unveil cutting-edge machine learning (ML) models that are both predictive and interpretable, tailored for the identification of potent AMPs targeting World Health Organization's (WHO) high-priority pathogens. Furthermore, we have developed ML models that consider the hemolysis of human erythrocytes, emphasizing their therapeutic potential. Anchored in the nuanced physical-chemical attributes gleaned from the three-dimensional (3D) helical conformations of AMPs, our optimized models have demonstrated commendable performance-boasting an accuracy exceeding 75% when evaluated against both low-sequence-identified peptides and recently unveiled AMPs. As a testament to their efficacy, we deployed these models to prioritize peptide sequences stemming from PEM-2 and subsequently probed the bioactivity of our algorithm-predicted peptides vis-à-vis WHO's priority pathogens. Intriguingly, several of these new AMPs outperformed the native PEM-2 in their antimicrobial prowess, thereby underscoring the robustness of our modeling approach. To elucidate ML model outcomes, we probe via Shapley Additive exPlanations (SHAP) values, uncovering intricate mechanisms guiding diverse actions against bacteria. Our state-of-the-art predictive models expedite the design of new AMPs, offering a robust countermeasure to antibiotic resistance. Our prediction tool is available to the public at https://ai-meta.chem.ncu.edu.tw/amp-meta.
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Affiliation(s)
- Cheng-Ting Tsai
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Chia-Wei Lin
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Gen-Lin Ye
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Shao-Chi Wu
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
| | - Philip Yao
- Aurora
High School, 109 W Pioneer Trail, Aurora, Ohio 44202, United States
| | - Ching-Ting Lin
- School
of Chinese Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Lei Wan
- School
of Chinese Medicine, China Medical University, No. 91 Hsueh-Shih Road, Taichung 40402, Taiwan
| | - Hui-Hsu Gavin Tsai
- Department
of Chemistry, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan 32001, Taiwan
- Research
Center of New Generation Light Driven Photovoltaic Modules, National Central University, Taoyuan 32001, Taiwan
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47
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Erba F, Mei G, Minicozzi V, Sabatucci A, Di Venere A, Maccarrone M. Conformational Dynamics of Lipoxygenases and Their Interaction with Biological Membranes. Int J Mol Sci 2024; 25:2241. [PMID: 38396917 PMCID: PMC10889196 DOI: 10.3390/ijms25042241] [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: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Lipoxygenases (LOXs) are a family of enzymes that includes different fatty acid oxygenases with a common tridimensional structure. The main functions of LOXs are the production of signaling compounds and the structural modifications of biological membranes. These features of LOXs, their widespread presence in all living organisms, and their involvement in human diseases have attracted the attention of the scientific community over the last decades, leading to several studies mainly focused on understanding their catalytic mechanism and designing effective inhibitors. The aim of this review is to discuss the state-of-the-art of a different, much less explored aspect of LOXs, that is, their interaction with lipid bilayers. To this end, the general architecture of six relevant LOXs (namely human 5-, 12-, and 15-LOX, rabbit 12/15-LOX, coral 8-LOX, and soybean 15-LOX), with different specificity towards the fatty acid substrates, is analyzed through the available crystallographic models. Then, their putative interface with a model membrane is examined in the frame of the conformational flexibility of LOXs, that is due to their peculiar tertiary structure. Finally, the possible future developments that emerge from the available data are discussed.
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Affiliation(s)
- Fulvio Erba
- Department of Clinical Science and Translational Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Giampiero Mei
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Velia Minicozzi
- Department of Physics and INFN, Tor Vergata University of Rome, Via Della Ricerca Scientifica 1, 00133 Rome, Italy;
| | - Annalaura Sabatucci
- Department of Biosciences and Technology for Food Agriculture and Environment, University of Teramo, Via Renato Balzarini 1, 64100 Teramo, Italy;
| | - Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy
- European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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48
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De Jesús-Pérez JJ, Gabrielle M, Raheem S, Fluck EC, Rohacs T, Moiseenkova-Bell VY. Structural mechanism of TRPV5 inhibition by econazole. Structure 2024; 32:148-156.e5. [PMID: 38141613 PMCID: PMC10872542 DOI: 10.1016/j.str.2023.11.012] [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: 08/03/2023] [Revised: 11/01/2023] [Accepted: 11/28/2023] [Indexed: 12/25/2023]
Abstract
The calcium-selective TRPV5 channel activated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is involved in calcium homeostasis. Recently, cryoelectron microscopy (cryo-EM) provided molecular details of TRPV5 modulation by exogenous and endogenous molecules. However, the details of TRPV5 inhibition by the antifungal agent econazole (ECN) remain elusive due to the low resolution of the currently available structure. In this study, we employ cryo-EM to comprehensively examine how the ECN inhibits TRPV5. By combining our structural findings with site-directed mutagenesis, calcium measurements, electrophysiology, and molecular dynamics simulations, we determined that residues F472 and L475 on the S4 helix, along with residue W495 on the S5 helix, collectively constitute the ECN-binding site. Additionally, the structure of TRPV5 in the presence of ECN and PI(4,5)P2, which does not show the bound activator, reveals a potential inhibition mechanism in which ECN competes with PI(4,5)P2, preventing the latter from binding, and ultimately pore closure.
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Affiliation(s)
- José J De Jesús-Pérez
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Gabrielle
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Sumiyya Raheem
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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49
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van Hilten N, Verwei N, Methorst J, Nase C, Bernatavicius A, Risselada HJ. PMIpred: a physics-informed web server for quantitative protein-membrane interaction prediction. Bioinformatics 2024; 40:btae069. [PMID: 38317055 PMCID: PMC11212490 DOI: 10.1093/bioinformatics/btae069] [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: 04/10/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/07/2024] Open
Abstract
MOTIVATION Many membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods to quantitatively predict sensing and binding free energies for protein sequences or structures are lacking, and such tools could greatly benefit the discovery of membrane-interacting motifs, as well as their de novo design. RESULTS Here, we trained a transformer neural network model on molecular dynamics data for >50 000 peptides that is able to accurately predict the (relative) membrane-binding free energy for any given amino acid sequence. Using this information, our physics-informed model is able to classify a peptide's membrane-associative activity as either non-binding, curvature sensing, or membrane binding. Moreover, this method can be applied to detect membrane-interaction regions in a wide variety of proteins, with comparable predictive performance as state-of-the-art data-driven tools like DREAMM, PPM3, and MODA, but with a wider applicability regarding protein diversity, and the added feature to distinguish curvature sensing from general membrane binding. AVAILABILITY AND IMPLEMENTATION We made these tools available as a web server, coined Protein-Membrane Interaction predictor (PMIpred), which can be accessed at https://pmipred.fkt.physik.tu-dortmund.de.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
| | - Nino Verwei
- Leiden Institute of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
| | - Jeroen Methorst
- Leiden Institute of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
| | - Carsten Nase
- Department of Physics, Technical University Dortmund, Dortmund 44227, Germany
| | - Andrius Bernatavicius
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden 2333 CA, Netherlands
- Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
- Department of Physics, Technical University Dortmund, Dortmund 44227, Germany
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50
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Farci D, Milenkovic S, Iesu L, Tanas M, Ceccarelli M, Piano D. Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans. J Biol Chem 2024; 300:105537. [PMID: 38072042 PMCID: PMC10828601 DOI: 10.1016/j.jbc.2023.105537] [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: 10/05/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024] Open
Abstract
The extremophile bacterium D. radiodurans boasts a distinctive cell envelope characterized by the regular arrangement of three protein complexes. Among these, the Type II Secretion System (T2SS) stands out as a pivotal structural component. We used cryo-electron microscopy to reveal unique features, such as an unconventional protein belt (DR_1364) around the main secretin (GspD), and a cap (DR_0940) found to be a separated subunit rather than integrated with GspD. Furthermore, a novel region at the N-terminus of the GspD constitutes an additional second gate, supplementing the one typically found in the outer membrane region. This T2SS was found to contribute to envelope integrity, while also playing a role in nucleic acid and nutrient trafficking. Studies on intact cell envelopes show a consistent T2SS structure repetition, highlighting its significance within the cellular framework.
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Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; R&D Department, ReGenFix Laboratories, Sardara, Italy.
| | - Stefan Milenkovic
- Department of Physics and IOM/CNR, Università degli Studi di Cagliari, Monserrato, Italy
| | - Luca Iesu
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Marta Tanas
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Matteo Ceccarelli
- Department of Physics and IOM/CNR, Università degli Studi di Cagliari, Monserrato, Italy
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland; Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; R&D Department, ReGenFix Laboratories, Sardara, Italy.
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