1
|
Lozada C, Barlow TMA, Gonzalez S, Lubin-Germain N, Ballet S. Identification and Characteristics of Fusion Peptides Derived From Enveloped Viruses. Front Chem 2021; 9:689006. [PMID: 34497798 PMCID: PMC8419435 DOI: 10.3389/fchem.2021.689006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/10/2021] [Indexed: 01/28/2023] Open
Abstract
Membrane fusion events allow enveloped viruses to enter and infect cells. The study of these processes has led to the identification of a number of proteins that mediate this process. These proteins are classified according to their structure, which vary according to the viral genealogy. To date, three classes of fusion proteins have been defined, but current evidence points to the existence of additional classes. Despite their structural differences, viral fusion processes follow a common mechanism through which they exert their actions. Additional studies of the viral fusion proteins have demonstrated the key role of specific proteinogenic subsequences within these proteins, termed fusion peptides. Such peptides are able to interact and insert into membranes for which they hold interest from a pharmacological or therapeutic viewpoint. Here, the different characteristics of fusion peptides derived from viral fusion proteins are described. These criteria are useful to identify new fusion peptides. Moreover, this review describes the requirements of synthetic fusion peptides derived from fusion proteins to induce fusion by themselves. Several sequences of the viral glycoproteins E1 and E2 of HCV were, for example, identified to be able to induce fusion, which are reviewed here.
Collapse
Affiliation(s)
- Camille Lozada
- BioCIS, CNRS, CY Cergy-Paris Université, Cergy-Pontoise, France
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Thomas M. A. Barlow
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Simon Gonzalez
- BioCIS, CNRS, CY Cergy-Paris Université, Cergy-Pontoise, France
| | | | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
2
|
Gronnier J, Crowet JM, Habenstein B, Nasir MN, Bayle V, Hosy E, Platre MP, Gouguet P, Raffaele S, Martinez D, Grelard A, Loquet A, Simon-Plas F, Gerbeau-Pissot P, Der C, Bayer EM, Jaillais Y, Deleu M, Germain V, Lins L, Mongrand S. Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains. eLife 2017; 6:e26404. [PMID: 28758890 PMCID: PMC5536944 DOI: 10.7554/elife.26404] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022] Open
Abstract
Plasma Membrane is the primary structure for adjusting to ever changing conditions. PM sub-compartmentalization in domains is thought to orchestrate signaling. Yet, mechanisms governing membrane organization are mostly uncharacterized. The plant-specific REMORINs are proteins regulating hormonal crosstalk and host invasion. REMs are the best-characterized nanodomain markers via an uncharacterized moiety called REMORIN C-terminal Anchor. By coupling biophysical methods, super-resolution microscopy and physiology, we decipher an original mechanism regulating the dynamic and organization of nanodomains. We showed that targeting of REMORIN is independent of the COP-II-dependent secretory pathway and mediated by PI4P and sterol. REM-CA is an unconventional lipid-binding motif that confers nanodomain organization. Analyses of REM-CA mutants by single particle tracking demonstrate that mobility and supramolecular organization are critical for immunity. This study provides a unique mechanistic insight into how the tight control of spatial segregation is critical in the definition of PM domain necessary to support biological function.
Collapse
Affiliation(s)
- Julien Gronnier
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Jean-Marc Crowet
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Mehmet Nail Nasir
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, CNRS, University of BordeauxBordeauxFrance
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | | | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Axelle Grelard
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects (UMR5248 CBMN), CNRS, Université de Bordeaux, Institut Polytechnique BordeauxPessacFrance
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Patricia Gerbeau-Pissot
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Christophe Der
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F-21000 Dijon, ERL 6003 CNRSDijonFrance
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1LyonFrance
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux InterfacesGX ABT, Université de LiègeGemblouxBelgium
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de BordeauxBordeauxFrance
| |
Collapse
|
3
|
Olson MA, Lee MS, Yeh IC. Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations. J Comput Chem 2017; 38:1342-1352. [PMID: 28130780 DOI: 10.1002/jcc.24717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 12/24/2022]
Abstract
This work presents replica-exchange molecular dynamics simulations of inserting a 16-residue Ebola virus fusion peptide into a membrane bilayer. A computational approach is applied for modeling the peptide at the explicit all-atom level and the membrane-aqueous bilayer by a generalized Born continuum model with a smoothed switching function (GBSW). We provide an assessment of the model calculations in terms of three metrics: (1) the ability to reproduce the NMR structure of the peptide determined in the presence of SDS micelles and comparable structural data on other fusion peptides; (2) determination of the effects of the mutation Trp-8 to Ala and sequence discrimination of the homologous Marburg virus; and (3) calculation of potentials of mean force for estimating the partitioning free energy and their comparison to predictions from the Wimley-White interfacial hydrophobicity scale. We found the GBSW implicit membrane model to produce results of limited accuracy in conformational properties of the peptide when compared to the NMR structure, yet the model resolution is sufficient to determine the effect of sequence differentiation on peptide-membrane integration. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Mark A Olson
- Department of Cell Biology and Biochemistry, Molecular and Translational Sciences, USAMRIID, Fredrick, Maryland
| | - Michael S Lee
- Computational Sciences Division, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland
| | - In-Chul Yeh
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, U.S. Army Medical Research and Materiel Command, Fredrick, Maryland
| |
Collapse
|
4
|
Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:581-92. [DOI: 10.1016/j.bbamem.2014.11.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/22/2014] [Accepted: 11/05/2014] [Indexed: 01/07/2023]
|
5
|
Deleu M, Crowet JM, Nasir MN, Lins L. Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3171-3190. [DOI: 10.1016/j.bbamem.2014.08.023] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
|
6
|
Hall BA, Halim KA, Buyan A, Emmanouil B, Sansom MSP. Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices. J Chem Theory Comput 2014; 10:2165-75. [PMID: 26580541 PMCID: PMC4871227 DOI: 10.1021/ct500003g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analyzed via coarse grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions, large (N ca. 100) ensembles of CGMD simulations are needed. To facilitate the running and analysis of such ensembles of simulations, we have developed Sidekick, an automated pipeline software for performing high throughput CGMD simulations of α-helical peptides in lipid bilayer membranes. Through an end-to-end approach, which takes as input a helix sequence and outputs analytical metrics derived from CGMD simulations, we are able to predict the orientation and likelihood of insertion into a lipid bilayer of a given helix of a family of helix sequences. We illustrate this software via analyses of insertion into a membrane of short hydrophobic TM helices containing a single cationic arginine residue positioned at different positions along the length of the helix. From analyses of these ensembles of simulations, we estimate apparent energy barriers to insertion which are comparable to experimentally determined values. In a second application, we use CGMD simulations to examine the self-assembly of dimers of TM helices from the ErbB1 receptor tyrosine kinase and analyze the numbers of simulation repeats necessary to obtain convergence of simple descriptors of the mode of packing of the two helices within a dimer. Our approach offers a proof-of-principle platform for the further employment of automation in large ensemble CGMD simulations of membrane proteins.
Collapse
Affiliation(s)
- Benjamin A Hall
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
- current address: Microsoft Research Cambridge, 21 Station Road, Cambridge, CB1 2FB
| | - Khairul Abd Halim
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
| | - Amanda Buyan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
| | - Beatrice Emmanouil
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU
| |
Collapse
|
7
|
Gapsys V, de Groot BL, Briones R. Computational analysis of local membrane properties. J Comput Aided Mol Des 2013; 27:845-58. [PMID: 24150904 PMCID: PMC3882000 DOI: 10.1007/s10822-013-9684-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
In the field of biomolecular simulations, dynamics of phospholipid membranes is of special interest. A number of proteins, including channels, transporters, receptors and short peptides are embedded in lipid bilayers and tightly interact with phospholipids. While the experimental measurements report on the spatial and/or temporal average membrane properties, simulation results are not restricted to the average properties. In the current study, we present a collection of methods for an efficient local membrane property calculation, comprising bilayer thickness, area per lipid, deuterium order parameters, Gaussian and mean curvature. The local membrane property calculation allows for a direct mapping of the membrane features, which subsequently can be used for further analysis and visualization of the processes of interest. The main features of the described methods are highlighted in a number of membrane systems, namely: a pure dimyristoyl-phosphatidyl-choline (DMPC) bilayer, a fusion peptide interacting with a membrane, voltage-dependent anion channel protein embedded in a DMPC bilayer, cholesterol enriched bilayer and a coarse grained simulation of a curved palmitoyl-oleoyl-phosphatidyl-choline lipid membrane. The local membrane property analysis proves to provide an intuitive and detailed view on the observables that are otherwise interpreted as averaged bilayer properties.
Collapse
Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany,
| | | | | |
Collapse
|
8
|
Li H, Gorfe AA. Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field. PLoS One 2013; 8:e71018. [PMID: 23923044 PMCID: PMC3724741 DOI: 10.1371/journal.pone.0071018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/28/2013] [Indexed: 11/25/2022] Open
Abstract
Lipid-anchored Ras oncoproteins assemble into transient, nano-sized substructures on the plasma membrane. These substructures, called nanoclusters, were proposed to be crucial for high-fidelity signal transmission in cells. However, the molecular basis of Ras nanoclustering is poorly understood. In this work, we used coarse-grained (CG) molecular dynamics simulations to investigate the molecular mechanism by which full-length H-ras proteins form nanoclusters in a model membrane. We chose two different conformations of H-ras that were proposed to represent the active and inactive state of the protein, and a domain-forming model bilayer made up of di16:0-PC (DPPC), di18:2-PC (DLiPC) and cholesterol. We found that, irrespective of the initial conformation, Ras molecules assembled into a single large aggregate. However, the two binding modes, which are characterized by the different orientation of the G-domain with respect to the membrane, differ in dynamics and organization during and after aggregation. Some of these differences involve regions of Ras that are important for effector/modulator binding, which may partly explain observed differences in the ability of active and inactive H-ras nanoclusters to recruit effectors. The simulations also revealed some limitations in the CG force field to study protein assembly in solution, which we discuss in the context of proposed potential avenues of improvement.
Collapse
Affiliation(s)
- Hualin Li
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, United States of America
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, United States of America
| |
Collapse
|
9
|
|