1
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Iyer SS, Srivastava A. Membrane lateral organization from potential energy disconnectivity graph. Biophys Chem 2024; 313:107284. [PMID: 39002248 DOI: 10.1016/j.bpc.2024.107284] [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: 03/29/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024]
Abstract
Understanding the thermodynamic and kinetic properties of biomolecules requires elucidation of their complex energy landscape. A disconnectivity graph analysis of the energy landscape provides a framework for mapping the multi-dimensional landscape onto a two-dimensional representation while preserving the key features of the energy landscape. Several studies show that the structure or shape of the disconnectity graph is directly associated with the function of protein and nucleic acid molecules. In this review, we discuss how disconnectivity analysis of the potential energy surface can be extended to lipid molecules to glean important information about membrane organization. The shape of the disconnectivity graphs can be used to predict the lateral organization of multi-component lipid bilayer. We hope that this review encourages the use of disconnectivity graphs routinely by membrane biophysicists to predict the lateral organization of lipids.
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Affiliation(s)
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India.
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2
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Zhao M, Lopes LJS, Sahni H, Yadav A, Do HN, Reddy T, López CA, Neale C, Gnanakaran S. Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606381. [PMID: 39131401 PMCID: PMC11312619 DOI: 10.1101/2024.08.02.606381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
A fundamental understanding of how HIV-1 envelope (Env) protein facilitates fusion is still lacking. The HIV-1 fusion peptide, consisting of 15 to 22 residues, is the N-terminus of the gp41 subunit of the Env protein. Further, this peptide, a promising vaccine candidate, initiates viral entry into target cells by inserting and anchoring into human immune cells. The influence of membrane lipid reorganization and the conformational changes of the fusion peptide during the membrane insertion and anchoring processes, which can significantly affect HIV-1 cell entry, remains largely unexplored due to the limitations of experimental measurements. In this work, we investigate the insertion of the fusion peptide into an immune cell membrane mimic through multiscale molecular dynamics simulations. We mimic the native T-cell by constructing a 9-lipid asymmetric membrane, along with geometrical restraints accounting for insertion in the context of gp41. To account for the slow timescale of lipid mixing while enabling conformational changes, we implement a protocol to go back and forth between atomistic and coarse-grained simulations. Our study provides a molecular understanding of the interactions between the HIV-1 fusion peptide and the T-cell membrane, highlighting the importance of conformational flexibility of fusion peptides and local lipid reorganization in stabilizing the anchoring of gp41 into the targeted host membrane during the early events of HIV-1 cell entry. Importantly, we identify a motif within the fusion peptide critical for fusion that can be further manipulated in future immunological studies.
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Affiliation(s)
- Mingfei Zhao
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | | | - Harshita Sahni
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
- Department of Computer Science, University of New Mexico, Albuquerque NM, USA
| | - Anju Yadav
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso TX, USA
| | - Hung N Do
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - Tyler Reddy
- CCS-7 Applied Computer Science Group, Los Alamos National Laboratory, Los Alamos NM USA
| | - Cesar A López
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - Chris Neale
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - S Gnanakaran
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
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3
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Rajendra D, Maroli N, Dixit NM, Maiti PK. Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells. J Biomol Struct Dyn 2023:1-11. [PMID: 38111161 DOI: 10.1080/07391102.2023.2294835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023]
Abstract
High mutation and replication rates of HIV-1 result in the continuous generation of variants, allowing it to adapt to changing host environments. Mutations often have deleterious effects, but variants carrying them are rapidly purged. Surprisingly, a particular variant incapable of entering host cells was found to be rescued by host antibodies targeting HIV-1. Understanding the molecular mechanism of this rescue is important to develop and improve antibody-based therapies. To unravel the underlying mechanisms, we performed fully atomistic molecular dynamics simulations of the HIV-1 gp41 trimer responsible for viral entry into host cells, its entry-deficient variant, and its complex with the rescuing antibody. We find that the Q563R mutation, which the entry-deficient variant carries, prevents the native conformation of the gp41 6-helix bundle required for entry and stabilizes an alternative conformation instead. This is the consequence of substantial changes in the secondary structure and interactions between the domains of gp41. Binding of the antibody F240 to gp41 reverses these changes and re-establishes the native conformation, resulting in rescue. To test the generality of this mechanism, we performed simulations with the entry-deficient L565A variant and antibody 3D6. We find that 3D6 binding was able to reverse structural and interaction changes introduced by the mutation and restore the native gp41 conformation. Viral variants may not only escape antibodies but be aided by them in their survival, potentially compromising antibody-based therapies, including vaccination and passive immunization. Our simulation framework could serve as a tool to assess the likelihood of such resistance against specific antibodies.Communicated by Ramaswamy H. SarmaCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharanish Rajendra
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
| | - Nikhil Maroli
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
- Department of Bioengineering, Indian Institute of Science, Bengaluru, India
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru, India
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4
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Kruse E, Abdalrahman T, Selhorst P, Franz T. Mathematical model for force and energy of virion-cell interactions during full engulfment in HIV: Impact of virion maturation and host cell morphology. Biomech Model Mechanobiol 2023; 22:1847-1855. [PMID: 37322329 PMCID: PMC10613145 DOI: 10.1007/s10237-023-01736-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/04/2023] [Indexed: 06/17/2023]
Abstract
Viral endocytosis involves elastic cell deformation, driven by chemical adhesion energy, and depends on physical interactions between the virion and cell membrane. These interactions are not easy to quantify experimentally. Hence, this study aimed to develop a mathematical model of the interactions of HIV particles with host cells and explore the effects of mechanical and morphological parameters during full virion engulfment. The invagination force and engulfment energy were described as viscoelastic and linear-elastic functions of radius and elastic modulus of virion and cell, ligand-receptor energy density and engulfment depth. The influence of changes in the virion-cell contact geometry representing different immune cells and ultrastructural membrane features and the decrease in virion radius and shedding of gp120 proteins during maturation on invagination force and engulfment energy was investigated. A low invagination force and high ligand-receptor energy are associated with high virion entry ability. The required invagination force was the same for immune cells of different sizes but lower for a local convex geometry of the cell membrane at the virion length scale. This suggests that localized membrane features of immune cells play a role in viral entry ability. The available engulfment energy decreased during virion maturation, indicating the involvement of additional biological or biochemical changes in viral entry. The developed mathematical model offers potential for the mechanobiological assessment of the invagination of enveloped viruses towards improving the prevention and treatment of viral infections.
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Affiliation(s)
- Elizabeth Kruse
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Tamer Abdalrahman
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa
| | - Philippe Selhorst
- Division of Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Thomas Franz
- Biomedical Engineering Research Centre, Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Observatory, South Africa.
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.
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5
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Di Bartolo AL, Tomes CN, Mayorga LS, Masone D. Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains. J Chem Theory Comput 2022; 18:4544-4554. [PMID: 35759758 DOI: 10.1021/acs.jctc.2c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fusion pore controls the release of exocytotic vesicle contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore (membrane fusion, nucleation, and expansion) that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve toward full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Claudia N Tomes
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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6
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Nieto-Garai JA, Contreras FX, Arboleya A, Lorizate M. Role of Protein-Lipid Interactions in Viral Entry. Adv Biol (Weinh) 2022; 6:e2101264. [PMID: 35119227 DOI: 10.1002/adbi.202101264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/19/2021] [Indexed: 12/25/2022]
Abstract
The viral entry consists of several sequential events that ensure the attachment of the virus to the host cell and the introduction of its genetic material for the continuation of the replication cycle. Both cellular and viral lipids have gained a wider focus in recent years in the field of viral entry, as they are found to play key roles in different steps of the process. The specific role is summarized that lipids and lipid membrane nanostructures play in viral attachment, fusion, and immune evasion and how they can be targeted with antiviral therapies. Finally, some of the limitations of techniques commonly used for protein-lipid interactions studies are discussed, and new emerging tools are reviewed that can be applied to this field.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - Aroa Arboleya
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain.,Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, E-48940, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country, Leioa, E-48940, Spain.,Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain
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Tran N, Oh Y, Sutherland M, Cui Q, Hong M. Cholesterol-Mediated Clustering of the HIV Fusion Protein gp41 in Lipid Bilayers. J Mol Biol 2021; 434:167345. [PMID: 34762895 DOI: 10.1016/j.jmb.2021.167345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/26/2021] [Accepted: 10/31/2021] [Indexed: 11/16/2022]
Abstract
The envelope glycoprotein (Env) of the human immunodeficient virus (HIV-1) is known to cluster on the viral membrane surface to attach to target cells and cause membrane fusion for HIV-1 infection. However, the molecular structural mechanisms that drive Env clustering remain opaque. Here, we use solid-state NMR spectroscopy and molecular dynamics (MD) simulations to investigate nanometer-scale clustering of the membrane-proximal external region (MPER) and transmembrane domain (TMD) of gp41, the fusion protein component of Env. Using 19F solid-state NMR experiments of mixed fluorinated peptides, we show that MPER-TMD trimers form clusters with interdigitated MPER helices in cholesterol-containing membranes. Inter-trimer 19F-19F cross peaks, which are indicative of spatial contacts within ∼2 nm, are observed in cholesterol-rich virus-mimetic membranes but are suppressed in cholesterol-free model membranes. Water-peptide and lipid-peptide cross peaks in 2D 1H-19F correlation spectra indicate that the MPER is well embedded in model phosphocholine membranes but is more exposed to the surface of the virus-mimetic membrane. These experimental results are reproduced in coarse-grained and atomistic molecular dynamics simulations, which suggest that the effects of cholesterol on gp41 clustering is likely via indirect modulation of the MPER orientation. Cholesterol binding to the helix-turn-helix region of the MPER-TMD causes a parallel orientation of the MPER with the membrane surface, thus allowing MPERs of neighboring trimers to interact with each other to cause clustering. These solid-state NMR data and molecular dynamics simulations suggest that MPER and cholesterol cooperatively govern the clustering of gp41 trimers during virus-cell membrane fusion.
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Affiliation(s)
- Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Younghoon Oh
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, United States
| | - Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, United States; Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, United States; Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, United States.
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States. https://twitter.com/MeiHongLab
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