1
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Jennings J, Bracey H, Hong J, Nguyen DT, Dasgupta R, Rivera AV, Sluis-Cremer N, Shi J, Aiken C. The HIV-1 capsid serves as a nanoscale reaction vessel for reverse transcription. PLoS Pathog 2024; 20:e1011810. [PMID: 39226318 PMCID: PMC11398657 DOI: 10.1371/journal.ppat.1011810] [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: 11/09/2023] [Revised: 09/13/2024] [Accepted: 08/08/2024] [Indexed: 09/05/2024] Open
Abstract
The viral capsid performs critical functions during HIV-1 infection and is a validated target for antiviral therapy. Previous studies have established that the proper structure and stability of the capsid are required for efficient HIV-1 reverse transcription in target cells. Moreover, it has recently been demonstrated that permeabilized virions and purified HIV-1 cores undergo efficient reverse transcription in vitro when the capsid is stabilized by addition of the host cell metabolite inositol hexakisphosphate (IP6). However, the molecular mechanism by which the capsid promotes reverse transcription is undefined. Here we show that wild type HIV-1 virions can undergo efficient reverse transcription in vitro in the absence of a membrane-permeabilizing agent. This activity, originally termed "natural endogenous reverse transcription" (NERT), depends on expression of the viral envelope glycoprotein during virus assembly and its incorporation into virions. Truncation of the gp41 cytoplasmic tail markedly reduced NERT activity, suggesting that gp41 licenses the entry of nucleotides into virions. By contrast to reverse transcription in permeabilized virions, NERT required neither the addition of IP6 nor a mature capsid, indicating that an intact viral membrane can substitute for the function of the viral capsid during reverse transcription in vitro. Collectively, these results demonstrate that the viral capsid functions as a nanoscale container for reverse transcription during HIV-1 infection.
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Affiliation(s)
- Jordan Jennings
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Harrison Bracey
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jun Hong
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Danny T Nguyen
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Rishav Dasgupta
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alondra Vázquez Rivera
- Division of Infectious Disease, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Nicolas Sluis-Cremer
- Division of Infectious Disease, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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2
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Sandberg JW, Santiago-McRae E, Ennis J, Brannigan G. The density-threshold affinity: Calculating lipid binding affinities from unbiased coarse-grained molecular dynamics simulations. Methods Enzymol 2024; 701:47-82. [PMID: 39025580 DOI: 10.1016/bs.mie.2024.03.008] [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] [Indexed: 07/20/2024]
Abstract
Many membrane proteins are sensitive to their local lipid environment. As structural methods for membrane proteins have improved, there is growing evidence of direct, specific binding of lipids to protein surfaces. Unfortunately the workhorse of understanding protein-small molecule interactions, the binding affinity for a given site, is experimentally inaccessible for these systems. Coarse-grained molecular dynamics simulations can be used to bridge this gap, and are relatively straightforward to learn. Such simulations allow users to observe spontaneous binding of lipids to membrane proteins and quantify localized densities of individual lipids or lipid fragments. In this chapter we outline a protocol for extracting binding affinities from these localized distributions, known as the "density threshold affinity." The density threshold affinity uses an adaptive and flexible definition of site occupancy that alleviates the need to distinguish between "bound'' lipids and bulk lipids that are simply diffusing through the site. Furthermore, the method allows "bead-level" resolution that is suitable for the case where lipids share binding sites, and circumvents ambiguities about a relevant reference state. This approach provides a convenient and straightforward method for comparing affinities of a single lipid species for multiple sites, multiple lipids for a single site, and/or a single lipid species modeled using multiple forcefields.
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Affiliation(s)
- Jesse W Sandberg
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Jahmal Ennis
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States; Department of Physics, Rutgers University, Camden, NJ, United States.
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3
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Coshic K, Maffeo C, Winogradoff D, Aksimentiev A. The structure and physical properties of a packaged bacteriophage particle. Nature 2024; 627:905-914. [PMID: 38448589 PMCID: PMC11196859 DOI: 10.1038/s41586-024-07150-4] [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: 09/01/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.
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Affiliation(s)
- Kush Coshic
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher Maffeo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Winogradoff
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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4
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Dinh T, Tber Z, Rey JS, Mengshetti S, Annamalai AS, Haney R, Briganti L, Amblard F, Fuchs JR, Cherepanov P, Kim K, Schinazi RF, Perilla JR, Kim B, Kvaratskhelia M. The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577387. [PMID: 38328097 PMCID: PMC10849636 DOI: 10.1101/2024.01.26.577387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are investigational antiretroviral agents which potently impair virion maturation by inducing hyper-multimerization of IN and inhibiting its interaction with viral genomic RNA. The pyrrolopyridine-based ALLINI pirmitegravir (PIR) has recently advanced into Phase 2a clinical trials. Previous cell culture based viral breakthrough assays identified the HIV-1(Y99H/A128T IN) variant that confers substantial resistance to this inhibitor. Here, we have elucidated the unexpected mechanism of viral resistance to PIR. While both Tyr99 and Ala128 are positioned within the inhibitor binding V-shaped cavity at the IN catalytic core domain (CCD) dimer interface, the Y99H/A128T IN mutations did not substantially affect direct binding of PIR to the CCD dimer or functional oligomerization of full-length IN. Instead, the drug-resistant mutations introduced a steric hindrance at the inhibitor mediated interface between CCD and C-terminal domain (CTD) and compromised CTD binding to the CCDY99H/A128T + PIR complex. Consequently, full-length INY99H/A128T was substantially less susceptible to the PIR induced hyper-multimerization than the WT protein, and HIV-1(Y99H/A128T IN) conferred >150-fold resistance to the inhibitor compared to the WT virus. By rationally modifying PIR we have developed its analog EKC110, which readily induced hyper-multimerization of INY99H/A128T in vitro and was ~14-fold more potent against HIV-1(Y99H/A128T IN) than the parent inhibitor. These findings suggest a path for developing improved PIR chemotypes with a higher barrier to resistance for their potential clinical use.
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Affiliation(s)
- Tung Dinh
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Zahira Tber
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Juan S Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Seema Mengshetti
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Arun S Annamalai
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Reed Haney
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - James R Fuchs
- College of Pharmacy, The Ohio State University, Columbus, Ohio, United States
| | - Peter Cherepanov
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Baek Kim
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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5
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Jennings J, Bracey H, Nguyen DT, Dasgupta R, Rivera AV, Sluis-Cremer N, Shi J, Aiken C. The HIV-1 capsid serves as a nanoscale reaction vessel for reverse transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566350. [PMID: 37986899 PMCID: PMC10659366 DOI: 10.1101/2023.11.08.566350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The viral capsid performs critical functions during HIV-1 infection and is a validated target for antiviral therapy. Previous studies have established that the proper structure and stability of the capsid are required for efficient HIV-1 reverse transcription in target cells. Moreover, it has recently been demonstrated that permeabilized virions and purified HIV-1 cores undergo efficient reverse transcription in vitro when the capsid is stabilized by addition of the host cell metabolite inositol hexakisphosphate (IP6). However, the molecular mechanism by which the capsid promotes reverse transcription is undefined. Here we show that wild type HIV-1 particles can undergo efficient reverse transcription in vitro in the absence of a membrane-permeabilizing agent. This activity, originally termed "natural endogenous reverse transcription" (NERT), depends on expression of the viral envelope glycoprotein during virus assembly and its incorporation into virions. Truncation of the gp41 cytoplasmic tail markedly reduced NERT activity, indicating that gp41 permits the entry of nucleotides into virions. Protease treatment of virions markedly reduced NERT suggesting the presence of a proteinaceous membrane channel. By contrast to reverse transcription in permeabilized virions, NERT required neither the addition of IP6 nor a mature capsid, indicating that an intact viral membrane can substitute for the function of the viral capsid during reverse transcription in vitro. Collectively, these results demonstrate that the viral capsid functions as a nanoscale container for reverse transcription during HIV-1 infection.
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Affiliation(s)
- Jordan Jennings
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Harrison Bracey
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Danny T. Nguyen
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Rishav Dasgupta
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alondra Vázquez Rivera
- Division of Infectious Disease, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Nicolas Sluis-Cremer
- Division of Infectious Disease, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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6
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Jana AK, Sharawy M, May ER. Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions. J Struct Biol 2023; 215:107964. [PMID: 37105277 PMCID: PMC10205670 DOI: 10.1016/j.jsb.2023.107964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/22/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Flock House virus (FHV) is an animal virus and considered a model system for non-enveloped viruses. It has a small, icosahedral capsid (T=3) and a bipartite positive-sense RNA genome. We present an extensive study of the FHV capsid dynamics from all-atom molecular dynamics simulations of the complete capsid. The simulations explore different biologically relevant conditions (neutral/low pH, with/without RNA in the capsid) using the CHARMM force field. The results show that low pH destabilizes the capsid, causing radial expansion, and RNA stabilizes the capsid. The finding of low pH destabilization is biologically relevant because the capsid is exposed to low pH in the endosome, where conformational changes occur leading to genome release. We also observe structural changes at the fivefold and twofold symmetry axes that likely relate to the externalization of membrane active γ peptides through the fivefold vertex and extrusion of RNA at the twofold axis. Simulations using the Amber force field at neutral pH are also performed and display similar characteristics to the CHARMM simulations.
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Affiliation(s)
- Asis K Jana
- DepartmentofMolecularandCellBiology, UniversityofConnecticut, Storrs, CT06269-3125, USA; Department of Microbiology and Biotechnology, Sister Nivedita University, New Town, West Bengal 700156, India
| | - Mahmoud Sharawy
- DepartmentofMolecularandCellBiology, UniversityofConnecticut, Storrs, CT06269-3125, USA
| | - Eric R May
- DepartmentofMolecularandCellBiology, UniversityofConnecticut, Storrs, CT06269-3125, USA.
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7
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Bryer AJ, Reddy T, Lyman E, Perilla JR. Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. PLoS Comput Biol 2022; 18:e1009781. [PMID: 35041642 PMCID: PMC8797243 DOI: 10.1371/journal.pcbi.1009781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 01/28/2022] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell's organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1's life cycle.
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Affiliation(s)
- Alexander J. Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - Tyler Reddy
- CCS-7 Applied Computer Science, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Edward Lyman
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, United States of America
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
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8
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Jones PE, Pérez-Segura C, Bryer AJ, Perilla JR, Hadden-Perilla JA. Molecular dynamics of the viral life cycle: progress and prospects. Curr Opin Virol 2021; 50:128-138. [PMID: 34464843 PMCID: PMC8651149 DOI: 10.1016/j.coviro.2021.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 01/29/2023]
Abstract
Molecular dynamics (MD) simulations across spatiotemporal resolutions are widely applied to study viruses and represent the central technique uniting the field of computational virology. We discuss the progress of MD in elucidating the dynamics of the viral life cycle, including the status of modeling intact extracellular virions and leveraging advanced simulations to mimic active life cycle processes. We further remark on the prospects of MD for continued contributions to the basic science characterization of viruses, especially given the increasing availability of high-quality experimental data and supercomputing power. Overall, integrative computational methods that are closely guided by experiments are unmatched in the level of detail they provide, enabling-now and in the future-new discoveries relevant to thwarting viral infection.
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Affiliation(s)
- Peter Eugene Jones
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
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9
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González-Arias F, Reddy T, Stone JE, Hadden-Perilla JA, Perilla JR. Scalable Analysis of Authentic Viral Envelopes on FRONTERA. Comput Sci Eng 2020; 22:11-20. [PMID: 33510584 PMCID: PMC7839976 DOI: 10.1109/mcse.2020.3020508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Enveloped viruses, such as SARS-CoV-2, infect cells via fusion of their envelope with the host membrane. By employing molecular simulations to characterize viral envelopes, researchers can gain insights into key determinants of infection. Here, the Frontera supercomputer is leveraged for large-scale modeling and analysis of authentic viral envelopes, whose lipid compositions are complex and realistic. Visual Molecular Dynamics (VMD) with support for MPI is employed, overcoming previous computational limitations and enabling investigation into virus biology at an unprecedented scale. The techniques applied here to an authentic HIV-1 envelope at two levels of spatial resolution (29 million particles and 280 million atoms) are broadly applicable to the study of other viruses. The authors are actively employing these techniques to develop and characterize an authentic SARS-CoV-2 envelope. A general framework for carrying out scalable analysis of simulation trajectories on Frontera is presented, expanding the utility of the machine in humanity’s ongoing fight against infectious diseases.
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