1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Mizrahi I, Bruinsma R, Rudnick J. Packaging contests between viral RNA molecules and kinetic selectivity. PLoS Comput Biol 2022; 18:e1009913. [PMID: 35363785 PMCID: PMC9022832 DOI: 10.1371/journal.pcbi.1009913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/21/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
The paper presents a statistical-mechanics model for the kinetic selection of viral RNA molecules by packaging signals during the nucleation stage of the assembly of small RNA viruses. The effects of the RNA secondary structure and folding geometry of the packaging signals on the assembly activation energy barrier are encoded by a pair of characteristics: the wrapping number and the maximum ladder distance. Kinetic selection is found to be optimal when assembly takes place under conditions of supersaturation and also when the concentration ratio of capsid protein and viral RNA concentrations equals the stoichiometric ratio of assembled viral particles. As a function of the height of the activation energy barrier, there is a form of order-disorder transition such that for sufficiently low activation energy barriers, kinetic selectivity is erased by entropic effects associated with the number of assembly pathways.
Collapse
Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, United States of America
- * E-mail:
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| |
Collapse
|
3
|
Jana AK, May ER. Atomistic dynamics of a viral infection process: Release of membrane lytic peptides from a non-enveloped virus. SCIENCE ADVANCES 2021; 7:7/16/eabe1761. [PMID: 33853772 PMCID: PMC8046363 DOI: 10.1126/sciadv.abe1761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/23/2021] [Indexed: 05/13/2023]
Abstract
Molecular simulations have played an instrumental role in uncovering the structural dynamics and physical properties of virus capsids. In this work, we move beyond equilibrium physicochemical characterization of a virus system to study a stage of the infection process that is required for viral proliferation. Despite many biochemical and functional studies, the molecular mechanism of host cell entry by non-enveloped viruses remains largely unresolved. Flock House virus (FHV) is a model system for non-enveloped viruses and is the subject of the current study. FHV infects through the acid-dependent endocytic pathway, where low pH triggers externalization of membrane-disrupting (γ) peptides from the capsid interior. Using all-atom equilibrium and enhanced sampling simulations, the mechanism and energetics of γ peptide liberation and the effect of pH on this process are investigated. Our computations agree with experimental findings and reveal nanoscopic details regarding the pH control mechanism, which are not readily accessible in experiments.
Collapse
Affiliation(s)
- Asis K Jana
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| |
Collapse
|
4
|
Abstract
Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.
Collapse
Affiliation(s)
| | - Julie M. Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
5
|
Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
Collapse
Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| |
Collapse
|
6
|
Jana AK, May ER. Structural and dynamic asymmetry in icosahedrally symmetric virus capsids. Curr Opin Virol 2020; 45:8-16. [PMID: 32615360 PMCID: PMC7746594 DOI: 10.1016/j.coviro.2020.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023]
Abstract
A common characteristic of virus capsids is icosahedral symmetry, yet these highly symmetric structures can display asymmetric features within their virions and undergo asymmetric dynamics. The fields of structural and computational biology have entered a new realm in the investigation of virus infection mechanisms, with the ability to observe symmetry-breaking features. This review will cover important studies on icosahedral virus structure and dynamics, covering both symmetric and asymmetric conformational changes. However, the main emphasis of the review will be towards recent studies employing cryo-electron microscopy or molecular dynamics simulations, which can uncover asymmetric aspects of these systems relevant to understanding viral physical-chemical properties and their biological impact.
Collapse
Affiliation(s)
- Asis K Jana
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| |
Collapse
|
7
|
Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics. Viruses 2020; 12:v12111273. [PMID: 33171826 PMCID: PMC7695174 DOI: 10.3390/v12111273] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a large assembly. We use cryo-EM reconstructions to simulate the DNA packaging-associated 3 nm expansion of the protein shell of an initially assembled phage T7 capsid (called procapsid or capsid I). This is accompanied by a disorder-order transition and expansion-associated externalization displacement of the 420 N-terminal tails of the shell proteins. For the simulations, we use an all-atom structure-based model (1.07 million atoms), which is specifically designed to probe the influence of molecular sterics on dynamics. We find that the rate at which the N-terminal tails undergo translocation depends heavily on their position within hexons and pentons. Specifically, trans-shell displacements of the hexon E subunits are the most frequent and hexon A subunits are the least frequent. The simulations also implicate numerous tail translocation intermediates during tail translocation that involve topological traps, as well as sterically induced barriers. The presented study establishes a foundation for understanding the precise relationship between molecular structure and phage maturation.
Collapse
|
8
|
Mesoscale model of the assembly and cross-linking of HPV virus-like particles. Virology 2019; 537:53-64. [PMID: 31450047 DOI: 10.1016/j.virol.2019.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 11/22/2022]
Abstract
We present a novel kinetic Monte Carlo model to simulate the real process time-scale of the assembly of Human Papillomavirus (HPV) virus-like particles (VLPs) incorporating the formation of intercapsomeric disulfide bonds. The objective was to develop insights into the underlying mechanisms of HPV VLP assembly and cross-linking during in vitro production of the HPV vaccine. The model integrates actual experimental data and detailed information of VLP geometrical structure in microscopic mechanistic steps. The principal novelty of this model is in the concurrent simulation of VLP assembly and cross-linking including a variable for spatial angular arrangement of capsomeres during their assembly that affects the overall rates of VLP assembly and cross-linking. The cross-linking modeled by using the mechanistic probability rules between involved cysteine residues. The model was utilized to better understand the actual process data and check on the hypothesis related to factors affecting the rates of HPV growth and maturation.
Collapse
|
9
|
Ramesh R, Lim XX, Raghuvamsi PV, Wu C, Wong SM, Anand GS. Uncovering metastability and disassembly hotspots in whole viral particles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:5-12. [PMID: 30553754 DOI: 10.1016/j.pbiomolbio.2018.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/26/2018] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
Viruses are metastable macromolecular assemblies that toggle between multiple conformational states through molecular rearrangements that are critical for mediating viral host entry. Viruses respond to different host specific environmental cues to form disassembly intermediates for the eventual release of genomic material required for replication. Although static snapshots of these intermediates have been captured through structural techniques such as X-ray crystallography and cryo-EM, the mechanistic details of these conformational rearrangements underpinning viral metastability have been poorly understood. Amide hydrogen deuterium exchange mass spectrometry (HDXMS) is a powerful tool that measures hydrogen bonding propensities to probe changes in the dynamics of different macromolecular interactions. Chaotropic agents such as urea can be used to disrupt hydrogen bonds between different subunits, thereby ranking regions of the virus that are critical in maintaining viral stability. By controlled urea denaturation with HDXMS, we have identified specific loci in a Turnip Crinkle Virus (TCV) model showing increased deuterium exchange with even minimally disruptive concentrations of urea. These loci represent dynamic disassembly hotspots. These hotspots are predominantly present at the quaternary contacts at the 3-fold and 5-fold axes. This approach can be applied to detect vulnerabilities in virus icosahedral structures to uncover the molecular mechanism of viral disassembly.
Collapse
Affiliation(s)
- Ranita Ramesh
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Xin Xiang Lim
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | | | - Chao Wu
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Sek Man Wong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore; Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
| | | |
Collapse
|
10
|
Aznar M, Roca-Bonet S, Reguera D. Viral nanomechanics with a virtual atomic force microscope. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:264001. [PMID: 29769436 PMCID: PMC7104910 DOI: 10.1088/1361-648x/aac57a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 05/07/2018] [Accepted: 05/15/2018] [Indexed: 05/22/2023]
Abstract
One of the most important components of a virus is the protein shell or capsid that encloses its genetic material. The main role of the capsid is to protect the viral genome against external aggressions, facilitating its safe and efficient encapsulation and delivery. As a consequence, viral capsids have developed astonishing mechanical properties that are crucial for viral function. These remarkable properties have started to be unveiled in single-virus nanoindentation experiments, and are opening the door to the use of viral-derived artificial nanocages for promising bio- and nano-technological applications. However, the interpretation of nanoindentation experiments is often difficult, requiring the support of theoretical and simulation analysis. Here we present a 'Virtual AFM' (VAFM), a Brownian Dynamics simulation of a coarse-grained model of virus aimed to mimic the standard setup of atomic force microscopy (AFM) nanoindentation experiments. Despite the heavy level of coarse-graining, these simulations provide valuable information which is not accessible in experiments. Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid's structural units. In particular, we will discuss the influence of adsorption, the tip radius, and the rigidity and shape of the shell on its mechanical response.
Collapse
Affiliation(s)
- María Aznar
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Sergi Roca-Bonet
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - David Reguera
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Martí i Franquès 1, 08028 Barcelona, Spain
| |
Collapse
|
11
|
Newton AC, Groenewold J, Kegel WK, Bolhuis PG. The role of multivalency in the association kinetics of patchy particle complexes. J Chem Phys 2018. [PMID: 28641424 DOI: 10.1063/1.4984966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Association and dissociation of particles are elementary steps in many natural and technological relevant processes. For many such processes, the presence of multiple binding sites is essential. For instance, protein complexes and regular structures such as virus shells are formed from elementary building blocks with multiple binding sites. Here we address a fundamental question concerning the role of multivalency of binding sites in the association kinetics of such complexes. Using single replica transition interface sampling simulations, we investigate the influence of the multivalency on the binding kinetics and the association mechanism of patchy particles that form polyhedral clusters. When the individual bond strength is fixed, the kinetics naturally is very dependent on the multivalency, with dissociation rate constants exponentially decreasing with the number of bonds. In contrast, we find that when the total bond energy per particle is kept constant, association and dissociation rate constants turn out rather independent of multivalency, although of course still very dependent on the total energy. The association and dissociation mechanisms, however, depend on the presence and nature of the intermediate states. For instance, pathways that visit intermediate states are less prevalent for particles with five binding sites compared to the case of particles with only three bonds. The presence of intermediate states can lead to kinetic trapping and malformed aggregates. We discuss implications for natural forming complexes such as virus shells and for the design of artificial colloidal patchy particles.
Collapse
Affiliation(s)
- Arthur C Newton
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jan Groenewold
- Van't Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Willem K Kegel
- Van't Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter G Bolhuis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
12
|
Hadden JA, Perilla JR, Schlicksup CJ, Venkatakrishnan B, Zlotnick A, Schulten K. All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits. eLife 2018; 7:32478. [PMID: 29708495 PMCID: PMC5927769 DOI: 10.7554/elife.32478] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid’s influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid’s triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids.
Collapse
Affiliation(s)
- Jodi A Hadden
- Department of Chemistry and Biochemistry, University of Delaware, Newark, United States
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, United States
| | | | | | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.,Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, United States
| |
Collapse
|
13
|
Sadre-Marandi F, Das P. Extension of Caspar-Klug theory to higher order pentagonal polyhedra. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2018. [DOI: 10.1515/cmb-2018-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract Many viral capsids follow an icosahedral fullerene-like structure, creating a caged polyhedral arrangement built entirely from hexagons and pentagons. Viral capsids consist of capsid proteins,which group into clusters of six (hexamers) or five (pentamers). Although the number of hexamers per capsid varies depending on the capsid size, Caspar-Klug Theory dictates there are exactly twelve pentamers needed to form a closed capsid.However, for a significant number of viruses, including viruses of the Papovaviridae family, the theory doesn’t apply. The anomaly of the Caspar-Klug Theory has raised a new question:“For which Caspar and Klug models can each hexamer be replaced with a pentamer while still following icosahedral symmetry?” This paper proposes an answer to this question by examining icosahedral viral capsid-like structures composed only of pentamers, called pentagonal polyhedra. The analysis shows that pentagonal polyhedra fall in a subclass of T, defined by P ≥ 7 and T = 1( mod 3).
Collapse
Affiliation(s)
- Farrah Sadre-Marandi
- 1Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Praachi Das
- 2Department of Mathematics, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
14
|
Machado MR, González HC, Pantano S. MD Simulations of Viruslike Particles with Supra CG Solvation Affordable to Desktop Computers. J Chem Theory Comput 2017; 13:5106-5116. [DOI: 10.1021/acs.jctc.7b00659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matı́as R. Machado
- Biomolecular Simulations
Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| | - Humberto C. González
- Biomolecular Simulations
Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| | - Sergio Pantano
- Biomolecular Simulations
Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay
| |
Collapse
|
15
|
Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nat Commun 2017; 8:15959. [PMID: 28722007 PMCID: PMC5524983 DOI: 10.1038/ncomms15959] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/12/2017] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ∼1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function. The large and complex HIV-1 capsid modulates several molecular events during HIV-1’s infective cycle. Here the authors use all-atom molecular dynamic simulations to probe the biophysical properties of the genome-free HIV-1 capsid.
Collapse
|
16
|
Abstract
During the life cycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article, we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly and thus should be taken into account in models that are used to estimate interaction parameters from experimental data.
Collapse
Affiliation(s)
- Guillermo R Lazaro
- Martin Fisher School of Physics, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University , Waltham, Massachusetts 02454, United States
| |
Collapse
|
17
|
Aggarwal A, May ER, Brooks CL, Klug WS. Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature. Phys Rev E 2016; 93:012417. [PMID: 26871111 DOI: 10.1103/physreve.93.012417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 06/05/2023]
Abstract
Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic thermal fluctuations obtained from molecular dynamics simulation at any coarse-grained scale using a potential of the mean-force approach. We present the results for a mutant of Sesbania mosaic virus capsid, where we calculate the elastic moduli at different scales and observe an apparent problem with the chosen reference configuration in some cases. We present a possible explanation using an elastic network model, where inducing random prestrain results in a similar behavior. This phenomenon provides a novel insight into the continuum nature of macromolecules and defines the limits on details that the elasticity theory can capture. Further investigation into prestrains could elucidate important aspects of conformational dynamics of macromolecules.
Collapse
Affiliation(s)
- Ankush Aggarwal
- Zienkiewicz Centre for Computational Engineering, Swansea University, Swansea SA1 8EN, United Kigdom
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Charles L Brooks
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - William S Klug
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California 90095, USA
| |
Collapse
|
18
|
Rahimi A, Varano AC, Demmert AC, Melanson LA, McDonald SM, Kelly DF. A Non-Symmetric Reconstruction Technique for Transcriptionally-Active Viral Assemblies. ACTA ACUST UNITED AC 2015; 2. [PMID: 27819069 PMCID: PMC5094455 DOI: 10.13188/2474-1914.1000004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The molecular mechanisms by which RNA viruses coordinate their transcriptional activities are not fully understood. For rotavirus, an important pediatric gastroenteric pathogen, transcription occurs within a double-layered particle that encloses the viral genome. To date, there remains very little structural information available for actively-transcribing rotavirus double-layered particles, which could provide new insights for antiviral development. To improve our vision of these viral assemblies, we developed a new combinatorial strategy that utilizes currently available high-resolution image processing tools. First, we employed a 3D classification routine that allowed us to sort transcriptionally-active rotavirus assemblies on the basis of their internal density. Next, we implemented an additional 3D refinement procedure using the most active class of DLPs. For comparison, the refined structures were computed in parallel by (1) enforcing icosahedral symmetry, and by (2) using no symmetry operators. Comparing the resulting structures, we were able to visualize the continuum that exists between viral capsid proteins and the viral RNA for the first time.
Collapse
Affiliation(s)
- Amina Rahimi
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | | | - Andrew C Demmert
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA
| | | | - Sarah M McDonald
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biomedical Sciences and Pathology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Virginia Tech Carilion School of Medicine, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
19
|
Boyd KJ, Bansal P, Feng J, May ER. Stability of Norwalk Virus Capsid Protein Interfaces Evaluated by in Silico Nanoindentation. Front Bioeng Biotechnol 2015; 3:103. [PMID: 26284238 PMCID: PMC4520240 DOI: 10.3389/fbioe.2015.00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/10/2015] [Indexed: 01/17/2023] Open
Abstract
Norwalk virus causes severe gastroenteritis for which there is currently no specific anti-viral therapy. A stage of the infection process is uncoating of the protein capsid to expose the viral genome and allow for viral replication. A mechanical characterization of the Norwalk virus may provide important information relating to the mechanism of uncoating. The mechanical strength of the Norwalk virus has previously been investigated using atomic force microscopy (AFM) nanoindentation experiments. Those experiments cannot resolve specific molecular interactions, and therefore, we have employed a molecular modeling approach to gain insights into the potential uncoating mechanism of the Norwalk capsid. In this study, we perform simulated nanoindentation using a coarse-grained structure-based model, which provides an estimate of the spring constant in good agreement with the experimentally determined value. We further analyze the fracture mechanisms and determine weak interfaces in the capsid structure, which are potential sites to inhibit uncoating by stabilization of these weak interfaces. We conclude by identifying potential target sites at the junction of a weak protein–protein interface.
Collapse
Affiliation(s)
- Kevin J Boyd
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, CT , USA
| | - Prakhar Bansal
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, CT , USA
| | - Jun Feng
- Department of Chemistry, West Virginia University , Morgantown, WV , USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, CT , USA
| |
Collapse
|
20
|
Affiliation(s)
- Fangqiang Zhu
- Department
of Physics, Indiana University - Purdue University, Indianapolis, Indiana 46202, United States
| | - Bo Chen
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
| |
Collapse
|
21
|
Abstract
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.
Collapse
|
22
|
Abstract
As they mature, many capsids undergo massive conformational changes that transform their stability, reactivity, and capacity for DNA. In some cases, maturation proceeds via one or more intermediate states. These structures represent local minima in a rich energy landscape that combines contributions from subunit folding, association of subunits into capsomers, and intercapsomer interactions. We have used scanning calorimetry and cryo-electron microscopy to explore the range of capsid conformations accessible to bacteriophage HK97. To separate conformational effects from those associated with covalent cross-linking (a stabilization mechanism of HK97), a cross-link-incompetent mutant was used. The mature capsid Head I undergoes an endothermic phase transition at 60°C in which it shrinks by 7%, primarily through changes in its hexamer conformation. The transition is reversible, with a half-life of ~3 min; however, >50% of reverted capsids are severely distorted or ruptured. This observation implies that such damage is a potential hazard of large-scale structural changes such as those involved in maturation. Assuming that the risk is lower for smaller changes, this suggests a rationalization for the existence of metastable intermediates: that they serve as stepping stones that preserve capsid integrity as it switches between the radically different conformations of its precursor and mature states. Large-scale conformational changes are widespread in virus maturation and infection processes. These changes are accompanied by the release of conformational free energy as the virion (or fusogenic glycoprotein) switches from a precursor state to its mature state. Each state corresponds to a local minimum in an energy landscape. The conformational changes in capsid maturation are so radical that the question arises of how maturing capsids avoid being torn apart. Offering proof of principle, severe damage is inflicted when a bacteriophage HK97 capsid reverts from the (nonphysiological) state that it enters when heated past 60°C. We suggest that capsid proteins have been selected in part by the criterion of being able to avoid sustaining collateral damage as they mature. One way of achieving this—as with the HK97 capsid—involves breaking the overall transition down into several smaller steps in which the risk of damage is reduced.
Collapse
|
23
|
May ER. Recent Developments in Molecular Simulation Approaches to Study Spherical Virus Capsids. MOLECULAR SIMULATION 2014; 40:878-888. [PMID: 25197162 DOI: 10.1080/08927022.2014.907899] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Viruses are a particularly challenging systems to study via molecular simulation methods. Virus capsids typically consist of over 100 subunit proteins and reach dimensions of over 100 nm; solvated viruses capsid systems can be over 1 million atoms in size. In this review, I will present recent developments which have attempted to overcome the significant computational expense to perform simulations which can inform experimental studies, make useful predictions about biological phenomena and calculate material properties relevant to nanotechnology design efforts.
Collapse
Affiliation(s)
- Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA 06269
| |
Collapse
|
24
|
Vashisth H, Skiniotis G, Brooks CL. Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chem Rev 2014; 114:3353-65. [PMID: 24446720 PMCID: PMC3983124 DOI: 10.1021/cr4005988] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Harish Vashisth
- Department
of Chemical Engineering, University of New
Hampshire, Durham, New Hampshire 03824, United States
| | - Georgios Skiniotis
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles Lee Brooks
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
25
|
Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
Collapse
|
26
|
May ER, Arora K, Brooks CL. pH-induced stability switching of the bacteriophage HK97 maturation pathway. J Am Chem Soc 2014; 136:3097-107. [PMID: 24495192 PMCID: PMC3985869 DOI: 10.1021/ja410860n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to shifting the stability between the states along the pathway under differing pH conditions. We further analyze these data to establish the connection between critical residues and important structural motifs which undergo reorganization during maturation. We go on to show how DNA packaging can induce spontaneous reorganization of the capsid during maturation.
Collapse
Affiliation(s)
- Eric R May
- Department of Molecular and Cell Biology, University of Connecticut , Storrs, Connecticut 06269, United States
| | | | | |
Collapse
|
27
|
Polles G, Indelicato G, Potestio R, Cermelli P, Twarock R, Micheletti C. Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition. PLoS Comput Biol 2013; 9:e1003331. [PMID: 24244139 PMCID: PMC3828136 DOI: 10.1371/journal.pcbi.1003331] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/13/2013] [Indexed: 02/05/2023] Open
Abstract
Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available. The genetic material of viruses is packaged inside capsids constituted from a few tens to thousands of proteins. The latter can organize in multimers that serve as fundamental blocks for the viral shell assembly or that control the capsid conformational transitions and response to mechanical stress. In this work, we introduce and apply a computational scheme that identifies the fundamental protein blocks from the structural fluctuations of the capsids in thermal equilibrium. These can be derived from phenomenological elastic network models with minimal computational expenditure. Accordingly, the basic functional protein units of a capsid can be obtained from the sole input of the capsid crystal structure. The method is applied to a heterogeneous set of viruses of various size and geometries. These include well-characterised instances for validation purposes, as well as debated ones for which predictions are formulated.
Collapse
Affiliation(s)
- Guido Polles
- International School for Advanced Studies (SISSA), Trieste, Italy
| | - Giuliana Indelicato
- York Centre for Complex Systems Analysis, Department of Mathematics, University of York, York, United Kingdom
| | | | - Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, Torino, Italy
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, Department of Mathematics, University of York, York, United Kingdom
| | | |
Collapse
|
28
|
Coarse-grain modelling of protein-protein interactions. Curr Opin Struct Biol 2013; 23:878-86. [PMID: 24172141 DOI: 10.1016/j.sbi.2013.09.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 08/29/2013] [Accepted: 09/17/2013] [Indexed: 11/24/2022]
Abstract
Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are separately described, but we note the parallel development that is present in both research fields with three important themes: firstly, combining CG modelling with knowledge-based approaches to predict and refine protein-protein complexes; secondly, using physics-based CG models for de novo prediction of protein-protein complexes; and thirdly modelling of large scale protein aggregates.
Collapse
|
29
|
Cermelli P, Indelicato G, Twarock R. Nonicosahedral pathways for capsid expansion. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032710. [PMID: 24125297 DOI: 10.1103/physreve.88.032710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 06/26/2013] [Indexed: 06/02/2023]
Abstract
For a significant number of viruses a structural transition of the protein container that encapsulates the viral genome forms an important part of the life cycle and is a prerequisite for the particle becoming infectious. Despite many recent efforts the mechanism of this process is still not fully understood, and a complete characterization of the expansion pathways is still lacking. We present here a coarse-grained model that captures the essential features of the expansion process and allows us to investigate the conditions under which a viral capsid becomes unstable. Based on this model we demonstrate that the structural transitions in icosahedral viral capsids are likely to occur through a low-symmetry cascade of local expansion events spreading in a wavelike manner over the capsid surface.
Collapse
Affiliation(s)
- Paolo Cermelli
- Dipartimento di Matematica, Università di Torino, Torino, Italy
| | | | | |
Collapse
|
30
|
Abstract
All matter has to obey the general laws of physics and living matter is not an exception. Viruses have not only learnt how to cope with them, but have managed to use them for their own survival. In this chapter we will review some of the exciting physics behind viruses and discuss simple physical models that can shed some light on different aspects of the viral life cycle and viral properties. In particular, we will focus on how the structure and shape of the capsid, its assembly and stability, and the entry and exit of viral particles and their genomes can be understood using fundamental physics theories.
Collapse
Affiliation(s)
- Antoni Luque
- Department of Fundamental Physics, Universitat de Barcelona, c/Martí i Franquès 1, 08028, Barcelona, Spain
| | | |
Collapse
|
31
|
Abstract
The propensity for capsid disassembly and uncoating of human adenovirus is modulated by interactions with host cell molecules like integrins and alpha defensins. Here, we use atomic force microscopy (AFM) nanoindentation to elucidate, at the single-particle level, the mechanism by which binding of these host molecules affects virus particle elasticity. Our results demonstrate the direct link between integrin or defensin binding and the mechanical properties of the virus. We show that the structure and geometry of adenovirus result in an anisotropic elastic response that relates to icosahedral symmetry. This elastic response changes upon binding host molecules. Whereas integrin binding softens the vertex regions, binding of a human alpha defensin has exactly the opposite effect. Our results reveal that the ability of these host molecules to influence adenovirus disassembly correlates with a direct effect on the elastic strength of the penton region. Host factors that influence adenovirus infectivity thus modulate the elastic properties of the capsid. Our findings reveal a direct link between virus-host interactions and capsid mechanics.
Collapse
|
32
|
Vashisth H, Brooks CL. Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes. J Phys Chem Lett 2012; 3:3379-3384. [PMID: 23185650 PMCID: PMC3505029 DOI: 10.1021/jz301650q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have studied large-scale conformational transitions in the maltose-binding protein, and the nucleotide binding domains of a maltose-transporter using enhanced conformational sampling in Cartesian collective variables (CVs) with temperature-accelerated molecular dynamics (TAMD), and C(α)-based elastic network normal mode analysis. Significantly, every functional displacement in the TAMD-generated pathways of each protein could be rationalized via a single low-frequency soft mode, while a combination of 2 to 3 low-frequency modes were found to describe the entire conformational change suggesting that collective functional movement in TAMD trajectories is facilitated by the intrinsically accessible low-frequency normal modes. By applying a harmonic potential to facilitate functional motion in TAMD simulations, we also provide a recipe to reproducibly generate structural transitions in both proteins, which can be used to characterize large-scale conformational changes in other biomolecules.
Collapse
Affiliation(s)
| | - C. L. Brooks
- To whom correspondence should be addressed , Phone: (734)-647-6682. Fax: (734)-647-1604
| |
Collapse
|
33
|
May ER, Brooks CL. On the morphology of viral capsids: elastic properties and buckling transitions. J Phys Chem B 2012; 116:8604-9. [PMID: 22409201 DOI: 10.1021/jp300005g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The morphology of icosahedral viruses ranges from highly spherical to highly faceted, and for some viruses a shape transition occurs during the viral life cycle. This phenomena is predicted from continuum elasticity, via the buckling transition theory by Nelson (Phys. Rev. E 2003, 68, 051910), in which the shape is dependent on the Foppl-von Kármán number (γ), which is a ratio of the two-dimensional Young's modulus (Y) and the bending modulus (κ). However, until now, no direct calculations have been performed on atomic-level capsid structures to test the predictions of the theory. In this study, we employ a previously described multiscale method by May and Brooks (Phys. Rev. Lett. 2011, 106, 188101) to calculate Y and κ for the bacteriophage HK97, which undergoes a spherical to faceted transition during its viral life cycle. We observe a change in γ consistent with the buckling transition theory and also a significant reduction in κ, which facilitates formation of the faceted state. We go on to examine many capsids from the T = 3 and 7 classes using only elastic network models, which allows us to calculate the ratio Y/κ, without the expense of all-atom molecular dynamics. We observe for the T = 7 capsids, there is strong correlation between the shape of the capsid and γ; however, there is no such correlation for the smaller T = 3 viruses.
Collapse
Affiliation(s)
- Eric R May
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | |
Collapse
|