1
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Gómez-Moreno A, Ploss A. Mechanisms of Hepatitis B Virus cccDNA and Minichromosome Formation and HBV Gene Transcription. Viruses 2024; 16:609. [PMID: 38675950 PMCID: PMC11054251 DOI: 10.3390/v16040609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatitis B virus (HBV) is the etiologic agent of chronic hepatitis B, which puts at least 300 million patients at risk of developing fibrosis, cirrhosis, and hepatocellular carcinoma. HBV is a partially double-stranded DNA virus of the Hepadnaviridae family. While HBV was discovered more than 50 years ago, many aspects of its replicative cycle remain incompletely understood. Central to HBV persistence is the formation of covalently closed circular DNA (cccDNA) from the incoming relaxed circular DNA (rcDNA) genome. cccDNA persists as a chromatinized minichromosome and is the major template for HBV gene transcription. Here, we review how cccDNA and the viral minichromosome are formed and how viral gene transcription is regulated and highlight open questions in this area of research.
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Affiliation(s)
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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2
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Pusara S, Wenzel W, Kozlowska M. Impact of DNA on interactions between core proteins of Hepatitis B virus-like particles comprising different C-terminals. Int J Biol Macromol 2024; 263:130365. [PMID: 38401590 DOI: 10.1016/j.ijbiomac.2024.130365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
Hepatitis B virus (HBV) virus-like particles (VLPs) are promising therapeutic agents derived from HBV core proteins (Cp). This study investigates the assembly dynamics of HBV VLPs, which is crucial for their potential as drug carriers or gene delivery systems. Coarse-grained molecular dynamics simulations explore the impact of C-terminal domain length (in the Cp ranging from Cp149 to wild-type Cp183) on Cp assembly and stability, particularly in the presence of DNA. Our findings reveal that the C-terminal nucleic acid binding region significantly influences Cp assembly and stability of trimers comprising Cp dimers. Shorter C-terminal domains (Cp164, Cp167) enhance stability and protein-protein interactions, while interactions between naturally occurring Cp183 are destabilized in the absence of DNA. Interestingly, DNA addition further stabilizes Cp assemblies, and this effect is influenced by the length of the nucleic acid binding region. Shorter C-terminal domains show less dependency on DNA content. This stabilization is attributed to electrostatic forces between positively charged C-terminal chains and negatively charged nucleic acids. Our study sheds light on the molecular mechanisms governing protein-protein and protein-DNA interactions in HBV VLP assembly, providing insights into Cp processability and informing the development of efficient gene therapy carriers using VLP technology.
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Affiliation(s)
- Srdjan Pusara
- Institute of Nanotechnology, Karlsruhe Institute of Technology KIT, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology KIT, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology, Karlsruhe Institute of Technology KIT, Kaiserstraße 12, 76131 Karlsruhe, Germany.
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3
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Mills KR, Torabifard H. Computational approaches to investigate fluoride binding, selectivity and transport across the membrane. Methods Enzymol 2024; 696:109-154. [PMID: 38658077 DOI: 10.1016/bs.mie.2024.01.006] [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: 04/26/2024]
Abstract
The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.
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Affiliation(s)
- Kira R Mills
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, TX, United States
| | - Hedieh Torabifard
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, TX, United States.
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4
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Ghaemi Z, Nafiu O, Tajkhorshid E, Gruebele M, Hu J. A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions. Sci Rep 2023; 13:21392. [PMID: 38049515 PMCID: PMC10695947 DOI: 10.1038/s41598-023-45998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 10/26/2023] [Indexed: 12/06/2023] Open
Abstract
Despite a vaccine, hepatitis B virus (HBV) remains a world-wide source of infections and deaths. We develop a whole-cell computational platform combining spatial and kinetic models describing the infection cycle of HBV in a hepatocyte host. We simulate key parts of the infection cycle with this whole-cell platform for 10 min of biological time, to predict infection progression, map out virus-host and virus-drug interactions. We find that starting from an established infection, decreasing the copy number of the viral envelope proteins shifts the dominant infection pathway from capsid secretion to re-importing the capsids into the nucleus, resulting in more nuclear-localized viral covalently closed circular DNA (cccDNA) and boosting transcription. This scenario can mimic the consequence of drugs designed to manipulate viral gene expression. Mutating capsid proteins facilitates capsid destabilization and disassembly at nuclear pore complexes, resulting in an increase in cccDNA copy number. However, excessive destabilization leads to premature cytoplasmic disassembly and does not increase the cccDNA counts. Finally, our simulations can predict the best drug dosage and its administration timing to reduce the cccDNA counts. Our adaptable computational platform can be parameterized to study other viruses and identify the most central viral pathways that can be targeted by drugs.
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Affiliation(s)
- Zhaleh Ghaemi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- National Science Foundation Science and Technology Center for Quantitative Cell Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Oluwadara Nafiu
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Emad Tajkhorshid
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- National Science Foundation Science and Technology Center for Quantitative Cell Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- National Science Foundation Science and Technology Center for Quantitative Cell Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jianming Hu
- Department of Microbiology and Immunology, Pennsylvania State University, Hershey, PA, 17033, USA
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5
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Luo H, Ma Y, Ren Y, Li Z, Sheng Y, Wang Y, Su Z, Bi J, Zhang S. Study of self-assembling properties of HBc-VLP derivatives aided by molecular dynamic simulations from a thermodynamic perspective. J Biomol Struct Dyn 2023:1-14. [PMID: 37908124 DOI: 10.1080/07391102.2023.2273438] [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: 06/05/2023] [Accepted: 10/14/2023] [Indexed: 11/02/2023]
Abstract
Self-assembling protein nanoparticles showed promise for vaccine design due to efficient antigen presentations and safety. However, the unpredictable formations of epitopes-fused protein assemblies remain challenging in the upstream design. This study suggests employing molecular dynamic (MD) simulations to investigate the assembly properties of Hepatitis B core protein (HBc) from thermodynamic perspectives. Eight HBc derivatives were expressed in E. coli, with their self-assembly properties characterised by high-performance liquid chromatography and transmission electron microscopy. MD simulations on the dimers, based on AlphaFold-predicted 3D structures, analysed the derivative at the atomic level. Results revealed that HBc derivatives can form dissociative polymers or large multi-subunit structures due to assembly failures. The instability of the dimer in aqueous solvents or inappropriate intradimer distances could cause major assembly failures. Polar solvation energies played a vital role too in forming assemble-incompetent dimers. Importantly, our study demonstrated that MD simulations on dimers can provide preliminary predictions on the assembly properties of HBc derivatives, thus aiding vaccine design by lowering the risk of self-assembling failures in engineered proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, Australia
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Yanan Sheng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, Australia
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, PR China
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6
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Elizalde MM, Giadans CG, Campos RH, Flichman DM. Impact of core protein naturally selected mutants associated with HBeAg-negative status in HBV biosynthesis. J Med Virol 2023; 95:e29195. [PMID: 37881005 DOI: 10.1002/jmv.29195] [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: 07/12/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
Hepatitis B e antigen (HBeAg) loss represents a late stage of chronic hepatitis B virus (HBV) infection associated with a drastic decrease in HBV-DNA, a lower risk of disease progression, and the occurrence of several mutations in the preCore/core region. However, the underlying mechanisms supporting the downregulation of viral replication have yet to be elucidated. In the present study, the analysis of the frequency of subgenotype D1 core protein (HBc) mutations associated with HBeAg status revealed a higher mutation rate in HBeAg-negative sequences compared to HBeAg-positive ones. Particularly, 22 amino acids exhibited a higher frequency of mutation in HBeAg-negative sequences, while the remaining residues showed a high degree of conservation. Subsequently, the assessment of HBc mutants derived from HBeAg-negative patients in viral structure and replicative capacity revealed that HBc mutations have the ability to modulate the subcellular localization of the protein (either when the protein was expressed alone or in the context of viral replication), capsid assembly, and, depending on specific mutation patterns, alter covalently closed circular DNA (cccDNA) recycling and up- or downregulate viral replication. In conclusion, HBc mutations associated with HBeAg-negative status impact on various stages of the HBV life cycle modulating viral replication during the HBeAg-negative stage of infection.
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Affiliation(s)
- María Mercedes Elizalde
- Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Cecilia Graciela Giadans
- Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego Martín Flichman
- Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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7
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Clark AB, Safdari M, Zoorob S, Zandi R, van der Schoot P. Relaxational dynamics of the T-number conversion of virus capsids. J Chem Phys 2023; 159:084904. [PMID: 37610017 DOI: 10.1063/5.0160822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023] Open
Abstract
We extend a recently proposed kinetic theory of virus capsid assembly based on Model A kinetics and study the dynamics of the interconversion of virus capsids of different sizes triggered by a quench, that is, by sudden changes in the solution conditions. The work is inspired by in vitro experiments on functionalized coat proteins of the plant virus cowpea chlorotic mottle virus, which undergo a reversible transition between two different shell sizes (T = 1 and T = 3) upon changing the acidity and salinity of the solution. We find that the relaxation dynamics are governed by two time scales that, in almost all cases, can be identified as two distinct processes. Initially, the monomers and one of the two types of capsids respond to the quench. Subsequently, the monomer concentration remains essentially constant, and the conversion between the two capsid species completes. In the intermediate stages, a long-lived metastable steady state may present itself, where the thermodynamically less stable species predominate. We conclude that a Model A based relaxational model can reasonably describe the early and intermediate stages of the conversion experiments. However, it fails to provide a good representation of the time evolution of the state of assembly of the coat proteins in the very late stages of equilibration when one of the two species disappears from the solution. It appears that explicitly incorporating the nucleation barriers to assembly and disassembly is crucial for an accurate description of the experimental findings, at least under conditions where these barriers are sufficiently large.
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Affiliation(s)
- Alexander Bryan Clark
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Mohammadamin Safdari
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Selim Zoorob
- Biophysics Graduate Program, University of California, Riverside, California 92521, USA
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
- Biophysics Graduate Program, University of California, Riverside, California 92521, USA
| | - Paul van der Schoot
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Postbus 513, 5600 MB Eindhoven, The Netherlands
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8
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Spivak M, Stone JE, Ribeiro J, Saam J, Freddolino PL, Bernardi RC, Tajkhorshid E. VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. J Chem Inf Model 2023; 63:4664-4678. [PMID: 37506321 PMCID: PMC10516160 DOI: 10.1021/acs.jcim.3c00658] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Modeling and simulation of small molecules such as drugs and biological cofactors have been both a major focus of computational chemistry for decades and a growing need among computational biophysicists who seek to investigate the interaction of different types of ligands with biomolecules. Of particular interest in this regard are quantum mechanical (QM) calculations that are used to more accurately describe such small molecules, which can be of heterogeneous structures and chemistry, either in purely QM calculations or in hybrid QM/molecular mechanics (MM) simulations. QM programs are also used to develop MM force field parameters for small molecules to be used along with established force fields for biomolecules in classical simulations. With this growing need in mind, here we report a set of software tools developed and closely integrated within the broadly used molecular visualization/analysis program, VMD, that allow the user to construct, modify, and parametrize small molecules and prepare them for QM, hybrid QM/MM, or classical simulations. The tools also provide interactive analysis and visualization capabilities in an easy-to-use and integrated environment. In this paper, we briefly report on these tools and their major features and capabilities, along with examples of how they can facilitate molecular research in computational biophysics that might be otherwise prohibitively complex.
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Affiliation(s)
- Mariano Spivak
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - John E Stone
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - João Ribeiro
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jan Saam
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Rafael C Bernardi
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, Center for Biophyics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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10
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Mohajerani F, Tyukodi B, Schlicksup CJ, Hadden-Perilla JA, Zlotnick A, Hagan MF. Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism. ACS NANO 2022; 16:13845-13859. [PMID: 36054910 PMCID: PMC10273259 DOI: 10.1021/acsnano.2c02119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hepatitis B virus (HBV) is an endemic, chronic virus that leads to 800000 deaths per year. Central to the HBV lifecycle, the viral core has a protein capsid assembled from many copies of a single protein. The capsid protein adopts different (quasi-equivalent) conformations to form icosahedral capsids containing 180 or 240 proteins: T = 3 or T = 4, respectively, in Caspar-Klug nomenclature. HBV capsid assembly has become an important target for recently developed antivirals; nonetheless, the assembly pathways and mechanisms that control HBV dimorphism remain unclear. We describe computer simulations of the HBV assembly, using a coarse-grained model that has parameters learned from all-atom molecular dynamics simulations of a complete HBV capsid and yet is computationally tractable. Dynamical simulations with the resulting model reproduce experimental observations of HBV assembly pathways and products. By constructing Markov state models and employing transition path theory, we identify pathways leading to T = 3, T = 4, and other experimentally observed capsid morphologies. The analysis shows that capsid polymorphism is promoted by the low HBV capsid bending modulus, where the key factors controlling polymorphism are the conformational energy landscape and protein-protein binding affinities.
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Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts02453, United States
| | - Botond Tyukodi
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts02453, United States
- Department of Physics, Babeş-Bolyai University, 400084Cluj-Napoca, Romania
| | - Christopher J Schlicksup
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana47405, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware19716, United States
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana47405, United States
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts02453, United States
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11
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Xi J, Cui X, Liu K, Liu H, Wang J, Hu J. Region-Specific Hepatitis B Virus Genome Exposure from Nucleocapsid Modulated by Capsid Linker Sequence and Inhibitor: Implications for Uncoating. J Virol 2022; 96:e0039922. [PMID: 35389266 PMCID: PMC9044944 DOI: 10.1128/jvi.00399-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/20/2022] Open
Abstract
Hepatitis B virus (HBV) contains a partially double-stranded, relaxed circular (RC) DNA genome synthesized within a nucleocapsid (NC) in the host cell cytoplasm. The release of RC DNA from the NC, in an ill-defined process called uncoating, to the nucleus is required for its conversion to the covalently closed circular (CCC) DNA, the viral episome serving as the transcriptional template for all viral RNAs necessary for replication and, thus, essential for establishing and sustaining viral infection. In efforts to better understand uncoating, we analyzed HBV core (HBc) mutants that show various levels of nuclear CCC DNA but little to no cytoplasmic RC DNA. We found that RC DNA could be synthesized by these mutants outside the cell, but in contrast to the wild type (wt), the mutant NCs were unable to protect RC DNA from digestion by the endogenous nuclease(s) in cellular lysates or exogenous DNase. Subcellular fractionation suggested that the major RC DNA-degrading activity was membrane associated. Digestion with sequence-specific and nonspecific DNases revealed the exposure of specific regions of RC DNA from the mutant NC. Similarly, treatment of wt NCs with a core inhibitor known to increase CCC DNA by affecting uncoating also led to region-specific exposure of RC DNA. Furthermore, a subpopulation of untreated wild type (wt) mature NCs showed site-specific exposure of RC DNA as well. Competition between RC DNA degradation and its conversion to CCC DNA during NC uncoating thus likely plays an important role in the establishment and persistence of HBV infection and has implications for the development of capsid-targeted antivirals. IMPORTANCE Disassembly of the hepatitis B virus (HBV) nucleocapsid (NC) to release its genomic DNA, in an ill-understood process called uncoating, is required to form the viral nuclear episome in the host cell nucleus, a viral DNA essential for establishing and sustaining HBV infection. The elimination of the HBV nuclear episome remains the holy grail for the development of an HBV cure. We report here that the HBV genomic DNA is exposed in a region-specific manner during uncoating, which is enhanced by mutations of the capsid protein and a capsid-targeted antiviral compound. The exposure of the viral genome can result in its rapid degradation or, alternatively, can enhance the formation of the nuclear episome, thus having a major impact on HBV infection and persistence. These results are thus important for understanding fundamental mechanisms of HBV replication and persistence and for the ongoing pursuit of an HBV cure.
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Affiliation(s)
- Ji Xi
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Xiuji Cui
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Kuancheng Liu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Haitao Liu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Joseph Wang
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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12
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Pavlova A, Bassit L, Cox BD, Korablyov M, Chipot C, Patel D, Lynch DL, Amblard F, Schinazi RF, Gumbart JC. The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates. J Med Chem 2022; 65:4854-4864. [PMID: 35290049 PMCID: PMC9026740 DOI: 10.1021/acs.jmedchem.1c02040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Interfering with the self-assembly of virus nucleocapsids is a promising approach for the development of novel antiviral agents. Applied to hepatitis B virus (HBV), this approach has led to several classes of capsid assembly modulators (CAMs) that target the virus by either accelerating nucleocapsid assembly or misdirecting it into noncapsid-like particles, thereby inhibiting the HBV replication cycle. Here, we have assessed the structures of early nucleocapsid assembly intermediates, bound with and without CAMs, using molecular dynamics simulations. We find that distinct conformations of the intermediates are induced depending on whether the bound CAM accelerates or misdirects assembly. Specifically, the assembly intermediates with bound misdirecting CAMs appear to be flattened relative to those with bound accelerators. Finally, the potency of CAMs within the same class was studied. We find that an increased number of contacts with the capsid protein and favorable binding energies inferred from free energy perturbation calculations are indicative of increased potency.
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Affiliation(s)
- Anna Pavlova
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Bryan D Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Maksym Korablyov
- MIT Media Lab, Massachusetts Institute of Technology, Boston, Massachusetts 02139, United States
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Laboratoire international associé CNRS-UIUC, UMR 7019, Université de Lorraine, B.P. 70239, 54506 Vandæuvre-lès-Nancy, France
| | - Dharmeshkumar Patel
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Diane L Lynch
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - James C Gumbart
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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