4.8 Article

Multiscale Modeling of Hepatitis B Virus Capsid Assembly and Its Dimorphism

Related references

Note: Only part of the references are listed.
Article Physics, Condensed Matter

Tiling a tubule: how increasing complexity improves the yield of self-limited assembly

Thomas E. Videbaek et al.

Summary: The ability to design and synthesize complicated colloidal particles allows for the self-assembly of complex structures, but thermal fluctuations can lead to off-target assembly. This study investigates strategies to limit off-target assembly by using multiple types of subunits, and shows how the assembly specificity can be improved by introducing tiling rules for assembling tubules from multiple species of triangles.

JOURNAL OF PHYSICS-CONDENSED MATTER (2022)

Article Chemistry, Multidisciplinary

Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries

Botond Tyukodi et al.

Summary: This study investigates the assembly thermodynamics of a particle-based model for geometrically frustrated assembly using computational modeling. The results show the occurrence of finite-temperature self-limiting assembly within a certain range of parameters and identify mechanisms that promote unbounded growth.

ACS NANO (2022)

Article Biochemistry & Molecular Biology

Hysteresis in Hepatitis B Virus (HBV) Requires Assembly of Near-Perfect Capsids

Caleb A. Starr et al.

Summary: By studying the dissociation of HBV capsids in vitro, it was found that the dissociation of capsid proteins has a hysteresis effect. Labile capsid dissociation corresponds to a similar pseudocritical concentration of assembly, while the dissociation of stable capsids corresponds to a subfemtomolar pseudocritical concentration, showing hysteresis. The proportion of stable capsids increases with the integrity of the Cp preparation and the ionic strength. These results suggest that hysteresis arises from the ideal capsid lattice structure.

BIOCHEMISTRY (2022)

Article Materials Science, Multidisciplinary

Programmable polymorphism of a virus-like particle

Artur P. Biela et al.

Summary: Virus-like particles (VLPs) have potential for drug delivery systems and vaccine development, but controlling their size and morphology is challenging. In this study, amino acid sequences were inserted into MS2 bacteriophage VLPs to control their size and shape. The resulting VLP size and geometry can be controlled by altering the length and type of the insert.

COMMUNICATIONS MATERIALS (2022)

Article Multidisciplinary Sciences

Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation

Aaron Tan et al.

Summary: This study elucidates the crucial role of HIV-1 Gag in viral assembly and the structural features of partial CA hexamers at lattice edges. Molecular dynamics simulations and free energy calculations reveal that partial hexamers are more prone to helix-to-coil transitions compared to complete six-helix bundles.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Chemistry, Multidisciplinary

Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control

Farzaneh Mohajerani et al.

Summary: This article discusses the assembly process of protein shells around a complex, inspired by bacterial microcompartments. It predicts the relationships between shell size, amount of encapsulated cargo, and assembly pathways through interactions between scaffold proteins and cargo. The results have implications for synthetic biology efforts and shed light on how cells utilize self-assembly and liquid-liquid phase separation to organize their interiors.

ACS NANO (2021)

Article Biophysics

A multiscale coarse-grained model of the SARS-CoV-2 virion

Alvin Yu et al.

Summary: This article presents the current status and ongoing development of a largely bottom-up coarse-grained (CG) model of the SARS-CoV-2 virion. The CG model was constructed using data from cryo-electron microscopy, x-ray crystallography, and computational predictions to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into the complete virion model. The CG model allows for capturing viral behavior that is difficult to observe in atomistic simulations and can be iteratively improved with new data.

BIOPHYSICAL JOURNAL (2021)

Article Multidisciplinary Sciences

Virus self-assembly proceeds through contact-rich energy minima

Pedro Buzon et al.

Summary: The assembly pathway and energy balance of hepatitis B virus (HBV) were revealed using fluorescence optical tweezers and high-speed atomic force microscopy. A specific, contact-rich pentameric arrangement of HBV capsid proteins was identified as a key intermediate in the assembly process, which is driven by a free energy change per condensed nucleotide. These findings have important implications for understanding the assembly of HBV and other viruses, as well as for developing new antiviral strategies and designing self-assembling nanomaterials.

SCIENCE ADVANCES (2021)

Article Virology

All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

Carolina Perez-Segura et al.

Summary: The research reveals a new alternative state that can lead to a significant opening of the intradimer interface, as well as the discovery of a new salt bridge that mediates direct communication between the spike tip and fulcrum.

VIRUSES-BASEL (2021)

Article Materials Science, Multidisciplinary

HBV Core-Directed Antivirals and Importin β Can Synergistically Disrupt Capsids

Christine Kim et al.

MICROSCOPY AND MICROANALYSIS (2021)

Article Chemistry, Physical

Programmable icosahedral shell system for virus trapping

Christian Sigl et al.

Summary: This study introduces a programmable icosahedral canvas for the self-assembly of icosahedral shells with viral trapping and antiviral properties. It demonstrates the potential of a new broad-spectrum antiviral platform that could alleviate many threats to global public health.

NATURE MATERIALS (2021)

Article Multidisciplinary Sciences

Molecular mechanism of capsid disassembly in hepatitis B virus

Zhaleh Ghaemi et al.

Summary: The disassembly process of HBV capsid involves structurally heterogeneous cracks mainly within hexameric sites, with only a small subset of capsid protein monomers engaged in each instance of disassembly. Specific residues at interfaces between dimers within hexamers, such as R127, I139, Y132, N136, A137, and V149, are identified as hot spots for disassembly by avoiding overstabilization of capsids, and are evolutionarily conserved.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Chemistry, Multidisciplinary

How a Virus Circumvents Energy Barriers to Form Symmetric Shells

Sanaz Panahandeh et al.

ACS NANO (2020)

Review Physics, Multidisciplinary

On virus growth and form

Roya Zandi et al.

PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2020)

Article Chemistry, Multidisciplinary

Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism

Jacob D. Durrant et al.

ACS CENTRAL SCIENCE (2020)

Article Multidisciplinary Sciences

TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid

Alvin Yu et al.

NATURE COMMUNICATIONS (2020)

Article Chemistry, Multidisciplinary

Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly

Roi Asor et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Biochemical Research Methods

Expression of quasi-equivalence and capsid dimorphism in the Hepadnaviridae

Weimin Wu et al.

PLoS Computational Biology (2020)

Article Chemistry, Analytical

Higher Resolution Charge Detection Mass Spectrometry

Aaron R. Todd et al.

ANALYTICAL CHEMISTRY (2020)

Review Pharmacology & Pharmacy

Targeting the multifunctional HBV core protein as a potential cure for chronic hepatitis B

Usha Viswanathan et al.

ANTIVIRAL RESEARCH (2020)

Review Virology

Structural and dynamic asymmetry in icosahedrally symmetric virus capsids

Asis K. Jana et al.

CURRENT OPINION IN VIROLOGY (2020)

Article Chemistry, Physical

Nonsymmetrical Dynamics of the HBV Capsid Assembly and Disassembly Evidenced by Their Transient Species

Maelenn Chevreuil et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Chemistry, Multidisciplinary

Molecular latent space simulators

Hythem Sidky et al.

CHEMICAL SCIENCE (2020)

Article Chemistry, Multidisciplinary

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

Jiang Wang et al.

ACS CENTRAL SCIENCE (2019)

Article Chemistry, Physical

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

Aleksander E. P. Durumeric et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

Article Physics, Multidisciplinary

Ground States of Crystalline Caps: Generalized Jellium on Curved Space

Siyu Li et al.

PHYSICAL REVIEW LETTERS (2019)

Review Chemistry, Analytical

Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids

Panagiotis Kondylis et al.

ANALYTICAL CHEMISTRY (2019)

Article Chemistry, Multidisciplinary

Competition between Normative and Drug-Induced Virus Self-Assembly Observed with Single-Particle Methods

Panagiotis Kondylis et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Chemistry, Medicinal

Evolution of Intermediates during Capsid Assembly of Hepatitis B Virus with Phenylpropenamide-Based Antivirals

Panagiotis Kondylis et al.

ACS INFECTIOUS DISEASES (2019)

Article Chemistry, Physical

DeePCG: Constructing coarse-grained models via deep neural networks

Linfeng Zhang et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Physics, Condensed Matter

Self consistent field theory of virus assembly

Siyu Li et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2018)

Article Chemistry, Multidisciplinary

Multiple Pathways in Capsid Assembly

Corinne A. Lutomski et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Multidisciplinary Sciences

Robust nonequilibrium pathways to microcompartment assembly

Grant M. Rotskoff et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Virology

A modelling paradigm for RNA virus assembly

Reidun Twarock et al.

CURRENT OPINION IN VIROLOGY (2018)

Article Biochemical Research Methods

The role of the encapsulated cargo in microcompartment assembly

Farzaneh Mohajerani et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Multidisciplinary Sciences

Why large icosahedral viruses need scaffolding proteins

Siyu Li et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Chemistry, Multidisciplinary

Hepatitis B Virus Capsid Completion Occurs through Error Correction

Corinne A. Lutomski et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Multidisciplinary Sciences

Allosteric conformational changes of human HBV core protein transform its assembly

Chuang Liu et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

Charge Detection Mass Spectrometry Identifies Preferred Non-Icosahedral Polymorphs in the Self-Assembly of Woodchuck Hepatitis Virus Capsids

Elizabeth E. Pierson et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Chemistry, Physical

Allosteric Control of Icosahedral Capsid Assembly

Guillermo R. Lazaro et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2016)

Article Chemistry, Physical

All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

Juan R. Perilla et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016)

Article Multidisciplinary Sciences

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

John M. A. Grime et al.

NATURE COMMUNICATIONS (2016)

Article Virology

Recent advances in coarse-grained modeling of virus assembly

Michael F. Hagan et al.

CURRENT OPINION IN VIROLOGY (2016)

Article Biology

Many-molecule encapsulation by an icosahedral shell

Jason D. Perlmutter et al.

ELIFE (2016)

Review Chemistry, Physical

Mechanisms of Virus Assembly

Jason D. Perlmutter et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 66 (2015)

Article Biophysics

The Robust Assembly of Small Symmetric Nanoshells

Jef Wagner et al.

BIOPHYSICAL JOURNAL (2015)

Article Biochemistry & Molecular Biology

Fluid lipid membranes: From differential geometry to curvature stresses

Markus Deserno

CHEMISTRY AND PHYSICS OF LIPIDS (2015)

Article Chemistry, Medicinal

Monte Carlo Simulations of HIV Capsid Protein Homodimer

Fangqiang Zhu et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)

Article Physics, Condensed Matter

Adsorption of annealed branched polymers on curved surfaces

Jef Wagner et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2015)

Article Multidisciplinary Sciences

High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein

Klaus Klumpp et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Chemistry, Analytical

Single-Particle Electrophoresis in Nanochannels

Zachary D. Harms et al.

ANALYTICAL CHEMISTRY (2015)

Article Chemistry, Physical

Using Markov state models to study self-assembly

Matthew R. Perkett et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Multidisciplinary

Detection of Late Intermediates in Virus Capsid Assembly by Charge Detection Mass Spectrometry

Elizabeth E. Pierson et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Article Biochemical Research Methods

Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations

Daniel L. Parton et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Chemistry, Multidisciplinary

Characterization of Hepatitis B Virus Capsids by Resistive-Pulse Sensing

Kaimeng Zhou et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Chemistry, Multidisciplinary

Interrogating viral capsid assembly with ion mobility-mass spectrometry

Charlotte Uetrecht et al.

NATURE CHEMISTRY (2011)

Article Chemistry, Physical

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

Jan-Hendrik Prinz et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

Review Biochemistry & Molecular Biology

Virus assembly, allostery and antivirals

Adam Zlotnick et al.

TRENDS IN MICROBIOLOGY (2011)

Article Biochemistry & Molecular Biology

Trapping of Hepatitis B Virus Capsid Assembly Intermediates by Phenylpropenamide Assembly Accelerators

Sarah P. Katen et al.

ACS CHEMICAL BIOLOGY (2010)

Article Chemistry, Multidisciplinary

Emergent Complexity from Simple Anisotropic Building Blocks: Shells, Tubes, and Spirals

Szilard N. Fejer et al.

ACS NANO (2010)

Article Materials Science, Multidisciplinary

Visualization and analysis of atomistic simulation data with OVITO-the Open Visualization Tool

Alexander Stukowski

MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING (2010)

Review Physics, Multidisciplinary

Physical virology

W. H. Roos et al.

NATURE PHYSICS (2010)

Article Biochemistry & Molecular Biology

A Mutant Hepatitis B Virus Core Protein Mimics Inhibitors of Icosahedral Capsid Self-Assembly

Christina R. Bourne et al.

BIOCHEMISTRY (2009)

Article Chemistry, Multidisciplinary

Invariant Polymorphism in Virus Capsid Assembly

Hung D. Nguyen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Article Chemistry, Multidisciplinary

Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

Oren M. Elrad et al.

NANO LETTERS (2008)

Article Materials Science, Multidisciplinary

Systematic coarse graining of biomolecular and softw-matter systems

Gary S. Ayton et al.

MRS BULLETIN (2007)

Review Biochemistry & Molecular Biology

Inference of macromolecular assemblies from crystalline state

Evgeny Krissinel et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Stability and dynamics of virus capsids described by coarse-grained modeling

Anton Arkhipov et al.

STRUCTURE (2006)

Article Biochemistry & Molecular Biology

BAY 41-4109 has multiple effects on Hepatitis B virus capsid assembly

Stephen J. Stray et al.

JOURNAL OF MOLECULAR RECOGNITION (2006)

Article Biochemistry & Molecular Biology

Native hepatitis B virions and capsids visualized by electron cryornicroscopy

Kelly A. Dryden et al.

MOLECULAR CELL (2006)

Article Biotechnology & Applied Microbiology

An in vitro fluorescence screen to identify antivirals that disrupt hepatitis B virus capsid assembly

SJ Stray et al.

NATURE BIOTECHNOLOGY (2006)

Review Microbiology

Exploring icosahedral virus structures with viper

P Natarajan et al.

NATURE REVIEWS MICROBIOLOGY (2005)

Article Biochemistry & Molecular Biology

Zinc ions trigger conformational change and oligomerization of hepatitis B virus capsid protein

SJ Stray et al.

BIOCHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Weak protein-protein interactions are sufficient to drive assembly of hepatitis B virus capsids

P Ceres et al.

BIOCHEMISTRY (2002)