G. A. Voth

Divergent spike mutations impact the activation of the fusion core in Delta and Omicronvariants of SARS-CoV-2

This study uses molecular dynamics simulations to show how spike mutations in Delta and Omicron variants affect the structural flexibility and activation of the fusion core in the SARS-CoV-2 spike/ACE2 complex.

Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation

This study uses molecular dynamics simulations to analyze how HIV-1 matrix protein interactions with lipids change during viral maturation, identifying altered binding modes of PIP2 lipids.

Cooperative Membrane Binding of HIV-1 Matrix Proteins

This study investigates the membrane binding dynamics of HIV-1 MA protein trimers and their interactions with anionic phospholipids using molecular dynamics simulations.

The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes

This study identifies the SARS-CoV-2 nucleoprotein's ability to bind anionic lipids, supporting a model for its role in viral membrane association during assembly.

Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding

This study uses molecular dynamics simulations to investigate how HIV-1 Gag polyprotein conformation changes during multimerization and gRNA binding, revealing structural transitions and their functional implications.

HIV-1 Capsid Shape, Orientation, and Entropic Elasticity Regulate Translocationinto the Nuclear Pore Complex

This study uses simulations to show that HIV-1 capsid shape, orientation, and elasticity are critical for translocation through the nuclear pore complex.

Mechanism of Phosphate Release from Actin Filaments

The paper uses molecular dynamics simulations to study phosphate release from actin filaments, identifying Mg2+ dissociation as the rate-limiting step and revealing the role of R177 in gate opening and occlusion.

Cracked actin filaments as mechanosensitive receptors

This paper uses molecular dynamics simulations to show that mechanical strain on actin filaments creates a metastable cracked conformation, which serves as a binding site for LIM domain proteins.

Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules

This paper uses computational simulations to determine that a compacted microtubule lattice is necessary for GTP hydrolysis, with E254 as the catalytic residue, while an expanded lattice hinders hydrolysis.

The structure, catalytic mechanism, and inhibitor identification of phosphatidylinositol remodeling MBOAT7

This study determines the structure of MBOAT7, models its catalytic mechanism, and identifies potential inhibitors for therapeutic development.

Organization of Upstream ESCRT Machinery at the HIV-1 Budding Site

This study uses molecular dynamics simulations to investigate how ESCRT-I and ESCRT-II proteins interact with HIV-1 Gag lattice at the budding site, revealing their role in modulating membrane curvature and enabling scission.

Structure of SARS-CoV-2 M protein in lipid nanodiscs

The paper presents the cryo-EM structure of SARS-CoV-2 M protein in lipid nanodiscs, revealing its homodimer structure and potential role in viral assembly.

Critical Mechanistic Features of HIV-1 Viral Capsid Assembly

This study uses simulations to show IP6 promotes conical HIV-1 capsid formation by stabilizing curvature and shifting assembly kinetics.

Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly towards kinetically-trapped morphologies

This study uses simulations to show IP6 accelerates HIV-1 Gag assembly, promoting curvature and defects that may aid viral morphogenesis.

Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins

The paper designs proton-conducting channels that use transient water wires to achieve high selectivity for protons over sodium ions.

Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions

The paper investigates how IRSp53 clustering regulates filopodia initiation by recruiting VASP to form actin-based membrane protrusions.

Ion Permeation, Selectivity, and Electronic Polarization in Fluoride Channels

The paper uses computational methods to study fluoride permeation through fluoride channels, finding that electronic polarization plays a key role in F- selectivity and transport.

Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane

This study investigates how seipin's transmembrane segments contribute to triglyceride nucleation and lipid droplet budding using simulations and cell experiments.

Key Factors Governing Initial Stages of Lipid Droplet Formation

This study uses a coarse-grained model to investigate the biophysics of lipid droplet formation, showing that membrane rigidity and asymmetric tension influence TG nucleation and budding direction.

Strain and rupture of HIV-1 capsids during uncoating

This study uses molecular dynamics simulations and cryo-ET to show HIV-1 capsids exhibit strain patterns and rupture via crack propagation along high-strain regions.

Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter

This study uses multiscale modeling to show how proton flux drives the conformational changes and ligand transport in proton-coupled peptide transporters.

Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior

This study uses multiscale simulations to analyze how the D44N mutation in the influenza A M2 channel alters proton transport behavior compared to the wild-type.

A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces

This paper introduces a new collective variable based on graph theory to quantify water wire connectivity and proton translocation in confined spaces, revealing that water connectivity, not just presence, is critical for proton transport.

Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central tomaturation inhibition

This study uses molecular dynamics simulations to show that bevirimat's effectiveness against HIV-1 depends on preserving the six-helix bundle symmetry, with escape mutations causing symmetry loss.

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

This study uses coarse-grained models and cryo-ET data to show that SARS-CoV-2 spike trimers cooperatively bind to ACE2 dimers, promoting S1 dissociation and exposing the fusion machinery.

Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2

This study uses molecular dynamics to analyze lipid-protein and protein-protein interactions of SARS-CoV-2's M and E proteins to understand their roles in viral assembly and infectivity.

Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis

This study characterizes triolein's behavior in bilayer membranes and proposes a model for its role in lipid droplet biogenesis through membrane curvature induction.

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

This paper develops a multiscale coarse-grained model of the SARS-CoV-2 virion using structural data and all-atom simulations to enable large-scale viral process simulations.

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

This paper investigates the structure and dynamics of immature HIV-1 Gag lattice edges, revealing partial hexamers and their role in proteolytic maturation.

Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover

This paper evaluates the MARTINI coarse-grained model's adherence to statistical mechanics by comparing it with all-atom simulations, identifying issues in temperature transferability and enthalpy-entropy decomposition.