Gregory A. Voth
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View article: Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example
Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example Open
Cryoelectron microscopy (cryo-EM) structures of multiprotein complexes such as actin filaments help explain the mechanisms of assembly and interactions with partner proteins. Yet, rapid cooling during freezing may not preserve the conforma…
View article: Mechanism of Phosphatidylserine Lipid Scrambling by Human SERINC3, an HIV-1 Restriction Factor
Mechanism of Phosphatidylserine Lipid Scrambling by Human SERINC3, an HIV-1 Restriction Factor Open
The HIV-1 restriction factor, hSERINC3, functions as a lipid scramblase, translocating lipids across the bilayer in reconstituted proteoliposomes and the viral envelope. Phosphatidylserine(PS) scrambling and exposure at the outer leaflet a…
View article: Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins
Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins Open
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates viral entry by binding its receptor-binding domain (RBD) to the host receptor ACE2. Spike mutations in different variants have been experimentally s…
View article: On the Mechanism of Ezrin Activation
On the Mechanism of Ezrin Activation Open
Ezrin is a peripheral membrane protein that contributes to the organization and stability of cellular membrane structures by reversibly linking the plasma membrane to actin filaments. The formation of this membrane-actin linkage has been e…
View article: Membrane Remodeling by the Collective Action of Caveolin-1
Membrane Remodeling by the Collective Action of Caveolin-1 Open
Caveolin-1 proteins scaffold 50-100nm large invaginations in the plasma membrane to mediate critical cellular processes. As revealed recently by cryo-electron microscopy, several caveolin-1 protomers can fold into a disk-like structure tha…
View article: Adaptations in <i>Plasmodium</i> tubulin determine unique microtubule architectures, mechanics and drug susceptibility
Adaptations in <i>Plasmodium</i> tubulin determine unique microtubule architectures, mechanics and drug susceptibility Open
Microtubules are ubiquitous yet diverse cytoskeleton filaments. However, tubulin conservation presents challenges in understanding the origins of diverse microtubule architectures. The mechanisms by which microtubule architecture varies th…
View article: Structural Heterogeneity of the Membrane-Interacting Region of the HIV-1 Envelope Glycoprotein
Structural Heterogeneity of the Membrane-Interacting Region of the HIV-1 Envelope Glycoprotein Open
The HIV-1 envelope glycoprotein (Env) trimer (gp120/gp41) 3 forms the key functional envelope spike and is the target of neutralizing antibodies. The glycoprotein gp41 component mediates the fusion of viral and host cell membranes. In addi…
View article: Systematic Bottom-Up Coarse-Graining of Hydrated Excess Proton Transport Across Scales
Systematic Bottom-Up Coarse-Graining of Hydrated Excess Proton Transport Across Scales Open
Proton transport is a multiscale phenomenon critical to chemistry, physics, biology, and materials science, yet development of a high-fidelity multiscale model bridging quantum to mesoscale dynamics remains a major challenge due to reactiv…
View article: Mechanism for oil-phase separation by the lipid droplet assembly complex
Mechanism for oil-phase separation by the lipid droplet assembly complex Open
Summary Cells store metabolic energy as triglyceride (TG) oils in lipid droplets (LDs). LDs form de novo from the endoplasmic reticulum. How the lipid droplet assembly complex (LDAC), composed of seipin and LDAF1 1,2 , catalyzes the organi…
View article: Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example
Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example Open
Cryo-electron microscopy (cryo-EM) structures of multi-protein complexes such as actin filaments help explain the mechanisms of assembly and interactions with partner proteins. Yet, rapid cooling during freezing may not preserve the confor…
View article: The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport
The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport Open
The model multi-drug efflux pump from Escherichia coli , EmrE, can perform multiple types of transport leading to different biological outcomes, conferring resistance to some drug substrates and enhancing susceptibility to others. While tr…
View article: The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport
The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport Open
The model multi-drug efflux pump from Escherichia coli, EmrE, can perform multiple types of transport leading to different biological outcomes, conferring resistance to some drug substrates and enhancing susceptibility to others. While tra…
View article: A Non-Canonical Interface of SNX9 PX Domain Selectively Sequesters PI(3,4)P2 Lipids, Protecting Them from Hydrolysis
A Non-Canonical Interface of SNX9 PX Domain Selectively Sequesters PI(3,4)P2 Lipids, Protecting Them from Hydrolysis Open
Plasma membrane remodeling processes are tightly regulated by the spatiotemporal distribution and dynamic conversion of phosphoinositidyl lipids (PIPs). This regulation is controlled by the recruitment of proteins such as sorting nexin 9 (…
View article: On the Curvature and Relaxation of Microtubule Plus-end Tips
On the Curvature and Relaxation of Microtubule Plus-end Tips Open
Microtubules are essential cytoskeletal components with a broad range of functions in which the structure and dynamics of their plus-end tips play critical roles. Existing mechanistic models explain the tips curving dynamics in different w…
View article: Lenacapavir-induced Lattice Hyperstabilization is Central to HIV-1 Capsid Failure at the Nuclear Pore Complex and in the Cytoplasm
Lenacapavir-induced Lattice Hyperstabilization is Central to HIV-1 Capsid Failure at the Nuclear Pore Complex and in the Cytoplasm Open
Lenacapavir (LEN) is the first HIV-1 capsid inhibitor approved for clinical use. It inhibits multiple steps of the viral life cycle; however, the molecular details of the effect of LEN on capsid structure and the mechanistic steps of the i…
View article: A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes
A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes Open
Bottom-up coarse-graining refers to the development of low-resolution simulation models that are thermodynamically consistent with certain distributions from fully atomistic simulations. Force-matching and relative entropy minimization rep…
View article: Kinetic implications of IP <sub>6</sub> anion binding on the molecular switch of HIV-1 capsid assembly
Kinetic implications of IP <sub>6</sub> anion binding on the molecular switch of HIV-1 capsid assembly Open
HIV-1 capsid (CA) proteins self-assemble into a fullerene-shaped CA, enabling cellular transport and nuclear entry of the viral genome. A structural switch comprising the Thr-Val-Gly- Gly (TVGG) motif either assumes a disordered coil or a …
View article: Adversarial Training for Dynamics Matching in Coarse-Grained Models
Adversarial Training for Dynamics Matching in Coarse-Grained Models Open
Molecular dynamics (MD) simulations are essential for studying complex molecular systems, but their high computational cost limits scalability. Coarse-grained (CG) models reduce this cost by simplifying the system, yet traditional approach…
View article: A Non-Canonical Interface of SNX9 PX Domain Selectively Sequesters PI(3,4)P<sub>2</sub>Lipids, Protecting Them from Hydrolysis
A Non-Canonical Interface of SNX9 PX Domain Selectively Sequesters PI(3,4)P<sub>2</sub>Lipids, Protecting Them from Hydrolysis Open
Plasma membrane remodeling processes are tightly regulated by the spatiotemporal distribution and dynamic conversion of phosphoinositidyl lipids (PIPs). This regulation is controlled by the recruitment of proteins such as sorting nexin 9 (…
View article: MSBack: Multiscale Backmapping of Highly Coarse-grained Proteins Using Constrained Diffusion
MSBack: Multiscale Backmapping of Highly Coarse-grained Proteins Using Constrained Diffusion Open
Coarse-grained (CG)molecular dynamics is a powerful tool for simulating the collective behavior of biomolecules. However, the structural information lost during coarse-graining prevents the CG configurations from being more widely useful (…
View article: Coarse-Graining in Quantum Mechanics: Distinguishable and Indistinguishable Particles
Coarse-Graining in Quantum Mechanics: Distinguishable and Indistinguishable Particles Open
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused …
View article: Molecular mechanism of Arp2/3 complex activation by nucleation-promoting factors and an actin monomer
Molecular mechanism of Arp2/3 complex activation by nucleation-promoting factors and an actin monomer Open
Arp (actin-related protein) 2/3 complex nucleates actin filament branches on the sides of preexisting actin filaments during cell and organelle movements. We used computer simulations of mammalian Arp2/3 complex to address fundamental ques…
View article: PLUMED Tutorials: A collaborative, community-driven learning ecosystem
PLUMED Tutorials: A collaborative, community-driven learning ecosystem Open
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users pre…
View article: The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport
The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport Open
The model multi-drug efflux pump from Escherichia coli , EmrE, can perform multiple types of transport leading to different biological outcomes, conferring resistance to some drug substrates and enhancing susceptibility to others. While tr…
View article: The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport
The C-terminus of the multi-drug efflux pump EmrE prevents proton leak by gating transport Open
The model multi-drug efflux pump from Escherichia coli, EmrE, can perform multiple types of transport leading to different biological outcomes, conferring resistance to some drug substrates and enhancing susceptibility to others. While tra…
View article: Entropy-based methods for formulating bottom-up ultra-coarse-grained models
Entropy-based methods for formulating bottom-up ultra-coarse-grained models Open
Bottom-up coarse-grained (CG) modeling is an effective means of bypassing the limited spatiotemporal scales of conventional atomistic molecular dynamics while retaining essential information from the atomistic model. A central challenge in…