H.-X. Zhou

Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions

The paper introduces FMAPS(q), a method to calculate protein solution structure factors using atomistic modeling of protein-protein interactions, showing agreement with experimental scattering data.

Multiple modes of DNA compaction by protamine

This study investigates how protamine compacts DNA through multiple modes, forming bends, loops, and coils that contribute to transcription silencing in sperm cells.

ATP Mediates Phase Separation of Disordered Basic Proteins by Bridging Intermolecular Interaction Networks

This study shows ATP mediates phase separation of basic intrinsically disordered proteins by acting as bridges between protein chains, forming liquid-like droplets with unique physical properties.

A Common Pathway for Detergent-Assisted Oligomerization of Aβ42

This study identifies a common oligomerization pathway for Aβ42 stabilized by SDS and DPC micelles, revealing structural and stabilizing mechanisms.

Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein

The paper determines the dimeric structure of the SARS-CoV-2 E protein using NMR and simulations, identifying a hydrophobic pore and potential drug-binding site.

Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence

The paper uses atomistic modeling to show that a single amino-acid substitution in γ-crystallin affects liquid-liquid phase equilibrium and critical temperature.

Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch

This study shows Mg2+ ions stabilize the SAM/SAH riboswitch structure and influence ligand binding and conformational changes through inner and outer-shell coordination.

Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

This paper introduces SeqDYN, a sequence-based method to predict residue-specific backbone dynamics of IDPs, identifying key amino acids involved in slow dynamics.

Structural Model for Self-Limiting β-strand Arrangement Within an Alzheimer's Amyloid-β Oligomer

The paper presents a structural model of an Alzheimer's Aβ42 oligomer based on solid-state NMR and cryo-EM data, explaining its stability and ion permeability.

Why Does Synergistic Activation of WASP, but Not N-WASP, by Cdc42 and PIP2 Require Cdc42 Prenylation?

The paper uses molecular dynamics simulations to show that Cdc42 prenylation is required for synergistic activation of WASP with PIP2, but not N-WASP.

Partial Mimicry of the Microtubule Binding of Tau by Its Membrane Binding

The paper uses molecular dynamics simulations to show that tau's membrane binding partially mimics its microtubule binding, with conserved residues forming similar interactions.

Membrane Tethering of SepF, a Membrane Anchor for the Mycobacterium tuberculosis Z-ring

This study identifies how SepF, a membrane anchor in Mtb, tethers to acidic membranes through specific residues, stabilizing Z-ring proximity for recruitment of FtsW and CrgA.

An Arg/Ala-Rich Helix in the N-Terminal Region of M. tuberculosis FtsQ Anchors FtsZ to Membranes

This paper identifies an Arg/Ala-rich helix in M. tuberculosis FtsQ that anchors FtsZ to membranes, influencing Z-ring formation and curvature.

SpiDec: Computing Binodals and Interfacial Tension of Biomolecular Condensates From Simulations of Spinodal Decomposition

SpiDec computes binodals and interfacial tension of biomolecular condensates from spinodal decomposition simulations of intrinsically disordered proteins.

Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

This study investigates how sequence-dependent backbone dynamics in intrinsically disordered proteins (IDPs) influence their functional versatility through molecular dynamics simulations.

Artificial Intelligence Guided Conformational Mining of Intrinsically Disordered Proteins

This paper uses generative autoencoders to predict conformational ensembles of intrinsically disordered proteins from short molecular dynamics simulations.

Multiphase Organization Is a Second Phase Transition Within Multi-Component Biomolecular Condensates

The paper develops a mean-field theory and validates it with simulations to show that multiphase organization in biomolecular condensates arises from two phase transitions driven by differences in self and cross-species attraction strengths.

Preferential interactions of a crowder protein with the specific binding site of a native protein complex

This paper investigates how crowder proteins affect the binding affinity and kinetics of the EIN-HPr protein complex using NMR and atomistic modeling, revealing preferential interactions that destabilize the complex.

Binding Free energy Decomposition and Multiple Unbinding Paths of Buried Ligands in a PreQ1 Riboswitch

This study uses molecular dynamics simulations to analyze binding free energy and unbinding paths of ligands in a PreQ1 riboswitch, identifying key nucleotide contributions and structural changes.

A Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening

The paper develops a machine learning pipeline for virtual drug screening that reduces compound libraries and classifies hits as true or false positives using a dense neural network.

Removing Thermostat Distortions of Protein Dynamics in Constant-Temperature Molecular Dynamics Simulations

This paper shows that Langevin thermostats distort protein dynamics in simulations and presents a correction scheme to remove these distortions, validated by NMR data.

Shear Relaxation Governs Dynamic Processes of Biomolecular Condensates

The paper measures the mechanical properties of biomolecular condensates and shows that shear stress relaxation, not viscocapillary effects, governs their fusion dynamics.

Macromolecular Regulators Have Matching Effects on the Phase Equilibrium and Interfacial Tension of Biomolecular Condensates

This study uses molecular dynamics simulations to show that regulators of phase-separated biomolecular condensates affect interfacial tension and phase equilibrium in matching ways.

Shape Recovery of Deformed Biomolecular Droplets: Dependence on Condensate Viscoelasticity

This study presents an analytical solution for the shape recovery dynamics of viscoelastic biomolecular droplets, showing multi-exponential behavior compared to the exponential behavior of viscous droplets.

Viscoelasticity of biomolecular condensates conforms to the Jeffreys model

The paper shows that the viscoelasticity of biomolecular condensates follows the Jeffreys model, with distinct exponential and viscous components affected by salt concentration.

Extreme Fuzzy Association of an Intrinsically Disordered Protein with Acidic Membranes

The paper characterizes the extreme fuzzy membrane association of the disordered N-terminal region of ChiZ using NMR and simulations, revealing sequence-interaction dynamics.

Fusion Speed of Biomolecular Condensates

The paper measures fusion speeds of biomolecular condensates and finds they vary by two orders of magnitude, correlating with macromolecular packing density and structure.

A Tug of War Between Condensate Phases in a Minimal Macromolecular System

The paper demonstrates phase behaviors in a minimal macromolecular system involving oppositely charged proteins and polyelectrolytes, revealing physical rules underlying membraneless organelles.

Sequence-dependent correlated segments in the intrinsically disordered region of ChiZ

The paper characterizes the conformational dynamics of an intrinsically disordered protein using NMR, SAXS, and MD simulations, identifying sequence-dependent correlated segments.

Membrane Association and Functional Mechanism of Synaptotagmin-1 in Triggering Vesicle Fusion

This study uses molecular dynamics simulations to show how Ca2+-bound synaptotagmin-1 facilitates vesicle fusion by interacting with both vesicle and plasma membranes through its C2 domains.