D. M. Zuckerman

Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change

The paper develops MMIST, a computational approach linking live-cell morphodynamics to gene expression changes during cell state transitions.

From average transient transporter currents to microscopic mechanism -- A Bayesian analysis

This paper uses Bayesian analysis to evaluate the ability of SSME data to identify kinetic parameters and mechanisms of secondary active transporters.

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software

The paper provides advanced tutorials for WESTPA 2.0, demonstrating new features for rare-events sampling in molecular simulations.

Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

This paper quantifies cooperative multisite binding in the protein LC8 using Bayesian inference, finding positive cooperativity in LC8-client peptide interactions but not in NudE-dynein intermediate chain interactions.

Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM

This paper develops a pipeline to analyze multivalent IDP oligomers using single-particle EM, correcting compositional heterogeneity and revealing new insights into their structure and function.

Type two secretion systems secretins are necessary for exopolymeric slime secretion in cyanobacteria and myxobacteria

The paper identifies secretins PilQ/GspD as essential for exopolymeric slime secretion in cyanobacteria and myxobacteria, expanding the known functions of these outer membrane structures.

Ligand-mediated structural dynamics of a mammalian pancreatic KATP channel

The paper investigates how ligands affect the structural dynamics of pancreatic KATP channels using cryo-EM and molecular dynamics simulations.

WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications

The paper introduces WESTPA 2.0, an upgraded software package for weighted ensemble simulations, enhancing efficiency and analysis of longer-timescale applications.

Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

The paper determines cryoEM structures of vascular KATP channels bound to Mg-nucleotides and reveals a conformational pathway for activation.

What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models

This study evaluates the ability of Markov state models (MSMs) to reproduce path-based observables in protein folding, finding they are reliable only when state lifetimes exceed the lag time, and history-augmented MSMs improve reliability.

Structure and function of a novel osmoregulated periplasmic fiber-forming high-molecular-weight carbohydrate of Myxococcus xanthus

This paper identifies a novel high-molecular-weight fiber-forming polysaccharide in Myxococcus xanthus that functions as an osmoregulated periplasmic glucan, replacing canonical OPGs and stabilizing the cell envelope during spore formation.

Connexin 46 and connexin 50 gap junction channel open stability and unitary conductance are shaped by structural and dynamic features of their N-terminal domains

This study investigates how structural and dynamic features of the N-terminal domains of connexin 46 and 50 influence gap junction channel stability and conductance through molecular dynamics simulations and electrophysiology.

Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 A

This study uses CryoEM to resolve the structure of connexin-46/50 gap junction channels in a lipid environment, revealing how lipid interactions stabilize the channel and influence its function.

Should virus capsids assemble perfectly? Theory and observation of defects

The paper quantifies conditions for viral capsid defects using a statistical mechanics model and confirms ~15% defective particles in cryoEM studies.

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

This paper introduces a computational method to explore alternative mechanisms of molecular machines, finding diverse reaction pathways for cotransport with proofreading capabilities.

HER2 Cancer Protrusion Growth Signaling Regulated by Unhindered, Localized Filopodial Dynamics

This study investigates how HER2 dynamics in filopodia regulate protrusion growth and signaling in breast cancer cells, revealing distinct motion patterns and functional roles in protrusion-based signaling.

Computational estimation of ms-sec atomistic folding times

The paper estimates atomistic protein folding times using weighted ensemble simulations on GPUs, showing reduced computational cost compared to conventional MD simulations.

High-throughput single-particle tracking reveals nested membrane nanodomain organization that dictates Ras diffusion and trafficking

This study uses single-particle tracking to show that KRas diffusion and trafficking are regulated by nested membrane nanodomains in U2OS cells.

Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α

This paper introduces a flexible docking method for protein-ligand interactions using mixed-resolution Monte Carlo, showing improved performance over existing methods for estrogen receptor α.

Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells

The paper demonstrates stochastic simulation for visualizing gene expression and error correction in cells, using case studies and code samples for educational purposes.