J. S. Hub

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

The paper quantifies protein hydration shell structure using small-angle scattering data and molecular dynamics simulations, showing force fields vary in their agreement with experimental results.

Viral fusion proteins of class II and III recognize and reorganize complex biological membranes

This study investigates how class II and III viral fusion proteins recognize and reorganize host membranes through lipid binding pockets, revealing distinct mechanisms that enhance membrane disorder and fusion.

Atomistic ensemble of active SHP2 phosphatase

The paper presents an atomistic ensemble of the constitutively active SHP2E76K phosphatase using molecular dynamics simulations and SAXS data.

Converging PMF calculations of antibiotic permeation across an outer membrane porin with sub-kilocalorie per mole accuracy

This paper investigates the convergence of potentials of mean force for antibiotic permeation through an outer membrane porin using advanced umbrella sampling techniques.

Molecular simulations reveal the free energy landscape and transition state of membrane electroporation

The paper uses molecular dynamics simulations to study membrane electroporation, revealing discrepancies in free energy barriers and proposing a modified continuum model.

Equivalence of charge imbalance and external electric fields during free energy calculations of membrane electroporation

The paper compares two methods for modeling transmembrane potentials in membrane electroporation and shows they produce equivalent results under specific electrostatic conditions.

Simulated tempering-enhanced umbrella sampling improves convergence of free energy calculations of drug membrane permeation

This study introduces STeUS, a method combining simulated tempering and umbrella sampling to improve convergence of free energy calculations for drug membrane permeation, showing significant acceleration for bulky molecules.

Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions

This study reveals the atomic-scale conformational transitions of Prp43 during RNA translocation using molecular dynamics simulations.

Revealing allostery in PTPN11 SH2 domains from MD simulations

The paper uses MD simulations and PCA to analyze SH2 domain conformations, revealing differences in dynamics between N-SH2 and C-SH2 domains that suggest distinct functional roles.

Structure and ensemble refinement against SAXS data: combining MD simulations with Bayesian inference or with the maximum entropy principle

This paper describes methods to integrate SAXS data with MD simulations to refine atomic structures and ensembles, using Bayesian inference and maximum entropy principles.

DNA opening during transcription initiation by RNA polymerase II in atomic detail

This study uses molecular dynamics simulations to reveal the atomic details of DNA opening during transcription initiation by RNA polymerase II, showing how protein loops interact with DNA to break hydrogen bonds and stabilize the open bubble.

Free energies of stalk formation in the lipidomics era

The paper computes free energies of stalk formation in membranes with varying lipid compositions to show how lipid diversity affects membrane fusion energetics.

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

This study challenges the 'allosteric switch' model of SHP2 activation by showing that N-SH2 binding cleft opening has minimal impact on activation, while central β-sheet opening is more significant.

An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase

This study identifies an allosteric interaction that controls SHP2 activation by stabilizing the N-SH2 domain, revealing how ligand binding influences its conformation and activity.

A joint reaction coordinate for computing the free energy landscape of pore nucleation and pore expansion in lipid membranes

This study introduces a joint reaction coordinate to compute the free energy landscape of pore nucleation and expansion in lipid membranes, revealing barriers, metastability, and energetic costs.

Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase

This study uses molecular dynamics simulations to analyze the structural determinants of phosphopeptide binding to the N-SH2 domain of SHP2, identifying key residues and interactions that influence binding affinity and specificity.

SAXS Curves of Detergent Micelles: Effects of Asymmetry, Shape Fluctuations, Disorder, and Atomic Details

The paper investigates how atomic details, asymmetry, shape fluctuations, and disorder affect SAXS curves of DDM micelles using simulations and experiments.

Merging in-solution X-ray and neutron scattering data allows fine structural analysis of membrane-protein detergent complexes

The paper combines SAXS and SANS data to analyze unlabeled membrane-protein detergent complexes, providing more detailed structural information than either method alone.