R. C. Wade

The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming

This paper uses molecular dynamics simulations to show that heparan sulfate and N-glycans stabilize the SARS-CoV-2 spike:ACE2 complex and promote viral entry by triggering structural changes.

Comprehensive characterization of the neurogenic and neuroprotective action of a novel TrkB agonist using mouse and human stem cell models of Alzheimer's Disease

S100A1ct: a synthetic peptide derived from human S100A1 protein improves cardiac contractile performance and survival in pre-clinical heart failure models

This paper develops a synthetic peptide S100A1ct that improves cardiac function and survival in heart failure models by enhancing Ca2+ cycling and targeting SERCA2a and RyR2.

SUMO interacting motif (SIM) of S100A1 is critical for S100A1 post-translational protein stability

This study identifies a SUMO interacting motif in S100A1 that regulates its post-translational stability through SUMO-mediated interactions.

Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments

The paper introduces parameters for simulating dodecylphosphocholine in Martini 3 to enable protein insertion into micelles and bilayers by adjusting protein-water interactions.

Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance

The paper combines experiments and molecular simulations to identify optimal drug-salt-polymer combinations for improving biopharmaceutical performance of poorly water-soluble drugs.

Diffusion of small molecule drugs is affected by surface interactions and crowder proteins

This study examines how protein crowders affect the diffusion of small molecules, finding varied impacts based on molecular interactions and self-aggregation.

Robustness of trinucleosome compaction to A-tract mediated linker histone orientation

This study investigates whether A-tract mediated linker histone orientation affects trinucleosome compaction and stability, finding no significant differences in compaction or stability between DNA sequences with different A-tract positions.

A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations

The paper develops a multiscale method to compute gated ligand binding using molecular dynamics and Brownian dynamics simulations, applied to HIV-1 protease to quantify conformational gating effects on drug binding kinetics.

G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from {tau}RAMD Simulations

This paper uses {tau}RAMD simulations to study GPCR ligand dissociation rates and mechanisms, showing agreement with conventional MD simulations and revealing effects of allosteric modulation.

A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

The paper identifies a blueprint for high affinity SARS-CoV-2 Mpro inhibitors by analyzing protein dynamics and redefining druggability through virtual screening and pharmacophore modeling.

DNA-sequence dependent positioning of the linker histone in a nucleosome: a single-pair FRET study

This paper uses single-pair FRET to show that the linker histone H1.0b binds on-dyad to A-tract DNA via minor groove recognition, revealing a new mechanism for AT-rich DNA binding.

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

This study investigates the structural and functional interactions between membrane-bound CYP 1A1 and CPR, identifying ET-compatible arrangements and explaining lower ET rates compared to bacterial CYPs.

Halogen-aromatic π-interactions modulate inhibitor residence time

The paper shows that halogen-aromatic π-interactions increase inhibitor residence time in kinase-inhibitor complexes, providing a strategy to improve drug efficacy and selectivity.