P. C. Biggin

Exploring the Influence of Pore Shape on Conductance and Permeation

This paper introduces an algorithm using ellipsoidal probe particles to better characterize ion channel pore geometry, revealing that non-spherical probes improve conductance predictions compared to spherical ones.

Tackling hysteresis in conformational sampling - how to be forgetful with MEMENTO

This paper introduces MEMENTO, a method to generate conformational transition paths in proteins that reduces hysteresis in molecular dynamics simulations, outperforming traditional targeted MD approaches.

State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane

This study uses molecular dynamics simulations to show that lipid-protein interactions in glycine receptors depend on their functional state, revealing new sites for drug design.

Binding and activation of serotonergic G-protein coupled receptors by the multimodal antidepressant vortioxetine.

This study uses in silico analysis to examine vortioxetine's binding and activation mechanisms at 5-HT1A, 5-HT1B, and 5-HT7 receptors, revealing insights into agonist-antagonist behavior and activation without hydrogen bonding to helix 5.

The KDEL Trafficking Receptor Exploits pH to Tune the Strength of an Unusual Short Hydrogen Bond.

The paper shows that the KDEL receptor uses pH to strengthen a short hydrogen bond, enhancing peptide binding and enabling COPI-mediated retrieval of ER proteins.

A Refined Open State of the Glycine Receptor Obtained Via Molecular Dynamics Simulations

This study refines an open state of the glycine receptor using molecular dynamics simulations to achieve a stable structure and demonstrate chloride permeation.

Proton-control of transitions in an amino-acid transporter

The paper uses molecular dynamics simulations to study proton-coupled amino acid transport in GkApcT, showing that deprotonation of E115 facilitates the transition from inward-occluded to inward-open states.

Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase

This paper investigates how DNA polymerase I recognizes gapped DNA structures through conformational dynamics, revealing a bent DNA structure and using single-molecule FRET and simulations to support the findings.