A. Polasa

Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1

This study uses molecular dynamics simulations to compare conformational dynamics of inactive and active states of CB1 receptor, identifying key structural differences and electrostatic interactions that influence its function.

Cholesterol Dependence on the Conformational Changes of Metabotropic Glutamate Receptor 1

This study uses molecular dynamics simulations to show that cholesterol modulates conformational changes in mGluR1 dimers, with 10% cholesterol causing the most significant effects.

Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase

This study uses molecular dynamics simulations to investigate the structure and function of YidC in gram-negative bacteria, revealing its role in protein insertion and highlighting domain interactions.

An Investigation of the YidC-Mediated Membrane Insertion of Pf3 Coat Protein Using Molecular Dynamics Simulations

This study uses molecular dynamics simulations to investigate the YidC-mediated insertion of Pf3 coat protein, revealing the role of YidC's hydrophilic groove in protein transport.

Computational Elucidation of Recombinant Fusion Protein Effect on Peptide-Directed Nanoparticles

This study uses molecular dynamics simulations to analyze how peptide sequences and their binding to GFPuv affect nanoparticle properties and free energies.

Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel

This paper uses molecular dynamics simulations to elucidate the atomic-level activation mechanism of an engineered MscL channel triggered by pH changes, identifying key structural changes and interactions involved.

Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics

The paper simulates freely-diffusing single-molecule FRET data with conformational dynamics using Langevin dynamics to test analysis techniques for flexible proteins.

Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2

This study uses molecular dynamics simulations to compare the dynamic behavior of prefusion spike proteins in SARS-CoV-1 and SARS-CoV-2, finding that SARS-CoV-2's spike is more stable with a higher energy barrier for activation.