A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.

ABSTRACT: Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecul

SUBMITTER: Blazhynska M 

PROVIDER: S-EPMC11145395 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature