Journal Article Review Ppublish
PubMed: 40068541 DOI: 10.1016/j.sbi.2025.103029
Atomistic molecular dynamics simulations of intrinsically disordered proteins.
Curr Opin Struct Biol 92:103029
Authors: Fidha Nazreen Kunnath Muhammedkutty, Matthew MacAinsh, Huan-Xiang Zhou
Affiliations
- Department of Chemistry and Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
- Department of Chemistry and Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA; Department of Physics, University of Illinois Chicago, Chicago, IL, 60607, USA.
Abstract
Recent years have seen remarkable gains in the accuracy of atomistic molecular dynamics (MD) simulations of intrinsically disordered proteins (IDPs) and expansion in the types of calculated properties that can be directly compared with experimental measurements. These advances occurred due to the use of IDP-tested force fields and the porting of MD simulations to GPUs and other computational technologies. All-atom MD simulations are now explaining the sequence-dependent dynamics of IDPs; elucidating the mechanisms of their binding to other proteins, nucleic acids, and membranes; revealing the modes of drug action on them; and characterizing their phase separation. Artificial intelligence (AI) and machine learning (ML) are further expanding the reach of atomistic MD simulations.
MeSH
Molecular Biology, Intrinsically Disordered Proteins, Artificial Intelligence, Molecular Dynamics Simulation