Details

Autor(en) / Beteiligte

• Zhou, Rui
• Duan, Mojie

Titel

Metadynamics Simulations to Study the Structural Ensembles and Binding Processes of Intrinsically Disordered Proteins

Ist Teil von

• Methods in molecular biology (Clifton, N.J.), 2022, Vol.2405, p.169

Ort / Verlag

United States

Erscheinungsjahr

2022

Quelle

MEDLINE

Beschreibungen/Notizen

• The structures of intrinsically disordered proteins (IDPs) are highly dynamic. It is hard to characterize the structures of these proteins experimentally. Molecular dynamics (MD) simulation is a powerful tool in the understanding of protein dynamic structures and function. This chapter describes the application of metadynamics-based enhanced sampling methods in the study of phosphorylation regulation on the structure of kinase-inducible domains (KID). The structural properties of free pKID and KID were obtained by parallel tempering metadynamics combined with well-tempered ensemble (PTMetaD WTE) method, and the binding free energy surfaces of pKID/KID and KIX were characterized by bias-exchanged metadynamics (BE-MetaD) simulations.