Towards accurate, force field independent conformational ensembles of intrinsically disordered proteins DOI Creative Commons

Kaushik Borthakur,

Thomas R. Sisk, Francesco Paolo Panei

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 5, 2024

Abstract Determining accurate atomic resolution conformational ensembles of intrinsically disordered proteins (IDPs) is extremely challenging. Molecular dynamics (MD) simulations provide atomistic IDPs, but their accuracy highly dependent on the quality physical models, or force fields, used. Here, we demonstrate how to determine IDPs by integrating all-atom MD with experimental data from nuclear magnetic resonance (NMR) spectroscopy and small-angle x-ray scattering (SAXS) a simple, robust fully automated maximum entropy reweighting procedure. We that when this approach applied sufficient data, IDP derived different fields converge similar distributions. The procedure presented here facilitates integration extensive datasets enables calculation accurate, force-field independent IDPs.

Language: Английский

Simulation-based inference of single-molecule experiments DOI Creative Commons
Lars Dingeldein, Pilar Cossio, Roberto Covino

et al.

Current Opinion in Structural Biology, Journal Year: 2025, Volume and Issue: 91, P. 102988 - 102988

Published: Feb. 7, 2025

Language: Английский

Citations

0
Towards accurate, force field independent conformational ensembles of intrinsically disordered proteins DOI Creative Commons

Kaushik Borthakur,

Thomas R. Sisk, Francesco Paolo Panei

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 5, 2024

Abstract Determining accurate atomic resolution conformational ensembles of intrinsically disordered proteins (IDPs) is extremely challenging. Molecular dynamics (MD) simulations provide atomistic IDPs, but their accuracy highly dependent on the quality physical models, or force fields, used. Here, we demonstrate how to determine IDPs by integrating all-atom MD with experimental data from nuclear magnetic resonance (NMR) spectroscopy and small-angle x-ray scattering (SAXS) a simple, robust fully automated maximum entropy reweighting procedure. We that when this approach applied sufficient data, IDP derived different fields converge similar distributions. The procedure presented here facilitates integration extensive datasets enables calculation accurate, force-field independent IDPs.

Language: Английский

Citations

0