Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation
Year: 2025
Type: article
Abstract: Conformational heterogeneity is critical for protein function, but the validation of dynamic ensembles remains a challenge. In this study, we introduced an approach that integrates free MD simulations, using an AlphaFold-generated structure as the starting point, with experimental relaxation data to identify biologically relevant conformational ensembles. For the extracellular region of Streptococcus pneumoniae Psr Sp , we found that only certain segments of the MD long trajectory aligned well with experimental data. The defined ensembles revealed two regions with increased flexibility that play important functional roles.
DOI: 10.3390/ijms26188917
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,499
Awards: G1025878304, G146323832, G1478185116, G1672484559, G1739236827, G2591221073, Spot-on Biomolecular NMR with Deep Learning, Innovativ experimentell modellering av dynamiska proteiner, G4137403346, Structural and dynamic bases underlying enhanced T cell receptor recognition, G4368121392, G492119165, G4993729156, G5206042285, G5405804748, G6404504321, G6568840017, G6661857097, G6722985812, G6915171404, G7031648273, G712881263, Prediction of IDP Structural Ensembles with NMR-Assisted Artificial Intelligence, G7497989071, Structural and metabolic pathways underlying enhanced CD8 T cell activation in cancer and viral infection, G7961147055, G8137567645, G8251366663, G8318021217
OpenAlex ID: W4414253118