Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation.

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Lesovoy D, Roshchin K, Sala BM, Sandalova T, Achour A, Agback T, Agback P, Orekhov V

Int J Mol Sci 26 (18) - [2025-09-12; online 2025-09-12]

Conformational heterogeneity is essential for protein function, yet validating theoretical molecular dynamics (MD) ensembles remains a significant challenge. In this study, we present an approach that integrates free MD simulations, starting from an AlphaFold-generated structure, with refined experimental NMR-relaxation data to identify biologically relevant holistic time-resolved 4D conformational ensembles. Specifically, we select trajectory segments (RMSD plateaus) consistent with experimental observables. For the extracellular region of Streptococcus pneumoniae PsrSp, we found that only specific segments of the long MD trajectory aligned well with experimental data. The resulting ensembles revealed two regions with increased flexibility, both of which play important functional roles.

PubMed 41009484

DOI 10.3390/ijms26188917

Crossref 10.3390/ijms26188917

pmc: PMC12469643
pii: ijms26188917