Agback, Tatiana
- Department of Molecular Sciences, Swedish University of Agricultural Sciences
- University of Gothenburg
Abstract
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.
Keywords
4D dynamical conformation ensembles; Streptococcus pneumoniae protein; back-calculated NMR parameters; N-15 cross-correlated relaxation; pulse program optimization
Published in
International Journal of Molecular Sciences
2025, volume: 26, number: 18, article number: 8917
Publisher: MDPI
SLU Authors
Agback, Peter
- Department of Molecular Sciences, Swedish University of Agricultural Sciences
- Department of Molecular Sciences, Swedish University of Agricultural Sciences
UKÄ Subject classification
Molecular Biology
Publication identifier
- DOI: https://doi.org/10.3390/ijms26188917
Permanent link to this page (URI)
https://res.slu.se/id/publ/143969