Agback, Tatiana
- Institutionen för molekylära vetenskaper, Sveriges lantbruksuniversitet
- Göteborgs Universitet
Sammanfattning
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.
Nyckelord
4D dynamical conformation ensembles; Streptococcus pneumoniae protein; back-calculated NMR parameters; N-15 cross-correlated relaxation; pulse program optimization
Publicerad i
International Journal of Molecular Sciences
2025, volym: 26, nummer: 18, artikelnummer: 8917
Utgivare: MDPI
SLU författare
Agback, Peter
- Institutionen för molekylära vetenskaper, Sveriges lantbruksuniversitet
- Institutionen för molekylära vetenskaper, Sveriges lantbruksuniversitet
UKÄ forskningsämne
Molekylärbiologi
Publikationens identifierare
- DOI: https://doi.org/10.3390/ijms26188917
Permanent länk till denna sida (URI)
https://res.slu.se/id/publ/143969