Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation
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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.
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Cites
Highly accurate protein structure prediction with AlphaFold
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Scalable emulation of protein equilibrium ensembles with generative deep learning
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“For instance, Lewis et al. [67] demonstrated that ensembles can be constructed by analysing AlphaFold Database entries of homologous proteins with similar sequences, thereby providing alternative conformational landscapes not sampled in a single MD trajectory.”
Scalable emulation of protein equilibrium ensembles with generative deep learning
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- Authors
- Lesovoy, D., Roshchin, K., Sala, B. M., Sandalova, T., Achour, A., Agback, T., Agback, P., & Orekhov, V.
- Affiliations
- Institute of Bioorganic Chemistry (RU)
- Karolinska University Hospital (SE)
- Swedish University of Agricultural Sciences (SE)
- Corresponding author
- Agback, Peter
- Orekhov, Vladislav
- ORCID
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2025-09-12
- Volume
- 26
- Issue
- 18
- Pages
- 8917
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC12469643
- OpenAlex
- W4414253118
- Cited by
- 6
- References
- 9
- Citations by year
- 2026: 4 · 2025: 2
- FWCI
- 1.79
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences)) (acceptedVersion)
- Funders
- Swedish Foundation for Strategic Research (ITM17-0218, 21 1605 Pj 01 H, 10399, RSF 24-13-00413, 2021-05061, 2018-02874, 2023-03485, 2024-06251)
- Swedish Cancer Society (ITM17-0218, 21 1605 Pj 01 H, 10399, RSF 24-13-00413, 2021-05061, 2018-02874, 2023-03485, 2024-06251)
- Cancer och Allergi Fonden (ITM17-0218, 21 1605 Pj 01 H, 10399, RSF 24-13-00413, 2021-05061, 2018-02874, 2023-03485, 2024-06251)
- RSF (ITM17-0218, 21 1605 Pj 01 H, 10399, RSF 24-13-00413, 2021-05061, 2018-02874, 2023-03485, 2024-06251)
- Swedish Research Council (ITM17-0218, 21 1605 Pj 01 H, 10399, RSF 24-13-00413, 2021-05061, 2018-02874, 2023-03485, 2024-06251)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- protein conformational ensembles, conformational heterogeneity, AlphaFold, extracellular proteins, protein flexibility
- MeSH terms
- Amides, Bacterial Proteins, Nitrogen Isotopes, Magnetic Resonance Spectroscopy, Protein Conformation, Streptococcus pneumoniae, Nuclear Magnetic Resonance, Biomolecular, Molecular Dynamics Simulation
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