AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein
Open accessPublished version of a preprint
Abstract
We use AlphaFold2 (AF2) to model the monomer and dimer structures of an intrinsically disordered protein (IDP), Nvjp-1 , assisted by molecular dynamics (MD) simulations. We observe relatively rigid dimeric structures of Nvjp-1 when compared with the monomer structures. We suggest that protein conformations from multiple AF2 models and those from MD trajectories exhibit a coherent trend: the conformations of an IDP are deviated from each other and the conformations of a well-folded protein are consistent with each other. We use a residue-residue interaction network (RIN) derived from the contact map which show that the residue-residue interactions in Nvjp-1 are mainly transient; however, those in a well-folded protein are mainly persistent. Despite the variation in 3D shapes, we show that the AF2 models of both disordered and ordered proteins exhibit highly consistent profiles of the pLDDT (predicted local distance difference test) scores. These results indicate a potential protocol to justify the IDPs based on multiple AF2 models and MD simulations.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · cited 1× · see citing works
“The present AF2 structure database contains over 200 million protein models covering nearly all known protein sequences [25], including the human proteome [26].”
BackgroundPredicting multiple conformations via sequence clustering and AlphaFold2
Wayment-Steele, H. K., Ojoawo, A., Otten, R., Apitz, J. M., Pitsawong, W., Hömberger, M., Ovchinnikov, S., Colwell, L., & Kern, D. (2024) · Nature · doi:10.1038/s41586-023-06832-9 · Cited by 545 · see citing works
Single-sequence protein structure prediction using language models from deep learning
Chowdhury, R., Bouatta, N., Biswas, S., Rochereau, C., Church, G. M., Sorger, P. K., & AlQuraishi, M. (2021) · doi:10.1101/2021.08.02.454840 · Cited by 455 · see citing works
Single-sequence protein structure prediction using a language model and deep learning
Chowdhury, R., Bouatta, N., Biswas, S., Floristean, C., Kharkar, A., Roy, K., Rochereau, C., Ahdritz, G., Zhang, J., Church, G. M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01432-w · Cited by 455 · see citing works
Critical assessment of protein intrinsic disorder prediction
Necci, M., Piovesan, D., Predictors, C., Hoque, M. T., Walsh, I., Iqbal, S., Vendruscolo, M., Sormanni, P., Wang, C., Raimondi, D., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01117-3 · Cited by 343 · see citing works
High‐accuracy protein structure prediction in <scp>CASP14</scp>
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AlphaFold heralds a data-driven revolution in biology and medicine
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AlphaFold2: A Role for Disordered Protein/Region Prediction?
Wilson, C. J., Choy, W.-Y., & Karttunen, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094591 · Cited by 173 · see citing works
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- Authors
- Guo, H.-B., Huntington, B., Perminov, A., Smith, K., Hastings, N., Dennis, P., Kelley-Loughnane, N., & Berry, R.
- Affiliations
- United States Air Force Research Laboratory (US)
- United States Air Force Academy (US)
- Corresponding author
- Guo, Hao-Bo
- Berry, Rajiv
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2024-05-13
- Volume
- 19
- Issue
- 5
- Pages
- e0301866
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC11090348
- OpenAlex
- W4396853373
- Cited by
- 13
- References
- 9
- Citations by year
- 2026: 3 · 2025: 9 · 2024: 1
- FWCI
- 1.77
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- creativecommons.org/publicdomain/zero/1.0/ (vor)
- Locations
- PLoS ONE (publishedVersion, public-domain)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, public-domain)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Office of the Under Secretary of Defense for Research and Engineering (Applied Research for Advancement of S&T Priorities (ARAP) Program)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- intrinsically disordered proteins, AlphaFold2, protein dimerization, protein conformational heterogeneity, contact maps, protein structure prediction, molecular dynamics trajectories
- MeSH terms
- Protein Conformation, Protein Folding, Protein Multimerization, Molecular Dynamics Simulation, Intrinsically Disordered Proteins
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