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AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein
Open accessPreprint — published as 10.1371/journal.pone.0301866 · Paper page
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. The TOC figure:
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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
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Metadata
- 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
- openRxiv
- Published
- 2023-07-30
- Volume
- 19
- Issue
- 5
- Pages
- e0301866-e0301866
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC11090348
- OpenAlex
- W4396853373
- Cited by
- 13
- References
- 1
- 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
- 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
- Office of the Under Secretary of Defense
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › 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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