Computational modeling multiple conformational states of proteins with residual dipolar coupling data
Open accessAbstract
Solution nuclear magnetic resonance spectroscopy provides unique opportunities to study the structure and dynamics of biomolecules in aqueous environments. While spin relaxation methods are well recognized for their ability to probe timescales of motion, residual dipolar couplings (RDCs) provide access to amplitudes and directions of motion, characteristics that are important to the function of these molecules. Although observed in the 1960s, the acquisition and computational analysis of RDCs has gained significant momentum in recent years, and particularly applications to motion in proteins have become more numerous. This trend may well continue as RDCs can easily leverage structures produced by new computational methods (e.g., AlphaFold) to produce functional descriptions. In this report, we provide examples and a summary of the ways that RDCs have been used to confirm the existence of internal dynamics, characterize the type of dynamics, and recover atomic-scale structural ensembles that define the full range of conformational sampling.
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Experimental data, especially SAXS, NMR, and cryo-EM, have been described as guides for modeling ensembles and alternative conformations.
“The use of experimental data, especially SAXS, NMR, and cryo-EM, has also been described to guide modeling of ensembles and alternative conformations71,82,108.”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [82]
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- Authors
- Abdollahi, H., Prestegard, J. H., & Valafar, H.
- Affiliations
- University of South Carolina (US)
- University of Georgia (US)
- Corresponding author
- Abdollahi, Hamed
- Prestegard, James H.
- Valafar, Homayoun
- Venue
- Current Opinion in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2023-10
- Volume
- 82
- Pages
- 102655
- ISSN
- 0959-440X (ISSN-L)
- OpenAlex
- W4384296006
- Cited by
- 8
- References
- 62
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 2 · 2023: 2
- FWCI
- 0.21
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Current Opinion in Structural Biology (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (1R01GM134335, P20GM103499)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Molecular spectroscopy and chirality
- Keywords
- residual dipolar couplings, protein conformational ensembles, protein internal dynamics, solution NMR, structural ensembles, AlphaFold, spin relaxation
- MeSH terms
- Computer Simulation, Models, Molecular, Molecular Conformation, Proteins, Nuclear Magnetic Resonance, Biomolecular
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