Cited by 8Protein Structure and DynamicsAdvanced NMR Techniques and ApplicationsMolecular spectroscopy and chirality

Computational modeling multiple conformational states of proteins with residual dipolar coupling data

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Abdollahi, Hamed, Prestegard, James H., Valafar, Homayoun·2023·Current Opinion in Structural Biology

Abstract

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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Crossref · 10.1016/j.sbi.2023.102655

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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
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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