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Unraveling motion in proteins by combining NMR relaxometry and molecular dynamics simulations: A case study on ubiquitin
Open accessPublished version of a preprint
Abstract
Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods that permit the joint analysis of MD simulations and NMR relaxation experiments. We discuss their relative strengths and areas of applicability and demonstrate how they may be utilized to interpret the dynamics in MD simulations with the small protein ubiquitin as a test system. We focus on the aliphatic side chains given the rigidity of the backbone of this protein. We find encouraging agreement between experiment, Markov state models built in the χ1/χ2 rotamer space of isoleucine residues, explicit rotamer jump models, and a decomposition of the motion using ROMANCE. These methods allow us to ascribe the dynamics to specific rotamer jumps. Simulations with eight different combinations of force field and water model highlight how the different metrics may be employed to pinpoint force field deficiencies. Furthermore, the presented comparison offers a perspective on the utility of NMR relaxation to serve as validation data for the prediction of kinetics by state-of-the-art biomolecular force fields.
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Metadata
- Authors
- Champion, C., Lehner, M., Smith, A. A., Ferrage, F., Bolik-Coulon, N., & Riniker, S.
- Affiliations
- ETH Zurich (CH)
- Leipzig University (DE)
- Centre National de la Recherche Scientifique (FR)
- University of Toronto (CA)
- Corresponding author
- Riniker, Sereina
- ORCID
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2024-03-11
- Volume
- 160
- Issue
- 10
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W4392649013
- Cited by
- 11
- References
- 97
- Citations by year
- 2025: 8 · 2024: 3
- FWCI
- 1.49
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- The Journal of Chemical Physics (publishedVersion, cc-by)
- ChemRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by-nc-nd)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- Funders
- European Research Council (FET-Open call, Grant Agreement 899683 (HIRES-MULTIDYN))
- Deutsche Forschungsgemeinschaft (450148812)
- Canadian Institutes of Health Research (Postdoctoral Fellowship)
- 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 › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- ubiquitin, protein dynamics, NMR relaxometry, molecular dynamics simulation, Markov state models, romance, force field validation, water model, side chain mobility
- MeSH terms
- Magnetic Resonance Spectroscopy, Proteins, Nuclear Magnetic Resonance, Biomolecular, Ubiquitin, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
