NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations
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Calculating NMR relaxation effects for proteins with dynamics on multiple time scales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than 3 orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model-free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions. Using simulations of HIV-1 protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.
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Computation of NMR relaxation and order parameters from MSMs can be made straightforward through the use of the model-free framework approach of Lipari and Szabo, as demonstrated for HIV-1 protease.
“their computation from MSMs can be made straightforward through the use of the model-free framework approach of Lipari and Szabo, as recently demonstrated for HIV-1 protease [69].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [69]
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Actions of the A.M.A. House of Delegates.
Blasingame, F. J. L. (1960) · PubMed
- Authors
- Xia, J., Deng, N.-J., & Levy, R. M.
- Affiliations
- Rutgers, The State University of New Jersey (US)
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Corresponding author
- Levy, Ronald M.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-05-28
- Volume
- 117
- Issue
- 22
- Pages
- 6625-6634
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- PMC
- PMC3727231
- OpenAlex
- W1981737350
- Cited by
- 29
- References
- 93
- Citations by year
- 2025: 1 · 2022: 3 · 2021: 1 · 2020: 2 · 2018: 3 · 2016: 3 · 2015: 7 · 2014: 8
- FWCI
- 2.69
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- The Journal of Physical Chemistry B (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (1s10rr027444-01)
- National Institute of General Medical Sciences (R01GM030580, GM30580)
- National Center for Research Resources (S10-RR027444, S10RR022375)
- 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
- NMR relaxation, protein internal motions, conformational exchange, Markov state models, model-independent analysis, HIV-1 protease, order parameter, multiple time scales, free energy landscape
- MeSH terms
- Humans, Kinetics, Markov Chains, Magnetic Resonance Spectroscopy, HIV-1, HIV Protease, Molecular Dynamics Simulation
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