ArticleThe journal of physical chemistry. B2013
NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Deciphering the Allosteric Process of theThe journal of physical chemistry. B · 2020Article
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- Relaxation mode analysis for molecular dynamics simulations of proteins.Biophysical reviews · 2018Review
- Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily.Structure (London, England : 1993) · 2018Article
- Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies.Catalysts (Basel, Switzerland) · 2016Article
- Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments.Protein science : a publication of the Protein Society · 2016Article
- Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.Frontiers in molecular biosciences · 2016Review
- Enzyme dynamics from NMR spectroscopy.Accounts of chemical research · 2015Review
- Visualizing transient dark states by NMR spectroscopy.Quarterly reviews of biophysics · 2015Article
- Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations.Frontiers in plant science · 2015Review
- On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins.Journal of chemical theory and computation · 2014Article
- Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4.Nature communications · 2014Article
- Molecular dynamics of the proline switch and its role in Crk signaling.The journal of physical chemistry. B · 2014Article
- Markov state models of biomolecular conformational dynamics.Current opinion in structural biology · 2014Review
- Activation pathway of Src kinase reveals intermediate states as targets for drug design.Nature communications · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.