ArticleProceedings of the National Academy of Sciences of the United States of America2011
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
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- Uncertainties in Markov State Models of Small Proteins.Journal of chemical theory and computation · 2023Article
- Conformational exchange divergence along the evolutionary pathway of eosinophil-associated ribonucleases.Structure (London, England : 1993) · 2023Article
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- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Real-time observation of ligand-induced allosteric transitions in a PDZ domain.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Identification of Druggable Kinase Target Conformations Using Markov Model Metastable States Analysis of apo-Abl.Journal of chemical theory and computation · 2020Article
- Dynamic graphical models of molecular kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data.The journal of physical chemistry letters · 2019Article
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- Identification of kinetic order parameters for non-equilibrium dynamics.The Journal of chemical physics · 2019Article
- Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.Biophysical journal · 2019Article
- Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.The Journal of chemical physics · 2019Article
- Variational encoding of complex dynamics.Physical review. E · 2018Article
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7 authors.
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Abstract
There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is "dynamical fingerprints" which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.
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