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Noé F, Doose S, Daidone I, et al. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A. 2011;108(12):4822-7doi: 10.1073/pnas.1004646108.
Noé, F., Doose, S., Daidone, I., Löllmann, M., Sauer, M., Chodera, J. D., & Smith, J. C. (2011). Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proceedings of the National Academy of Sciences of the United States of America, 108(12), 4822-7. https://doi.org/10.1073/pnas.1004646108
Noé, Frank, et al. "Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments." Proceedings of the National Academy of Sciences of the United States of America vol. 108,12 (2011): 4822-7. doi: https://doi.org/10.1073/pnas.1004646108
Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4822-7. doi: 10.1073/pnas.1004646108. Epub 2011 Mar 02. PMID: 21368203; PMCID: PMC3064371.
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Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4822-7. doi: 10.1073/pnas.1004646108. Epub 2011 Mar 02.

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.

Proceedings of the National Academy of Sciences of the United States of America

Frank Noé, Sören Doose, Isabella Daidone, Marc Löllmann, Markus Sauer, John D Chodera, Jeremy C Smith

Affiliations

  1. Research Center Matheon, FU Berlin, Arnimallee 6, 14159 Berlin, Germany. [email protected]

PMID: 21368203 PMCID: PMC3064371 DOI: 10.1073/pnas.1004646108

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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