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Inference of Calmodulin's Ca2+-Dependent Free Energy Landscapes via Gaussian Mixture Model Validation
KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, School of Engineering Sciences (SCI), Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 1, p. 63-71Article in journal (Refereed) Published
Abstract [en]

A free energy landscape estimation method based on the well-known Gaussian mixture model (GMM) is used to compare the efficiencies of thermally enhanced sampling methods with respect to regular molecular dynamics. The simulations are carried out on two binding states of calmodulin, and the free energy estimation method is compared with other estimators using a toy model. We show that GMM with cross-validation provides a robust estimate that is not subject to overfitting. The continuous nature of Gaussians provides better estimates on sparse data than canonical histogramming. We find that diffusion properties determine the sampling method effectiveness, such that diffusion-dominated apo calmodulin is most efficiently sampled by regular molecular dynamics, while holo calmodulin, with its rugged free energy landscape, is better sampled by enhanced sampling methods.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018. Vol. 14, no 1, p. 63-71
Keyword [en]
Exchange Molecular-Dynamics, Calculating Free-Energies, Replica-Exchange, Biological-Systems, Simulations, Transitions, Algorithm, Mechanism, Efficient, Proteins
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Other Chemistry Topics
Identifiers
URN: urn:nbn:se:kth:diva-221690DOI: 10.1021/acs.jctc.7b00346ISI: 000419998300007PubMedID: 29144736Scopus ID: 2-s2.0-85040344833OAI: oai:DiVA.org:kth-221690DiVA, id: diva2:1176306
Funder
Knut and Alice Wallenberg Foundation, 1484505Carl Tryggers foundation , CTS-15:298Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180122

Available from: 2018-01-22 Created: 2018-01-22 Last updated: 2018-01-29Bibliographically approved

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Westerlund, Annie M.Harpole, TylerDelemotte, Lucie
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CiteExportLink to record
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  • apa
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