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Article

Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank

Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
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Int. J. Mol. Sci. 2018, 19(11), 3405; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19113405
Received: 6 October 2018 / Revised: 22 October 2018 / Accepted: 27 October 2018 / Published: 30 October 2018
(This article belongs to the Collection Protein Folding)
In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean force, which we determined from DNA and protein structures in the Protein Data Bank (PDB). We define a partition function from a set of PDB-derived PMFs, which efficiently compensates for the error introduced by the assumption of a homogeneous partition function from the PDB datasets. The bias based on the PDB-derived partitions is added in the form of a hybrid Hamiltonian using a renormalization method, which adds the PMF-enriched gradient to the system depending on a linear weighting factor and the underlying force field. We validated the method using simulations of dialanine, the folding of TrpCage, and the conformational sampling of the Dickerson–Drew DNA dodecamer. Our results show the potential for the PMF-enriched simulation technique to enrich the conformational space of biomolecules along their order parameters, while we also observe a considerable speed increase in the sampling by factors ranging from 13.1 to 82. The novel method can effectively be combined with enhanced sampling or coarse-graining methods to enrich conformational sampling with a partition derived from the PDB. View Full-Text
Keywords: enhanced molecular dynamics simulations; protein folding; DNA simulation enhanced molecular dynamics simulations; protein folding; DNA simulation
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MDPI and ACS Style

Peter, E.K.; Černý, J. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. Int. J. Mol. Sci. 2018, 19, 3405. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19113405

AMA Style

Peter EK, Černý J. Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank. International Journal of Molecular Sciences. 2018; 19(11):3405. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19113405

Chicago/Turabian Style

Peter, Emanuel K., and Jiří Černý. 2018. "Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank" International Journal of Molecular Sciences 19, no. 11: 3405. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19113405

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