Chapter title |
Nanoscale Dynamics and Energetics of Proteins and Protein-Nucleic Acid Complexes in Classical Molecular Dynamics Simulations
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Chapter number | 34 |
Book title |
Nanoscale Imaging
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Published in |
Methods in molecular biology, January 2018
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DOI | 10.1007/978-1-4939-8591-3_34 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8590-6, 978-1-4939-8591-3
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Authors |
Suresh Gorle, Lela Vuković, Gorle, Suresh, Vuković, Lela |
Abstract |
The present article describes techniques for classical simulations of proteins and protein-nucleic acid complexes, revealing their dynamics and protein-substrate binding energies. The approach is based on classical atomistic molecular dynamics (MD) simulations of the experimentally determined structures of the complexes. MD simulations can provide dynamics of complexes in realistic solvents on microsecond timescales, and the free energy methods are able to provide Gibbs free energies of binding of substrates, such as nucleic acids, to proteins. The chapter describes methodologies for the preparation of computer models of biomolecular complexes and free energy perturbation methodology for evaluating Gibbs free energies of binding. The applications are illustrated with examples of snapshots of proteins and their complexes with nucleic acids, as well as the precise Gibbs free energies of binding. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 1 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 1 | 100% |
Readers by discipline | Count | As % |
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Chemistry | 1 | 100% |