Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

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• 作者：Ji艡铆 艩poner ; Pavel Ban谩拧 ; Petr Jure膷ka ; Marie Zgarbov谩 ; Petra K眉hrov谩 ; Marek Havrila ; Miroslav Krepl ; Petr Stadlbauer ; Michal Otyepka
• 刊名：The Journal of Physical Chemistry Letters
• 出版年：2014
• 出版时间：May 15, 2014
• 年：2014
• 卷：5
• 期：10
• 页码：1771-1782
• 全文大小：537K
• 年卷期：v.5,no.10(May 15, 2014)
• ISSN：1948-7185

文摘

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.