Journal
BIOPOLYMERS
Volume 85, Issue 2, Pages 169-184Publisher
WILEY
DOI: 10.1002/bip.20620
Keywords
hydration and cation binding; molecular dynamics; nucleic acid-protein complex; RNA; structure-activity relationship
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Funding
- NIGMS NIH HHS [R01 GM062357, GM 62357] Funding Source: Medline
- Wellcome Trust [067507, GR 067507] Funding Source: Medline
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RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require a understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the techniques and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA-small molecule and RNA-protein complexes. Increased cooperation between theorists and experimentalists will allow expanded juducious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules. (c) 2006 Wiley Periodicals, Inc.
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