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Simulating Dynamics in RNA–Protein Complexes

  • John Eargle
  • Zaida Luthey-Schulten
Chapter
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 27)

Abstract

Simulation of RNA–protein complexes presents new challenges for computational studies. While the fields of protein folding and docking of protein complexes have matured sufficiently so that experimental and computational methods complement and cross-validate each other, methods for RNA folding and docking of RNA to proteins are still in their infancy. Part of the difficulty lies in the complex interactions of RNA with ions and water that differ considerably from those of proteins, due to the extreme electronegativity of RNA, and result in unique dynamics. Here we address challenging issues in the simulation of RNA and its interactions with solvent, ions, and proteins. A general discussion of the preparation and simulation of large RNA–protein systems with divalent cations and modified bases is given, followed by a critical summary of methods for analyzing the resulting MD trajectories.

Keywords

Molecular Dynamic Simulation Root Mean Square Deviation Molecular Dynamic Trajectory Force Field Parameter Free Energy Landscape 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors are supported by NSF Grants MCB-0844670 and PHY-0822613 and NIH P41 RR005969. We thank Ke Chen for creating the figures related to S4·h16 and Eduard Schreiner for providing the VMD Tcl script for calculating the angle between RNA helices.

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© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Center for Biophysics and Computational BiologyUrbanaUSA
  2. 2.Department of ChemistryUniversity of IllinoisUrbanaUSA

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