Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

Christina Bergonzo1, Rodrigo Galindo‐Murillo1, Thomas E. Cheatham1

1 Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 7.9
DOI:  10.1002/0471142700.nc0709s55
Online Posting Date:  December, 2013
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Abstract

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all‐atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Curr. Protoc. Nucleic Acid Chem. 55:7.9.1‐7.9.27. © 2013 by John Wiley & Sons, Inc.

Keywords: nucleic acid chemistry; nucleic acid structure and folding; structural analysis of biomolecules; experimental determination of structure

     
 
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Table of Contents

  • Electrostatics and Solvation
  • In Vacuo Representations
  • Implicit Solvent Models
  • Simulations in Explicit Solvent
  • Summary
  • Acknowledgments
  • Literature Cited
  • Figures
     
 
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Materials

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Literature Cited

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Internet Resources
  http://gbio‐pbil.ibcp.fr/ABC/
  Ascona B‐DNA Consortium Web site.
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