Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
RNA Simulation - Part I: SwS: Solvation Web Service for Nucleic Acids, a New Tool Dedicated to the Analysis of Nucleic Acids Solvation
The solvent (ions and water) is implicated in almost all molecular recognition phenomena involving biomolecules and, more specifically, nucleic acids. For instance, ligands approaching nucleic acid binding sites perceive the first solvation shell molecules before replacing some of them in order to establish direct contacts with the solute. Moreover, water molecules establish sometimes important solute/ligand bridges. Thus, a comprehensive knowledge of the first solvation shell structure is necessary in order to improve current drug design strategies.
We have developed a web service, called SwS (Solvation web Service for nucleic acids), which aims at providing a statistical overview of the first solvation shell structure around nucleic acid molecules based on available RNA and DNA crystallographic structures. The current version of SwS analyses the solvation (water, cations and anions) around the 33 DNA and RNA canonical and non-canonical base pair types linked by two or three hydrogen bonds. Solvent molecules composing their first solvation shell are extracted, ?pseudo-electron-density? maps are calculated. The most probable solvent binding sites are highlighted by using colors corresponding to their respective peak heights (from red/highest to blue/lowest; see figure). Data generated by SwS can be exploited at many levels. They can be used: (i) as reference data for validating molecular dynamics simulations; (ii) for helping crystallographers in the interpretation of solvent electron density maps; (iii) for drug design investigations involving nucleic acids; (iv) for pedagogic purpose; (v) but also by all those interested in nucleic acid structural aspects.
References and Footnotes