computer modeling in molecular biology.pdf

5 Modelling Nucleic Acids 125rotations about the short and long axis of the base pair). In standard RNA helices,the values of those parameters are 15.9" and 0", respectively. The values averagedover the last 50 ps of simulation are -24.3' and 18.7', respectively. The change insign of the inclination parameter is particularly striking and difficult to rationalize.Despite those unexplained structural deformations, the analysis of the hydrationof the RNA fragment was highly instructive. Cones of hydration around eachanionic phosphate oxygen (Figure 5-13) were systematically observed, as well aswater bridges connecting successive phosphate groups with lifetimes around 10 psand more. The structuring power of the ribose 02' atom on the polar environmentwas also apparent in the simulations, since the 02' preferentially accepts hydrogenbonding from water instead of being a hydrogen donor. The organized hydration inthe shallow groove of RNA helices and around unusual base pairs, like G-U pairs,already discussed on the basis of crystallographic results [45] could be describedmore precisely. The active structuring role of water molecules is not restricted tohelical regions, since very organized water networks were observed in the anticodonloop, involving especially the pseudouridine 32 and the methyl guanosine 37P3