computer modeling in molecular biology.pdf

76 Shoshana .I Wodak, Daniel van Belle, and Martine Prtfvostthe crystal structure, persist during the simulation (they occur in more than 60% ofthe conformations in the trajectory). The proportion of persisting crystallographichydrogen bonds decreases to 43 (70 in the sidechain-mainchain category, and then furtherto 17 %, in the sidechain-sidechain category. In parallel to the loss of crystallographichydrogen bonds we observe the formation of new intra-molecular hydrogenbonds not present in the crystal structure. However, most of them occur transientlywith only a very small number persisting in 6O%, or more, of the generated conformations.For example, among the 83 new hydrogen bonds formed between mainchainatoms, only about 10% persist, and among the 72 new sidechain-sidechainhydrogen bonds only 2 (about 3 070) persist. Figure 4-9 summarizes these data for themainchain hydrogen bonds in barnase.Figure 4-9. Hydrogen bonds formed between amide and carbonyl groups of the polypeptidebackbone during the 250 ps molecular dynamics simulation of solvated barnase. The sequenceposition of the amide groups is given vertically, and the hydrogen bonds that they formare plotted in the upper left diagonal. The sequence position of the carbonyl groups is givenhorizontally and their hydrogen bonds are plotted in the lower right diagonal. Only 4catagories of hydrogen bonds are plotted: hydrogen bonds observed in the crystal structure,and maintained in more than 60% of the conformations in the trajectory (B); hydrogenbonds observed in the crystal structure, and maintained in less than 60% of the conformations(0); new hydrogen bonds generated during the simulation and maintained in more than 60%of the conformations (a); new hydrogen bonds generated during the simulation and maintainedin less than 60% of the conformations (0).Protein-Solvent Hydrogen Bonds Involving the Backbone. In addition to intramolecularinteractions, polar groups can also form hydrogen bonds with watermolecules. The average number of hydrogen bonds formed during the simulationby mainchain amide and carbonyl groups with water molecules is displayed inFigure 4-10a. Data on intra-molecular hydrogen bonds formed between the same