computer modeling in molecular biology.pdf

4 Molecular Dynamics and Free Energy Calculations 77groups are shown in Figure 4-lob for comparison. We see that overall, backbonegroups are involved more often in hydrogen bonds with water molecules (a total of144 hydrogen bonds on the average) than with other protein atoms (a total of 60hydrogen bonds on the average). We find furthermore that carbonyl groups are moreoften involved in hydrogen bonds with water molecules than amide groups. This fitswith the general tendency of carbonyl groups to form more hydrogen bonds than10 10 20 30 40 50 60 70 80 90 100 110 NFigure 4-10. The average number of hydrogen bonds formed by backbone amides and carbony1groups of barnase during the 250 ps simulation of the protein-water system. The averagenumber of hydrogen bonds for each group ((NHb)NH or (NHb),,) is defined as the numberof conformations in which the corresponding group makes a hydrogen bond divided by thetotal number of conformations in the trajectory. The criteria for hydrogen bond formationare given in the legend of Figure 4-8. (a) displays the average number of hydrogen bonds madewith other protein atoms, by the backbone amides (above) and carbonyl groups (below) alongthe amino-acid sequence of barnase. (b) displays the same data, but counting only hydrogenbonds made with water molecules.