computer modeling in molecular biology.pdf

84 Shoshana 1 Wodak, Daniel van Belle, and Martine PrhostFigure 4-15. Mean square displacement correlation function of the water molecules aroundHJ’S of Ile in barnase. Were considered in the computations only isoleucines Ha’s that exposemore than 30% of their surface to solvent (residues 4 and 55). The diffusion coefficient Dis proportional to the slope of the correlation function at long time scales.significantly more mobile (D = 1.6 x s-’), but still much less mobile than bulkwater.To help interpret these observations, Eq. (4-11) was also used to compute the “selfdiffusion coefficient” of each type of reference proton around which the water shellswere analyzed. These coefficients are given in column 2 of Table 4-3.Table 4-3. Diffusion coefficients at the surface of barnase.GroupN-HAla HpIle H,LYS H,Dintrinsic (lo-’ m2 s-’)0.30.41.40.65DWarer (lo-’ m2 s-’)Intrinsic refers to the diffusion coefficient of the reference protein atoms and water refers tothe diffusion coefficient of the water molecules belonging to the first solvation shell aroundthese reference atoms (see Figure 4-14). In the calculation 21 amide protons were considered;8 Ala Ha protons belonging to Ala 32, 37,43 (3 out of the 7 Ala residues in barnase); 6 IleH,in Ile 4, 55 (2 out of the 8 Ile in barnase) and 14 LysHr in Lys 19, 39, 49, 62, 66, 98, 108(7 out of the 8 Lys residues in barnase).0.30.41.61.6We see that the “diffusion coefficient” of the Ile H, is about 4 times larger thanthose of the amide and p protons. This is consistent with the 6 protons being at theextremity of a flexible side-chain and therefore moving faster, than the amide and