computer modeling in molecular biology.pdf

Colour IllustrationsXI11Figure 4-4. The simulated barnase-water system. (a) The starting conformation of the system,consisting of one of the three barnase molecules in the asymmetric unit (molecule C) fromthe 2 A resolution refined crystal structure (represented by its molecular surface), 94crystallography determined water positions located within 4 A of a protein atom (in blue) and2265 randomly oriented water molecules (in red) placed on a cubic lattice in a rectangular box(dimensions : 49.68 x 37.16 x 49.68 A), (b) the same system after 50 ps. Colouring of the proteinsurface is chosen according to the value of the mean square displacement of the mainchainatoms: small displacement < 0.6 A (blue), medium < 1.2 A (yellow), large < 4.0 A(red). Water molecules displaying a very large displacement ( > 4.0 A) are coloured in pink andrepresent bulk water molecules. It can also be seen that water molecules trapped in cavitiesdisplay the same mean displacement as the surrounding protein atoms.(Text see page 69).