computer modeling in molecular biology.pdf

4 Molecular Dynamics and Free Energy Calculations 734.2.2.2 Variations of the Protein Accessible Surface Areaand VolumeOther parameters such as the protein accessible surface area and accessible volumewere also monitored along the trajectory (see Figure 4-7). These quantities, definedin the legend of Figure 4-7, were computed using an analytic algorithm implemented(AZ)Accessible surface(A3)22000 10 50 100 150 200 250(a)Accessible volume215002100020500 32 m:/,""y , , , , , , , , , , , , , , t (PS) , ,Figure 4-7. Accessible surface areas (A2) and volumes (A3) of barnase conformations alongthe 250 ps trajectory of the protein-water system. Areas (a) and volumes (b) were computedwith an analytical algorithm [54], using a probe radius of 1.4 A. The accessible volume isdefined as the volume contained within the accessible surface of the protein [54]. Values correspondingto the accessible surface area and the accessible volume of the crystal structurerespectively, 5800 A' and 20050 A3, are indicated by arrows. The largest changes in bothquantities occur during the thermalization and equilibration periods, which precede the250 ps production run.