computer modeling in molecular biology.pdf

4 Molecular Dynamics and Free Energy Calculations 63discussed in light of the experimentally determined measures of protein stabilitychanges caused by the mutation.4.2 Molecular Dynamics Simulationsof Barnase in WaterBarnase is an extra cellular ribonuclease from Bacillus amyloliquefaciens. It is ofparticular interest because, being small enough (1 10 residues), it is readily amenableto physical, chemical, spectroscopic and structural studies. Indeed, it has beenanalyzed by nuclear magnetic resonance spectroscopy (NMR) [27, 281. The crystalstructure of the free enzyme is known to 2.0 A resolution [29] and the structuredeterminations of its complexes with nucleotides [30, 311 and with the protein inhibitorbarstar [30], are being completed. Furthermore, barnase undergoes reversiblethermal and urea induced denaturation [32] and has served as a model system forstudying protein stability and folding by site directed mutagenesis [28]. It containsa significant amount of secondary structure, which comprises a P-sheet composedof 5 strands (residues 50-55, 70-75, 85-91, 94-101, and 106-108) and two a-helices(residues 6-18 and 26-34), as depicted in Figure 4-1.The 250 ps MD simulation of solvated barnase described in this section, is usedto analyze the detailed motional behaviour of this protein in solution and its interac-Figure 4-1. Ribbon drawing [51] of the barnase crystal structure [29].