computer modeling in molecular biology.pdf

98 Shoshana 1 Wodak, Daniel van Belle, and Martine Prkvost4.4 Concluding RemarksThis chapter described the application of molecular dynamics simulation techniquesto the study of the dynamic and thermodynamic properties of wild type barnase andof one of its stability mutants.Methodological and practical aspects involved in generating a 250 ps trajectoryof wild type barnase in water, were described. This trajectory was then analyzedfocusing on aspects of protein motion and protein-solvent interactions. The analysissuggests that the simulated system of 8777 atoms displayed a physically reasonablebehavior, a tribute to the progress achieved in improving the force-fields and simulationmethodology. Protein conformations deviated relatively little from the startingcrystal structure, during the simulations; the structure of the first water layer at theprotein surface, followed patterns previously observed for dilute solutions of smallmolecules; the simulations revealed a reduced mobility of the water molecules at theprotein surface, in agreement with experimental evidence from NMR spectroscopy,and with other simulation studies.It is however clear that the time scale of the simulations (250 ps) is still much tooshort to allow the system to sample the conformational states accessible to it underexperimental conditions, and/or that are biologically relevant. It may thus not alwaysbe possible to relate the detailed picture provided by simulations of this length to experimentaldata, a problem which also hampers its validation. This situation is improvinghowever, as computational tools, that allow a more efficient sampling ofconformational space are developed, and as the available computer power increases.The second part of this chapter, illustrated the application of molecular dynamicssimulations to the calculation of the free energy change produced by substituting Ile96 by Ala in the hydrophobic core of barnase. Despite the well known sampling problemsdiscussed above, free energy perturbation methods relying on moleculardynamics trajectories of 315 ps, are shown to yield computed free energy differenceswhich are in satisfactory agreement with the changes in the denaturation freeenergies, and in solvation free energies measured experimentally. It is important torealize however, that the error associated with the computed free energy values is ofthe same order as the values themselves, and hence that the reliability of the resultsdepends critically on the underlying assumptions. With due vigilance however, thedescribed free energy computation analysis is seen to provide useful insights into theorigins of the hydrophobic stabilization of proteins.