MD-SIMULATIONS IN PSEUDO-PARTICLE FLUIDS - APPLICATIONS TO ACTIVE-SITE PROTEIN COMPLEXES

Truncated protein-ligand active-site complexes were studied by molecul ar dynamics simulations. Pseudo-particles were used for the representa tion of the outer protein parts and the surrounding solvent. This pseu do-particle approach was applied to the MD simulation of adenylate kin ase wild type or mutant enzymes in complex with different ligands. For further validation of the method, the human leucocyte antigen HLA-B27 was simulated in complex with three different nonapeptides. All molec ular dynamics simulations were additionally compared with biochemical data. Despite the crude approximation of the outer protein parts and t he solvent environment, differences in binding properties of the ligan ds could be observed and correlated to experiments.