MD simulations in Pseudo-Particle Fluids: Applications to active-site Protein Complexes

Truncated protein-ligand active-site complexes were studied by molecular dynamics simulations. Pseudo-particles were used for the representation of the outer protein parts and the surrounding solvent. This pseudo-particle approach was applied to the MD simulation of adenylate kinase 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 molecular dynamics simulations were additionally compared with biochemical data. Despite the crude approximation of the outer protein parts and the solvent environment, differences in binding properties of the ligands could be observed and correlated to experiments.

Journal article

MD simulations in Pseudo-Particle Fluids: Applications to active-site Protein Complexes, Quantitative Structure-Activity Relationships 1995 14 (3), 229-241