The protein-protein interactions- molecular modelling study

The signal transduction and regulatory processes in cell are based on protein-protein interaction, and they are very sensitive to protein mutations. Herein I shall give an overview of our theoretical studies accomplished for two sets of protein complexes: Barnes- Barstar and complexes between Ras and its effectors, proteins Raf and RalGDS. Ras is a small guanosine triphosphate (GTP)-binding protein that serves as a switch in the mitogen-activating protein kinase pathway (MAPK). In its active, on conformation (GTP bound), Ras interacts with Raf, a Ser/Thr specific protein kinase, an immediate downstream target of Ras in MAPK. Another protein that Ras interacts with is Ral guanine nucleotide dissociation stimulator (RalGDS). This interaction is connected with the control of cytoskeletal rearrangements. Consequences of certain Ras mutations are uncontrolled growth and division of cells, and the mutated Ras proteins are frequently found in diverse human tumours. Barnase is the extracellular ribonuclease and Barstar is its intracellular inhibitor. This is one of the tightest known protein complexes with Kd of about 10-14M. We determined the dominating interactions in the above mentioned complexes (Fig. 1) and influence of the single point mutations on their stability, and derived the system specific QSAR (Quantitative Structure Activity Relationship) models for estimating binding free energy.1, 2 To find out what is the net electrostatic contribution to formation of these protein-complexes we accomplished Poisson-Boltzmann electrostatic calculations. The association rates of the designed mutants were calculated by using Brownian dynamics (BD) simulations.