Abstract

Protein kinases have become one of the principal targets in the drugs development in many pharmaceutical companies due to the critical role into intracellular signaling system [1-4]. In response to growth factors, the protein kinases activate a several metabolic pathways, which generate cellular response such as mitogenesis, proliferation, differentiation, migration, or induction of apoptosis. Many studies have focused on cancer because overexpression of protein kinases is frequently associated with many human cancers such as colon, pancreas, kidney, ovarian cancer and others. Since PKA is involved in the intracellular signaling system, this must be specific and act at a specific target in the cell. This specificity is essential for cell integrity and depends on the complementarity between the kinase and its substrate, and therefore, its structure tridimencional. We have carried out molecular dynamics (MD) simulations and MM/GBSA free energy calculations on the complex between the protein kinase A (PKA) and the specific peptide substrate Kemptide (LRRASLG). We made the same calculations on other PKA complexes that contain mutations of the arginines at the positions 2 and 3 of Kemptide. We predicted the mutation-caused shifts of the free energy changes from the free PKA to the PKA-substrate complex (∆∆GE→ES). The calculated shifts correlate with the experimental shifts of the free energy changes from the free PKA to the transition states (∆∆GE→TS) determined by the catalytic efficiency (kcat/KM) changes. Our results provide novel structural information about the atomic forces that contribute to the interactions between protein kinases and their substrates.