title: Conformational flexibility, binding energy, role of salt bridge and alanine-mutagenesis for c-Abl kinase complex.
abstract: Abl kinase plays a decisive role in the mechanism of the most fatal human pathogen chronic mylogenous leukemia (CML). Here, we have carried out a comprehensive study about the conformational flexibility, role of salt bridge and the protein- ligand interaction for this kinase with its well-known inhibitor, Imatinib. We have performed molecular dynamics simulations for conformational behavior, investigated the salt bridges and calculated the binding free energy of Imatinib with MM-PB/SA method for Abl kinase complex. We also explored the role of salt-bridge in the kinase complex and its effect on binding activity of inhibitors. Furthermore, to investigate the importance of those residues which form salt bridges, we mutated them by Alanine with the help of Alanine scanning program. We noticed significant variations in total free energy of Imatinib in all possible mutations. The binding free energy of ligand for kinase receptor was analyzed by molecular mechanics Poission Boltzmann surface area (MM-PB/SA) method. These results suggest that conserved glutamic acid and lysine are necessary for stability of complex.
authors.affiliation: Department of Physics, DDU Gorakhpur University, Gorakhpur, India. kshatresh@gmail.com
authors.forename: Kshatresh Dutta
authors.initials: KD
authors.lastname: Dubey
authors.forename: Rajendra Prasad
authors.initials: RP
authors.lastname: Ojha
mesh_terms: D000409:Alanine / Q000737:chemistry* / Q000235:genetics; D001549:Benzamides; D001665:Binding Sites; D018698:Glutamic Acid / Q000737:chemistry / Q000235:genetics; D006801:Humans; D006860:Hydrogen Bonding; D000068877:Imatinib Mesylate; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000201:enzymology; D008024:Ligands; D008239:Lysine / Q000737:chemistry / Q000235:genetics; D056004:Molecular Dynamics Simulation; D016296:Mutagenesis; D010879:Piperazines / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D016315:Proto-Oncogene Proteins c-abl / Q000737:chemistry* / Q000235:genetics; D011743:Pyrimidines / Q000737:chemistry*; D012492:Salts / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D001549:Benzamides; D008024:Ligands; D010879:Piperazines; D047428:Protein Kinase Inhibitors; D011743:Pyrimidines; D012492:Salts; D018698:Glutamic Acid; D000068877:Imatinib Mesylate; D016315:Proto-Oncogene Proteins c-abl; D008239:Lysine; D000409:Alanine