Brajesh Narayan1, Arman Fathizadeh2, Clark Templeton3, Peng He4, Shima Arasteh4, Ron Elber5, Nicolae-Viorel Buchete1, Ron M Levy4. 1. School of Physics, University College Dublin, Belfield, Dublin 4, Ireland. 2. Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, 201 E. 24(th) Street, 1 University Station (C0200), Austin, TX 78712-1229, USA. 3. McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keaton St. Stop C0400, Austin, TX 78712-1589, USA. 4. Department of Chemistry, Temple University, 1801 N Broad Street, Philadelphia, PA 19122, USA. 5. Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, 201 E. 24(th) Street, 1 University Station (C0200), Austin, TX 78712-1229, USA; Department of Chemistry, University of Texas at Austin, 2506 Speedway STOP A5300, Austin, TX 78712-1224, USA. Electronic address: ron@oden.utexas.edu.
Abstract
BACKGROUND: Kinases are a family of enzymes that catalyze the transfer of the ɤ-phosphate group from ATP to a protein's residue. Malfunctioning kinases are involved in many health problems such as cardiovascular diseases, diabetes, and cancer. Kinases transitions between multiple conformations of inactive to active forms attracted considerable interest. METHOD: A reaction coordinate is computed for the transition between the active to inactive conformation in Abl kinase with a focus on the DFG-in to DFG-out flip. The method of Rock Climbing is used to construct a path locally, which is subsequently optimized using a functional of the entire path. The discrete coordinate sets along the reaction path are used in a Milestoning calculation of the free energy landscape and the rate of the transition. RESULTS: The estimated transition times are between a few milliseconds and seconds, consistent with simulations of the kinetics and with indirect experimental data. The activation requires the transient dissociation of the salt bridge between Lys271 and Glu286. The salt bridge reforms once the DFG motif is stabilized by a locked conformation of Phe382. About ten residues are identified that contribute significantly to the process and are included as part of the reaction space. CONCLUSIONS: The transition from DFG-in to DFG-out in Abl kinase was simulated using atomic resolution of a fully solvated protein yielding detailed description of the kinetics and the mechanism of the DFG flip. The results are consistent with other computational methods that simulate the kinetics and with some indirect experimental measurements. GENERAL SIGNIFICANCE: The activation of kinases includes a conformational transition of the DFG motif that is important for enzyme activity but is not accessible to conventional Molecular Dynamics. We propose a detailed mechanism for the transition, at a timescale longer than conventional MD, using a combination of reaction path and Milestoning algorithms. The mechanism includes local structural adjustments near the binding site as well as collective interactions with more remote residues.
BACKGROUND:Kinases are a family of enzymes that catalyze the transfer of the ɤ-phosphate group from ATP to a protein's residue. Malfunctioning kinases are involved in many health problems such as cardiovascular diseases, diabetes, and cancer. Kinases transitions between multiple conformations of inactive to active forms attracted considerable interest. METHOD: A reaction coordinate is computed for the transition between the active to inactive conformation in Abl kinase with a focus on the DFG-in to DFG-out flip. The method of Rock Climbing is used to construct a path locally, which is subsequently optimized using a functional of the entire path. The discrete coordinate sets along the reaction path are used in a Milestoning calculation of the free energy landscape and the rate of the transition. RESULTS: The estimated transition times are between a few milliseconds and seconds, consistent with simulations of the kinetics and with indirect experimental data. The activation requires the transient dissociation of the salt bridge between Lys271 and Glu286. The salt bridge reforms once the DFG motif is stabilized by a locked conformation of Phe382. About ten residues are identified that contribute significantly to the process and are included as part of the reaction space. CONCLUSIONS: The transition from DFG-in to DFG-out in Abl kinase was simulated using atomic resolution of a fully solvated protein yielding detailed description of the kinetics and the mechanism of the DFG flip. The results are consistent with other computational methods that simulate the kinetics and with some indirect experimental measurements. GENERAL SIGNIFICANCE: The activation of kinases includes a conformational transition of the DFG motif that is important for enzyme activity but is not accessible to conventional Molecular Dynamics. We propose a detailed mechanism for the transition, at a timescale longer than conventional MD, using a combination of reaction path and Milestoning algorithms. The mechanism includes local structural adjustments near the binding site as well as collective interactions with more remote residues.
Authors: Navratna Vajpai; André Strauss; Gabriele Fendrich; Sandra W Cowan-Jacob; Paul W Manley; Stephan Grzesiek; Wolfgang Jahnke Journal: J Biol Chem Date: 2008-04-22 Impact factor: 5.157
Authors: R S K Vijayan; Peng He; Vivek Modi; Krisna C Duong-Ly; Haiching Ma; Jeffrey R Peterson; Roland L Dunbrack; Ronald M Levy Journal: J Med Chem Date: 2014-12-12 Impact factor: 7.446