Molecular mechanisms of activation in CDK2

Cyclin-dependent kinases (CDKs) are enzymes involved in crucial cellular processes. Their biological activity is directly linked to their high conformational variability, which involves large protein conformational rearrangements. We present here the application of an enhancing sampling technique to the study of conformational transitions between the open and closed state of CDKs. The analysis of the conformational intermediates supports the idea that the process is regulated by two important protein regions, which sequentially rearrange in order to allow the protein to reach its final conformation. Furthermore, the two paths involve additional (minor) protein rearrangements which are specific to the paths. Our results show that our procedure can provide reasonable transition pathways between the two protein forms at a very reduced computational cost. The robustness and the simplicity of our approach make it of general application to describe virtually any macromolecular conformational transitions.

[1]  K. Tai.  Conformational sampling for the impatient. , 2004, Biophysical chemistry.

[2]  Bradley M Dickson,et al.  αC helix as a switch in the conformational transition of Src/CDK-like kinase domains. , 2012, The journal of physical chemistry. B.

[3]  Philip D. Jeffrey,et al.  Crystal structure of the p27Kip1 cyclin-dependent-kinase inibitor bound to the cyclin A–Cdk2 complex , 1996, Nature.

[4]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[5]  M. Orozco,et al.  Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. , 2012, Journal of chemical theory and computation.

[6]  A. Laio,et al.  Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Huijong Han,et al.  Discovery of a potential allosteric ligand binding site in CDK2. , 2011, ACS chemical biology.

[8]  Osamu Miyashita,et al.  Conformational transitions of adenylate kinase: switching by cracking. , 2007, Journal of molecular biology.

[9]  Christian Bartels,et al.  Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations , 1997, J. Comput. Chem..

[10]  L. Johnson,et al.  Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2. , 2001, Molecular cell.

[11]  H J Berendsen,et al.  An efficient method for sampling the essential subspace of proteins. , 1996, Journal of biomolecular structure & dynamics.

[12]  Qiang Lu,et al.  Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles. , 2008, Journal of the American Chemical Society.

[13]  Mark A. Wilson,et al.  Intrinsic motions along an enzymatic reaction trajectory , 2007, Nature.

[14]  J. Chu,et al.  Illuminating the mechanistic roles of enzyme conformational dynamics , 2007, Proceedings of the National Academy of Sciences.

[15]  N. Pavletich.  Mechanisms of cyclin-dependent kinase regulation: structures of Cdks, their cyclin activators, and Cip and INK4 inhibitors. , 1999, Journal of molecular biology.

[16]  E. Lengyel,et al.  Tyrosine kinase mutations in human cancer. , 2007, Current molecular medicine.

[17]  Benoît Roux,et al.  Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms , 2008, PLoS Comput. Biol..

[18]  Kornelia Polyak,et al.  Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex , 1995, Nature.

[19]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[20]  A. Amadei,et al.  Protein Folding Pathways Revealed by Essential Dynamics Sampling. , 2008, Journal of chemical theory and computation.

[21]  Andrea Amadei,et al.  Essential dynamics: foundation and applications , 2012 .

[22]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[23]  Sung-Hou Kim,et al.  Crystal structure of cyclin-dependent kinase 2 , 1993, Nature.

[24]  L. Johnson.  Protein kinase inhibitors: contributions from structure to clinical compounds , 2009, Quarterly Reviews of Biophysics.

[25]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[26]  Andrea Amadei,et al.  Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. , 2003, Biophysical journal.

[27]  J. Kuriyan,et al.  Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. , 2011, Molecular cell.

[28]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[29]  Grubmüller,et al.  Predicting slow structural transitions in macromolecular systems: Conformational flooding. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[30]  L. Johnson,et al.  The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases , 1999, Nature Cell Biology.

[31]  John Kuriyan,et al.  Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). , 2001, Cancer research.

[32]  Bert L de Groot,et al.  The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study. , 2008, Structure.

[33]  J. Kuriyan,et al.  The Conformational Plasticity of Protein Kinases , 2002, Cell.

[34]  J. Sack.  CRYSTAL STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2-WT) COMPLEX WITH N-[5-[[[5-(1,1-DIMETHYLETHYL)-2-OXAZOLYL] METHYL]THIO]-2-THIAZOLYL]-4-PIPERIDINECARBOXAMIDE (BMS-387032) , 2015 .

[35]  Susan S. Taylor,et al.  Defining the Conserved Internal Architecture of a Protein Kinase , 2010, Biochimica et biophysica acta.

[36]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[37]  Benoît Roux,et al.  Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories , 2009, Proceedings of the National Academy of Sciences.

[38]  G. Superti-Furga,et al.  Structural Basis for the Autoinhibition of c-Abl Tyrosine Kinase , 2003, Cell.