title: Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes.
abstract: Cyclin-dependent kinases (CDKs) and their associated regulatory cyclins are central for timely regulation of cell-cycle progression. They constitute attractive pharmacological targets for development of anticancer therapeutics, since they are frequently deregulated in human cancers and contribute to sustained, uncontrolled tumor proliferation. Characterization of their structural/dynamic features is essential to gain in-depth insight into structure-activity relationships. In addition, the identification of druggable pockets or key intermediate conformations yields potential targets for the development of novel classes of inhibitors. Structural studies of CDK2/cyclin A have provided a wealth of information concerning monomeric/heterodimeric forms of this kinase. There is, however, much less structural information for other CDK/cyclin complexes, including CDK4/cyclin D1, which displays an alternative (open) position of the cyclin partner relative to CDK, contrasting with the closed CDK2/cyclin A conformation. In this study, we carried out normal-mode analysis and enhanced sampling simulations with our recently developed method, molecular dynamics with excited normal modes, to understand the conformational equilibrium on these complexes. Interestingly, the lowest-frequency normal mode computed for each complex described the transition between the open and closed conformations. Exploration of these motions with an explicit-solvent representation using molecular dynamics with excited normal modes confirmed that the closed conformation is the most stable for the CDK2/cyclin A complex, in agreement with their experimentally available structures. On the other hand, we clearly show that an open↔closed equilibrium may exist in CDK4/cyclin D1, with closed conformations resembling that captured for CDK2/cyclin A. Such conformational preferences may result from the distinct distributions of frustrated contacts in each complex. Using the same approach, the putative roles of the Thr(160) phosphoryl group and the T-loop conformation were investigated. These results provide a dynamic view of CDKs revealing intermediate conformations not yet characterized for CDK members other than CDK2, which will be useful for the design of inhibitors targeting critical conformational transitions.
authors.affiliation: Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France. Electronic address: nicolas.floquet@univ-montp1.fr.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Floquet
authors.affiliation: Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
authors.forename: Mauricio G S
authors.initials: MG
authors.lastname: Costa
authors.affiliation: Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
authors.forename: Paulo R
authors.initials: PR
authors.lastname: Batista
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Pedro
authors.initials: P
authors.lastname: Renault
authors.affiliation: Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Paulo M
authors.initials: PM
authors.lastname: Bisch
authors.affiliation: Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Raussin
authors.affiliation: Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Martinez
authors.affiliation: Institut des Biomolécules Max Mousseron (IBMM), Centre National de la Recherche Scientifique UMR 5247, Université de Montpellier, Ecole Normale Supérieure de Chimie de Montpellier, Faculté de Pharmacie, Montpellier, France.
authors.forename: May C
authors.initials: MC
authors.lastname: Morris
authors.affiliation: Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Cachan, France. Electronic address: david.perahia@ens-cachan.fr.
authors.forename: David
authors.initials: D
authors.lastname: Perahia
mesh_terms: D019925:Cyclin A / Q000737:chemistry / Q000378:metabolism*; D019938:Cyclin D1 / Q000737:chemistry / Q000378:metabolism*; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry / Q000378:metabolism*; D051358:Cyclin-Dependent Kinase 4 / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009038:Motion; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
chemical_list: D019925:Cyclin A; D012997:Solvents; D014867:Water; D019938:Cyclin D1; D051357:Cyclin-Dependent Kinase 2; D051358:Cyclin-Dependent Kinase 4