title: All-atomic molecular dynamic studies of human CDK8: insight into the A-loop, point mutations and binding with its partner CycC.
abstract: The Mediator, a conserved multisubunit protein complex in eukaryotic organisms, regulates gene expression by bridging sequence-specific DNA-binding transcription factors to the general RNA polymerase II machinery. In yeast, Mediator complex is organized in three core modules (head, middle and tail) and a separable 'CDK8 submodule' consisting of four subunits including Cyclin-dependent kinase CDK8 (CDK8), Cyclin C (CycC), MED12, and MED13. The 3-D structure of human CDK8-CycC complex has been recently experimentally determined. To take advantage of this structure and the improved theoretical calculation methods, we have performed molecular dynamic simulations to study dynamics of CDK8 and two CDK8 point mutations (D173A and D189N), which have been identified in human cancers, with and without full length of the A-loop, as well as the binding between CDK8 and CycC. We found that CDK8 structure gradually loses two helical structures during the 50-ns molecular dynamic simulation, likely due to the presence of the full-length A-loop. In addition, our studies showed the hydrogen bond occupation of the CDK8 A-loop increases during the first 20-ns MD simulation and stays stable during the later 30-ns MD simulation. Four residues in the A-loop of CDK8 have high hydrogen bond occupation, while the rest residues have low or no hydrogen bond occupation. The hydrogen bond dynamic study of the A-loop residues exhibits three types of changes: increasing, decreasing, and stable. Furthermore, the 3-D structures of CDK8 point mutations D173A, D189N, T196A and T196D have been built by molecular modeling and further investigated by 50-ns molecular dynamic simulations. D173A has the highest average potential energy, while T196D has the lowest average potential energy, indicating that T196D is the most stable structure. Finally, we calculated theoretical binding energy of CDK8 and CycC by MM/PBSA and MM/GBSA methods, and the negative values obtained from both methods demonstrate stability of CDK8-CycC complex. Taken together, these analyses will improve our understanding of the exact functions of CDK8 and the interaction with its partner CycC.
authors.affiliation: Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA. Electronic address: wxx6941@louisiana.edu.
authors.forename: Wu
authors.initials: W
authors.lastname: Xu
authors.affiliation: Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Amire-Brahimi
authors.affiliation: Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA.
authors.forename: Xiao-Jun
authors.initials: XJ
authors.lastname: Xie
authors.affiliation: Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
authors.forename: Liying
authors.initials: L
authors.lastname: Huang
authors.affiliation: Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA. Electronic address: ji@medicine.tamhsc.edu.
authors.forename: Jun-Yuan
authors.initials: JY
authors.lastname: Ji
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000595:Amino Acid Sequence; D001216:Asparagine / Q000737:chemistry*; D001224:Aspartic Acid / Q000737:chemistry*; D001665:Binding Sites; D056745:Cyclin C / Q000737:chemistry* / Q000235:genetics; D056850:Cyclin-Dependent Kinase 8 / Q000737:chemistry* / Q000235:genetics; D015870:Gene Expression; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D017354:Point Mutation; D011485:Protein Binding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013816:Thermodynamics
chemical_list: C503674:CCNC protein, human; D056745:Cyclin C; D001224:Aspartic Acid; D001216:Asparagine; C095686:CDK8 protein, human; D056850:Cyclin-Dependent Kinase 8; D000409:Alanine
keywords: CDK8; CycC; Molecular dynamics
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