title: Determining the Functions of HIV-1 Tat and a Second Magnesium Ion in the CDK9/Cyclin T1 Complex: A Molecular Dynamics Simulation Study.
abstract: The current paradigm of cyclin-dependent kinase (CDK) regulation based on the well-established CDK2 has been recently expanded. The determination of CDK9 crystal structures suggests the requirement of an additional regulatory protein, such as human immunodeficiency virus type 1 (HIV-1) Tat, to exert its physiological functions. In most kinases, the exact number and roles of the cofactor metal ions remain unappreciated, and the repertoire has thus gained increasing attention recently. Here, molecular dynamics (MD) simulations were implemented on CDK9 to explore the functional roles of HIV-1 Tat and the second Mg2+ ion at site 1 (Mg12+). The simulations unveiled that binding of HIV-1 Tat to CDK9 not only stabilized hydrogen bonds (H-bonds) between ATP and hinge residues Asp104 and Cys106, as well as between ATP and invariant Lys48, but also facilitated the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop. By contrast, these H-bonds cannot be formed in CDK9 owing to the absence of HIV-1 Tat. MD simulations further revealed that the Mg12+ ion, coupled with the Mg22+ ion, anchored to the triphosphate moiety of ATP in its catalytic competent conformation. This observation indicates the requirement of the Mg12+ ion for CDK9 to realize its function. Overall, the introduction of HIV-1 Tat and Mg12+ ion resulted in the active site architectural characteristics of phosphorylated CDK9. These data highlighted the functional roles of HIV-1 Tat and Mg12+ ion in the regulation of CDK9 activity, which contributes an important complementary understanding of CDK molecular underpinnings.
authors.affiliation: Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China.
authors.forename: Hai-Xiao
authors.initials: HX
authors.lastname: Jin
authors.affiliation: Department of Pharmacy, National University of Singapore, Singapore, Singapore.
authors.forename: Mei-Lin
authors.initials: ML
authors.lastname: Go
authors.affiliation: Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Yin
authors.affiliation: Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China.
authors.forename: Xiao-Ting
authors.initials: XT
authors.lastname: Qiu
authors.affiliation: Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Applied Marine Biotechnology Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China.
authors.forename: Xiao-Jun
authors.initials: XJ
authors.lastname: Yan
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001665:Binding Sites; D056906:Cyclin T / Q000737:chemistry / Q000378:metabolism*; D042863:Cyclin-Dependent Kinase 9 / Q000737:chemistry / Q000378:metabolism*; D015497:HIV-1 / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D008274:Magnesium / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D046912:Multiprotein Complexes / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000378:metabolism*
chemical_list: C503684:CCNT1 protein, human; D056906:Cyclin T; D046912:Multiprotein Complexes; D054322:tat Gene Products, Human Immunodeficiency Virus; D000255:Adenosine Triphosphate; C467969:CDK9 protein, human; D042863:Cyclin-Dependent Kinase 9; D008274:Magnesium