Cyclin-Dependent Protein Kinase-2 Regulation by
Phosphorylation, A Molecular Dynamics Study

D 2003

Cyclin-Dependent Protein Kinase-2 Regulation by Phosphorylation, A Molecular Dynamics Study

BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA

Basic information

Original name

Cyclin-Dependent Protein Kinase-2 Regulation by Phosphorylation, A Molecular Dynamics Study

Authors

BÁRTOVÁ, Iveta (203 Czech Republic, guarantor), Michal OTYEPKA (203 Czech Republic), Zdeněk KŘÍŽ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic)

Edition

2003. vyd. Wroclav, Cellular and Molecular Biology Letters, p. 574-575, 2 pp. 2003

Publisher

3rd International Conference Inhibitors of Protein Kinases

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10403 Physical chemistry

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/03:00009259

Organization unit

Faculty of Science

Keywords in English

molekular dynamics; CDK regulation; cell cycle

Abstract

V originále

Cyclin-dependent kinases (CDKs) are enzymes controlling the eukaryotic cell cycle. CDKs activity is regulated by complex mechanism that include binding to positive regulatory subunit and phosphorylation at positive and/or negative regulatory sites [1]. CDK2 requires for activation binding to cyclinA or cyclinE. CDK2 obtains full activity by phosphorylation of the Thr160 residue in the activation segment (T-loop) [2]. CDKs activity is natively inhibited in several ways, for example, by (de)phosphorylation, interactions with various natural protein inhibitors [3], etc. CDK2 can be negatively regulated by phosphorylation at Tyr15 and (theoretically) at Thr14 [4]. Human CDK2 contains the classical bi-lobal kinase fold [1]. The N-terminal domain is composed mainly of b-sheet, containing five anti-parallel b-strands, and one helix (the C-helix). The larger C-terminal domain is predominantly a-helical, and is linked to the N-terminal domain by a flexible hinge (see picture). The adenosine triphosphate is natural substrate of the CDK2. The ATP-binding site is located in the deep cleft between two lobes. The primary function of CDK is to catalyze the phosphoryl transfer of the g-phosphate of ATP to the hydroxyl of a serine or threonine residues in the protein target substrate [1]. This study compares behavior of monomeric CDK2, CDK2/cyclinA complex, and pT160-CDK2/cyclinA complex (CDK2/cyclinA complex phosphorylated at Thr160) using the molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER software package [5]. The inhibited forms of CDK2 were also studied. The complexes pT14,pT160-CDK2/cyclinA and pY15,pT160-CDK2/cyclinA were prepared by phosphorylation of the pT160-CDK2/cyclinA complex at Thr14 or Tyr15 residues in the Gly-rich loop (residues 11-18). Activation and inhibition of CDK2 by phosphorylation involves various conformational changes, including the reorientation of the phosphate part of the ATP and key residues involved in the ATP binding site. Conformational change of the ATP phosphate in the pT160-CDK2/cyclinA complex is important to form substrate binding site, and is thought to be critical for catalysis. This study is aimed at a detailed description of the molecular mechanism of CDK2 activation and deactivation by phosphorylation on the activatory, and inhibitory sites. Results of conformational behavior of ATP, T-loop, Gly-rich loop and key residues will be presented.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center

Citovat

BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA. Cyclin-Dependent Protein Kinase-2 Regulation by Phosphorylation, A Molecular Dynamics Study. In Cellular and Molecular Biology Letters. 2003rd ed. Wroclav: 3rd International Conference Inhibitors of Protein Kinases, 2003, p. 574-575.

@inproceedings{491006,
   author = {Bártová, Iveta and Otyepka, Michal and Kříž, Zdeněk and Koča, Jaroslav},
   address = {Wroclav},
   booktitle = {Cellular and Molecular Biology Letters},
   edition = {2003},
   keywords = {molekular dynamics; CDK regulation; cell cycle},
   language = {eng},
   location = {Wroclav},
   pages = {574-575},
   publisher = {3rd International Conference Inhibitors of Protein Kinases},
   title = {Cyclin-Dependent Protein Kinase-2 Regulation by Phosphorylation, A Molecular Dynamics Study},
   year = {2003}
}

TY  - JOUR
ID  - 491006
AU  - Bártová, Iveta - Otyepka, Michal - Kříž, Zdeněk - Koča, Jaroslav
PY  - 2003
TI  - Cyclin-Dependent Protein Kinase-2 Regulation by Phosphorylation, A Molecular Dynamics Study
PB  - 3rd International Conference Inhibitors of Protein Kinases
CY  - Wroclav
KW  - molekular dynamics
KW  - CDK regulation
KW  - cell cycle
N2  - Cyclin-dependent kinases (CDKs) are enzymes controlling the eukaryotic cell cycle. CDKs activity is regulated by complex mechanism that include binding to positive regulatory subunit and phosphorylation at positive and/or negative regulatory sites [1]. CDK2 requires for activation binding to cyclinA or cyclinE. CDK2 obtains full activity by phosphorylation of the Thr160 residue in the activation segment (T-loop) [2]. CDKs activity is natively inhibited in several ways, for example, by (de)phosphorylation, interactions with various natural protein inhibitors [3], etc. CDK2 can be negatively regulated by phosphorylation at Tyr15 and (theoretically) at Thr14 [4]. Human CDK2 contains the classical bi-lobal kinase fold [1]. The N-terminal domain is composed mainly of b-sheet, containing five anti-parallel b-strands, and one helix (the C-helix). The larger C-terminal domain is predominantly a-helical, and is linked to the N-terminal domain by a flexible hinge (see picture). The adenosine triphosphate is natural substrate of the CDK2. The ATP-binding site is located in the deep cleft between two lobes. The primary function of CDK is to catalyze the phosphoryl transfer of the g-phosphate of ATP to the hydroxyl of a serine or threonine residues in the protein target substrate [1]. This study compares behavior of monomeric CDK2, CDK2/cyclinA complex, and pT160-CDK2/cyclinA complex (CDK2/cyclinA complex phosphorylated at Thr160) using the molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER software package [5]. The inhibited forms of CDK2 were also studied. The complexes pT14,pT160-CDK2/cyclinA and pY15,pT160-CDK2/cyclinA were prepared by phosphorylation of the pT160-CDK2/cyclinA complex at Thr14 or Tyr15 residues in the Gly-rich loop (residues 11-18). Activation and inhibition of CDK2 by phosphorylation involves various conformational changes, including the reorientation of the phosphate part of the ATP and key residues involved in the ATP binding site. Conformational change of the ATP phosphate in the pT160-CDK2/cyclinA complex is important to form substrate binding site, and is thought to be critical for catalysis. This study is aimed at a detailed description of the molecular mechanism of CDK2 activation and deactivation by phosphorylation on the activatory, and inhibitory sites. Results of conformational behavior of ATP, T-loop, Gly-rich loop and key residues will be presented.
ER  -

BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA. Cyclin-Dependent Protein Kinase-2 Regulation by Phosphorylation, A Molecular Dynamics Study. In \textit{Cellular and Molecular Biology Letters}. 2003rd ed. Wroclav: 3rd International Conference Inhibitors of Protein Kinases, 2003, p.~574-575.

Detailed Information on Publication Record