Molecular Dynamics Simulations of CDK2/ATP Complex

D 2002

Molecular Dynamics Simulations of CDK2/ATP Complex

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

Basic information

Original name

Molecular Dynamics Simulations of CDK2/ATP Complex

Authors

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

Edition

Praha, Chemicke listy 6, p. 427-427, 2002

Publisher

54. Sjezd chemickych spolecnosti

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10610 Biophysics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/02:00007235

Organization unit

Faculty of Science

Keywords in English

Cyclin dependent kinase; ATP; Molecular dynamics

Abstract

V originále

Cyclin-dependent kinases (CDKs) are enzymes controlling the eukaryotic cell cycle. This is tightly regulated by the activity of CDKs. A CDK enzyme consists typically of a catalytic subunit, kinase, and a regulatory subunit, cyclin. CDKs are inactive as monomers. For activation requires binding to cyclins. Full activity CDKs obtain at binding with adenosine triphosphate (ATP) by phosphorylation of a threonine residue in the CDK [3]. Activity of these enzymes are inhibited in several ways, for examples, (de)phosphorylation, interaction with various natural protein inhibitors. This work describes behavior of CDK2/ATP complex using the molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER software package. Results of conformational behavior of ATP in CDK2/ATP complex will be presented. The interaction energies calculated between ATP and amino acids in the active site show the residues that are important for substrate recognition. The binding energie of ATP were calculated using MM-PB(GB)SA analysis. The results will be compared with binding energies of two inhibitors (roscovitine and isopentenyladenine) obtained from previous molecular dynamics simulations.

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

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

Citovat

BÁRTOVÁ, Iveta, Zdeněk KŘÍŽ, Michal OTYEPKA and Jaroslav KOČA. Molecular Dynamics Simulations of CDK2/ATP Complex. In Chemicke listy 6. Praha: 54. Sjezd chemickych spolecnosti, 2002, p. 427.

@inproceedings{483323,
   author = {Bártová, Iveta and Kříž, Zdeněk and Otyepka, Michal and Koča, Jaroslav},
   address = {Praha},
   booktitle = {Chemicke listy 6},
   keywords = {Cyclin dependent kinase; ATP; Molecular dynamics},
   language = {eng},
   location = {Praha},
   pages = {427-427},
   publisher = {54. Sjezd chemickych spolecnosti},
   title = {Molecular Dynamics Simulations of CDK2/ATP Complex},
   year = {2002}
}

TY  - JOUR
ID  - 483323
AU  - Bártová, Iveta - Kříž, Zdeněk - Otyepka, Michal - Koča, Jaroslav
PY  - 2002
TI  - Molecular Dynamics Simulations of CDK2/ATP Complex
PB  - 54. Sjezd chemickych spolecnosti
CY  - Praha
KW  - Cyclin dependent kinase
KW  - ATP
KW  - Molecular dynamics
N2  - Cyclin-dependent kinases (CDKs) are enzymes controlling the eukaryotic cell cycle. This is tightly regulated by the activity of CDKs. A CDK enzyme consists typically of a catalytic subunit, kinase, and a regulatory subunit, cyclin. CDKs are inactive as monomers. For activation requires binding to cyclins. Full activity CDKs obtain at binding with adenosine triphosphate (ATP) by phosphorylation of a threonine residue in the CDK [3]. Activity of these enzymes are inhibited in several ways, for examples, (de)phosphorylation, interaction with various natural protein inhibitors. This work describes behavior of CDK2/ATP complex using the molecular dynamics simulations with the Cornell et al. force field as implemented in the AMBER software package. Results of conformational behavior of ATP in CDK2/ATP complex will be presented. The interaction energies calculated between ATP and amino acids in the active site show the residues that are important for substrate recognition. The binding energie of ATP were calculated using MM-PB(GB)SA analysis. The results will be compared with binding energies of two inhibitors (roscovitine and isopentenyladenine) obtained from previous molecular dynamics simulations.
ER  -

BÁRTOVÁ, Iveta, Zdeněk KŘÍŽ, Michal OTYEPKA and Jaroslav KOČA. Molecular Dynamics Simulations of CDK2/ATP Complex. In \textit{Chemicke listy 6}. Praha: 54. Sjezd chemickych spolecnosti, 2002, p.~427.

Detailed Information on Publication Record