Analysis of CDK2 active-site hydration: A method to design new inhibitors

KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČA. Analysis of CDK2 active-site hydration: A method to design new inhibitors. Proteins: Structure, Function, and Bioinformatics. Wiley, vol. 55, No 3, p. 258-274. ISSN 0887-3585. 2004.

Basic information

• Original name: Analysis of CDK2 active-site hydration: A method to design new inhibitors
• Name in Czech: Analýza hydratace CDK2 aktivního místa
• Authors: KŘÍŽ, Zdeněk (203 Czech Republic, guarantor), Michal OTYEPKA (203 Czech Republic), Iveta BÁRTOVÁ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic).
• Edition: Proteins: Structure, Function, and Bioinformatics, Wiley, 2004, 0887-3585.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10403 Physical chemistry
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• Impact factor: Impact factor: 4.429
• RIV identification code: RIV/00216224:14310/04:00009962
• Organization unit: Faculty of Science
• UT WoS: 000220980600007
• Keywords in English: cyclin-dependent kinase; ATP; roscovitine; isopentenyladenine; molecular dynamics; hydration of proteins; structural water molecules
• Tags: ATP, cyclin-dependent kinase, hydration of proteins, isopentenyladenine, molecular dynamics, roscovitine, structural water molecules

Abstract

The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine complex simulation, two water molecules that arrange interaction between the inhibitor and the enzyme via an H-bond were observed. Two stable water molecules in the trajectory of the free CDK2 were found that occupy the same position as the nitrogens N3 and N9 of the isopentenyladenine or N1 and N6 nitrogens of the adenosine triphosphate (ATP). The positions of structural water molecules were compared with the positions of substrate polar groups and crystallographic water molecules found in the Brookhaven Protein Data Bank for various CDK2 complexes. It was concluded that tracing tightly bound water molecules may substantially help in designing new inhibitors

Abstract (in Czech)

The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine complex simulation, two water molecules that arrange interaction between the inhibitor and the enzyme via an H-bond were observed. Two stable water molecules in the trajectory of the free CDK2 were found that occupy the same position as the nitrogens N3 and N9 of the isopentenyladenine or N1 and N6 nitrogens of the adenosine triphosphate (ATP). The positions of structural water molecules were compared with the positions of substrate polar groups and crystallographic water molecules found in the Brookhaven Protein Data Bank for various CDK2 complexes. It was concluded that tracing tightly bound water molecules may substantially help in designing new inhibitors

Links

• GV201/98/K041, research and development project: Name: HCILAB - Laboratoř interakcí člověka s počítačem

Investor: Czech Science Foundation, HCILAB - Human-Computer Interactions Laboratory

• MSM 143100005, plan (intention): Name: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Structure-function Relationships and their role in the Metabolism