Molecular Dynamics Study of Protein-Ligand Interactions

KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČA. Molecular Dynamics Study of Protein-Ligand Interactions. In Cellular and Molecular Biology Letters. Wroclaw: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw, 2005. p. 111-112. ISBN 1425-8153.

Basic information

• Original name: Molecular Dynamics Study of Protein-Ligand Interactions
• Name in Czech: Studioum interakci protein-ligand pomoci molekulove dynamiky
• Authors: KŘÍŽ, Zdeněk (203 Czech Republic, guarantor), Michal OTYEPKA (203 Czech Republic), Iveta BÁRTOVÁ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic).
• Edition: Wroclaw, Cellular and Molecular Biology Letters, p. 111-112, 2 pp. 2005.
• Publisher: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10403 Physical chemistry
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• RIV identification code: RIV/00216224:14310/05:00013838
• Organization unit: Faculty of Science
• ISBN: 1425-8153
• Keywords in English: Molecular Dynamics; Interaction Energy; Cyclin Dependent Kinase; Olomoucine; Roscovitine; Bohemine
• Tags: Bohemine, Cyclin dependent kinase, Interaction Energy, molecular dynamics, Olomoucine, roscovitine

Abstract

Detailed knowledge of interactions inside the proteins plays an important role in drug design. Experimental methods such as X-crystallography, NMR spectroscopy and neutron diffraction are typical experimental methods to analyze these interactions at atomic level. These experimental methods can, in some cases, be complemented by molecular modeling methods. The molecular docking combined with flexible conformational search, molecular dynamics and quantum dynamics are the most used modeling methods at this time. Recently, the interactions of solvent molecules with cyclin dependent kinase (CDK2) using molecular dynamics were studied in our laboratory [1]. The previous study was extended by including solvation into interaction energies between protein and ligands acording to ref. [2]. Our molecular dynamics study was performed on complexes of cyclin-dependent kinase CDK2 with natural substrate ATP and with inhibitors roscovitine, olomoucine [3] and olomoucine II [4]. The X-ray crystallographic data was used as starting points for molecular dynamics study performed by the AMBER program suite [5]. The composition of van der Waals and electrostatic interactions between the CDK2 and ligand, including interactions between CDK2, ligand and solvent molecules, were calculated along the MD trajectories.

Abstract (in Czech)

Detailed knowledge of interactions inside the proteins plays an important role in drug design. Experimental methods such as X-crystallography, NMR spectroscopy and neutron diffraction are typical experimental methods to analyze these interactions at atomic level. These experimental methods can, in some cases, be complemented by molecular modeling methods. The molecular docking combined with flexible conformational search, molecular dynamics and quantum dynamics are the most used modeling methods at this time. Recently, the interactions of solvent molecules with cyclin dependent kinase (CDK2) using molecular dynamics were studied in our laboratory [1]. The previous study was extended by including solvation into interaction energies between protein and ligands acording to ref. [2]. Our molecular dynamics study was performed on complexes of cyclin-dependent kinase CDK2 with natural substrate ATP and with inhibitors roscovitine, olomoucine [3] and olomoucine II [4]. The X-ray crystallographic data was used as starting points for molecular dynamics study performed by the AMBER program suite [5]. The composition of van der Waals and electrostatic interactions between the CDK2 and ligand, including interactions between CDK2, ligand and solvent molecules, were calculated along the MD trajectories.

Links

• MSM0021622413, plan (intention): Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment