Molecular Dynamics Study of Protein-Ligand Interactions

KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ a 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, s. 111-112. ISBN 1425-8153.

Základní údaje

• Originální název: Molecular Dynamics Study of Protein-Ligand Interactions
• Název česky: Studioum interakci protein-ligand pomoci molekulove dynamiky
• Autoři: KŘÍŽ, Zdeněk (203 Česká republika, garant), Michal OTYEPKA (203 Česká republika), Iveta BÁRTOVÁ (203 Česká republika) a Jaroslav KOČA (203 Česká republika).
• Vydání: Wroclaw, Cellular and Molecular Biology Letters, od s. 111-112, 2 s. 2005.
• Nakladatel: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Stať ve sborníku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Česká republika
• Utajení: není předmětem státního či obchodního tajemství
• Kód RIV: RIV/00216224:14310/05:00013838
• Organizační jednotka: Přírodovědecká fakulta
• ISBN: 1425-8153
• Klíčová slova anglicky: Molecular Dynamics; Interaction Energy; Cyclin Dependent Kinase; Olomoucine; Roscovitine; Bohemine
• Štítky: Bohemine, Cyclin dependent kinase, Interaction Energy, molecular dynamics, Olomoucine, roscovitine

Anotace

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.

Anotace česky

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.

Návaznosti

• MSM0021622413, záměr: Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím