Molecular Dynamics Study of Protein-Ligand Interactions
| Authors | |
|---|---|
| Year of publication | 2005 |
| Type | Article in Proceedings |
| Conference | Cellular and Molecular Biology Letters |
| MU Faculty or unit | |
| Citation | |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | Molecular Dynamics; Interaction Energy; Cyclin Dependent Kinase; Olomoucine; Roscovitine; Bohemine |
| Description | 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. |
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