Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical Calculations

• Published in: Chemistry : a European journal Vol. 12; no. 16; pp. 4297 - 4304
• Main Authors: Dobeš, Petr, Otyepka, Michal, Strnad, Miroslav, Hobza, Pavel
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 24-05-2006; WILEY‐VCH Verlag
• Subjects: ab initio calculations; Amino Acid Sequence; cyclin-dependent kinase; Cyclin-Dependent Kinase 2 - chemistry; density functional calculations; Humans; Mathematical Computing; Models, Chemical; molecular mechanics; Protein Conformation; Protein Kinase Inhibitors - chemistry; Purines - chemistry; roscovitine; Thermodynamics
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.200501269

The interaction between roscovitine and cyclin‐dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum‐chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug‐cc‐pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled‐cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density‐functional tight‐binding methods covering dispersion energy (DFTB‐D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein–inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.
The total stabilisation energy between roscovitine and cyclin‐dependent kinase 2 (shown here) is very large (66 kcal mol−1) and originates predominantly from dispersion energy. A few amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas many amino acids make a negligible contribution.