Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.
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.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic.
Petr
P
Dobes
Michal
M
Otyepka
Miroslav
M
Strnad
Pavel
P
Hobza
D000595:Amino Acid Sequence; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry*; D006801:Humans; D008432:Mathematical Computing; D008956:Models, Chemical; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D011687:Purines / Q000737:chemistry*; D000077546:Roscovitine; D013816:Thermodynamics
D047428:Protein Kinase Inhibitors; D011687:Purines; D000077546:Roscovitine; D051357:Cyclin-Dependent Kinase 2