Kernel energy method: application to insulin.

ABSTRACT: In two recent articles a method has been described for calculating the total energy of large molecules. The method is called the kernel energy method (KEM) and requires knowledge of the crystal structure of interest. Calculations are simplified by adopting the approximation that a full molecule could be represented by smaller kernels of atoms. The KEM was illustrated with peptides ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate results. The use of the KEM does not depend upon a particular choice of basis functions and is applicable across quantum computational methods of differing levels of accuracy. These earlier investigations suggested that the KEM could be used to calculate the ab initio quantum mechanical energy of proteins. An application has been made with the protein insulin, composed of 51 aa. Accurate KEM Hartree-Fock energies are obtained for the separate A and B chains of insulin and for their composite structure in the full insulin molecule. A limited basis is used to make possible calculation of the full insulin molecule, which can be used as a standard of accuracy for the KEM calculation. The KEM result obtained is E(KEM) = -21104.7656 a.u. It differs from a full molecule Hartree-Fock result by only 0.000002%. The solvent molecules can be treated effectively as a separate kernel. The KEM result for the fully solvated insulin molecule is E(KEM) = -26275.4127 a.u., differing from the full molecule Hartree-Fock result by as little as 0.000023%.

SUBMITTER: Huang L 

PROVIDER: S-EPMC1200310 | biostudies-literature | 2005 Sep

REPOSITORIES: biostudies-literature