Application of the PM6 method to modeling proteins

• Published in: Journal of molecular modeling Vol. 15; no. 7; pp. 765 - 805
• Main Author: Stewart, James J. P.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.07.2009
• Subjects: Algorithms; Binding Sites; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Chemistry, Organic - methods; Collagen - chemistry; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Crystallography, X-Ray; Green Fluorescent Proteins - chemistry; Metalloproteins - chemistry; Models, Molecular; Molecular Medicine; Original Paper; Protein Structure, Quaternary; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins - chemistry; Reproducibility of Results; Theoretical and Computational Chemistry; Proteins; Young’s modulus; MOZYME; PM6; Salt bridge; Metalloenzymes; Hydrogen bonding
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-008-0420-y

The applicability of the newly developed PM6 method for modeling proteins is investigated. In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent field (SCF) equations was replaced with a localized molecular orbital method (MOZYME), Baker’s Eigenfollowing technique for geometry optimization was replaced with the L-BFGS function minimizer, and some of the integrals used in the NDDO set of approximations were replaced with point-charge and polarization functions. The resulting method was used in the unconstrained geometry optimization of 45 proteins ranging in size from a simple nonapeptide of 244 atoms to an importin consisting of 14,566 atoms. For most systems, PM6 gave structures in good agreement with the reported X-ray structures. Some derived properties, such as pKa and bulk elastic modulus, were also calculated. The applicability of PM6 to model transition states was investigated by simulating a hypothetical reaction step in the chymotrypsin-catalyzed hydrolysis of a peptide bond. A proposed technique for generating accurate protein geometries, starting with X-ray structures, was examined.