The objective of this project is to develop and use computational methods to analyze and compare the energies of charged groups in proteins; analyze electron and proton transfers in three photosynthetic proteins; and survey the environment of acidic, basic, and redox active groups in a large number protein active sites to characterize electrostatic factors in protein design. This project will test the MCCE (Multi Conformation Continuum Electrostatics) program, developed at CCNY, by calculating pKas for charges added into Staphylococcal nuclease and will develop tools to evaluate proton pathways in proteins. Photosystem I, photosystem II, and bacterial RCs will be compared. These are analogous proteins that use essentially the same cofactors. However, the free energy of cofactor ionization is very different in the different proteins, varying by as much as 18 Kcal/mol. MCCE calculations will determine the contribution of electrostatic interactions to the observed chemistry. The importance of short-range interactions such as hydrogen bonds and long-range interactions with charged residues will be determined. Changes in protonation states and rotamer preferences of surrounding residues will be followed for each reaction. In addition, work will be carried out in collaboration with Batista and Brudvig of Yale to look at the proton coupling to the electron transfer reactions that occur in the Mn cluster of the oxygen-evolving complex of PSII. Several thousand proteins will be studied to determine interactions of charged groups in different protein contexts. Analysis will focus on ligand and substrate binding in protein active sites. The pKas of active site residues will be calculated in a different group of proteins. The pKas and Ems of cofactors (eg. flavins, iron-sulfur clusters) will be determined in diverse proteins. The factors that determine the affinity of common charged groups on substrates or cofactors (eg. phosphate groups) will be determined. Systems where convergent evolution brings the same active site amino acids together in very different proteins will be examined. MCCE will determine the pKas of active site residues to see how the protein generates these values.
MCCE will continue to be freely available and a new completely rewritten version is now being distributed. Other labs are beginning to publish results of calculations using the publicly accessible, early version of the program. In addition, a searchable form of the database analysis of pKas will be posted on the web. A public searchable web site with experimental and calculated pKas and Ems will be developed and maintained. CCNY, a public city university, has an extremely diverse, multi-ethnic student body. The database project has been and will continue to be carried out by a succession of talented undergraduates with some involvement of high school students.