Saturday, October 27, 2007
Ballroom Posters (Greenville Hyatt Regency Hotel)
834

Effect of Protein Environment on pKa of Bovine Carboxypeptidase

Mitchell C. Patterson and Robert W. Zurales. Middle Georgia College, Cochran, GA

Two mechanisms have been proposed for the enzyme carboxypeptidase. In one, a hydroxide ion bound to a zinc ion attacks the carbon of a peptide bond. In the second, a water molecule bound to the zinc ion is displaced by the carbonyl oxygen. Our group previously calculated the pKa of a small model of carboxypeptidase than included a zinc ion bound to a water/hydroxide, two imidazole rings, and an acetate ion. It was found that the water molecule had an increased acidity in nonpolar solvents. We now report our results for a larger model. We obtained atomic coordinates from the Protein Data Bank and included groups that were hydrogen bonded to our smaller system. We added two acid groups (modeled by acetate ions), one arginine side chain, and six water molecules. The bond lengths, angles and dihedral angles for added hydrogen atoms were treated as variables but other bond lengths, angles and dihedral angles were treated as constants. We performed one calculation assuming a water molecule and one assuming a hydroxide ion bound to the zinc ion. The optimization took about two months on a PC. We found that our predicted pKa agreed with our smaller model when the smaller model had water as the solvent. We suggest that water is the species bound to zinc in the enzyme carboxypeptidase.