Investigation of electrostatics in a hydogen bond network

Abstract

Proteins are important for many reasons -- chief among them are that many enzymes are proteins. Without enzymes, most biochemical reactions would not take place. Comparisons between proteins or amino acid sequences that differ only slightly from one another can provide estimates of energy gained or lost as a result of those differences. In this project, the use of site-directed mutagenesis will allow us to introduce minor changes into a protein. The differences in the conformation stability of the wild type and mutant proteins permit us to study the influence of a specific amino acid's side chain to its environment. In a protein, there are several interactions that can be studied. Our particular area of focus on this project is electrostatics. We work with one protein in particular, HPr, which is isolated from two different bacterial sources. The two proteins differ with respect to amino acid sequence, yet are able to retain a singular function. Similarly, the region of interest, although defined by different amino acids, still retains comparable folding patterns between the proteins. In either protein, a negatively charged amino acid is fixed in position by its interaction with other neighboring amino acids. We believe that the amino acid is important in stabilizing the area via electrostatic interactions between both negatively and positively charged amino acids. We will test this hypothesis by making several mutant proteins and measuring their conformational stability. The mutant D30T bsHPr showed a decrease in energy of ~1.0 kcal/mol. An attempt to determine the pKa of the wild type residue was unsuccessful because studies could not be conducted at low pH values. D72K bsHPr was also made. This was a difficult protein to purify; studies that were done on it were inconclusive. In general, it can be concluded that the amino acid residues within the wild type form stabilizing interactions. The absence of charged residues at key locations within a defined region lead to decreases in energy for the protein.