Theoretical Studies of the Energetics and Dynamics of the Aqueous and Ionic Environment about Proteins: Crystals of Streptomyces Griseus Protease A

Abstract

Many biological macromolecules, including proteins and nucleic acids, exist and operate within an aqueous environment which plays a crucial role both in determining the structural properties of the macromolecule and in its function. An understanding of the nature of the interactions between these molecules and water is therefore important in developing a full picture of the behaviour of macromolecules in biological systems. Furthermore, with the recent development of practical methods to “engineer” changes into the structure of proteins, it has become almost commonplace to synthesise new mutant proteins, with the goal of changing the specificity or catalytic efficiency of enzymes, or the optimal conditions (temperature, pH etc.) under which these enzymes operate by making simple changes in the amino acid sequence of the protein. This protein “engineering” work has given a new impetus to efforts to elucidate the principles which underly the structure and function of macromolecules and, again, an understanding of interactions with solvent constitutes an important part of these efforts. The solvent in biological systems, however, defies description at the molecular level by conventional experimental techniques due to its disordered or semi-ordered nature. To study this solvent one can turn to simulation techniques, including molecular dynamics and Monte Carlo. We have used these techniques to study the energetics and dynamics of both the water and counter ions in the crystal of the protein Streptomyces griseus Protease A (SGPA) (whose structure has been solved to 1.5A resolution with an R-factor of 12.1%).