Study on the Dynamic and Static Effects of Sulfur Atoms on Protein Structure

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In this research project, we tried to thoroughly elucidate the principles that dictate the dynamic behavior and the stability of protein structures by means of several methods from an organic-chemistry point of view. As the result, we could point out for the first time the possibility of the sulfur atoms in proteins playing roles on the functions as well as the evolution.Four sub-projects were simultaneously run in order to approach the unprecedented roles of the sulfur.1. Static roles of sulfur atoms in proteins.2. Dynamic roles of sulfur atoms in proteins.3. Chemical modification of sulfur atoms in proteins.4. Theoretical approach by molecular simulation.In sub-project 1, molecular structures of phospholipase A2 were analyzed by using the coordination data obtained from protein data bank, and four S…O and one S…N nonbonded interactions were characterized. It was found that these weak interactions exist near the active site and have strong correlation with molecular evolution of phosphilipase A2. In sub-project 2, new selenium reagents were applied to oxidative folding experiments of ribonuclease A that has four SS bonds. Significant importance of SS rearrangement processes for formation of the stable native-like structures was clearly demonstrated. In sub-project 3, the transformation reactions from cystine to selenocysteine derivatives were developed. The reaction would be useful for the design and synthesis of various peptides and proteins containing selenium atoms instead of the sulfur atoms. In sub-project 4, a high-speed molecular simulation program was developed based on the single amino acid potential (SAAP) force field. The SAAP potentials in water were shown to be a very important factor for determining folded structures of proteins.