Structural and Functional Roles of Modules in Protein Architecture

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A globular protein consists of compact modules. Module boundaries of proteins are closely correlated with intron positions in the genes encoding the proteins. This fact implies that exon-shuffling in genes is module shuffling in protein level and modules themselves were primitive enzymes. The purpose of this project is to obtain supporting evidences of modules as primitive enzymes and to understand the principle of protein design in nature. Proteins used in this study were barnase that is a bacterial RNase, RNA polymerase II, transcription repressors of procaryotes and ribonuclear proteins in chloroplast, etc. Barnase was decomposed into six modules(M1-M6). Hydrogen bonds were located predominantly within modules in barnase. This fact shows that hydrogen bond formation contributes to determine the compact conformation of modules in barnase architecture. We synthesized modules chemically and carried out experimental study on conformation of each module in solution and its function. Three modules (M2, M3 and M6) were revealed to have an enzymatic function as RNase. This is the first report on the enzymatic function of modules. Our results clearly imply that the modules carried a role as primitive enzymes in early evolution. We also determined the secondary structures of modules M2 and M3 using 2D-NMR and distance geometry. They had the similar secondary structures to those found in intact barnase. Furthermore, we found a barnase-like domain in RNA polymerase II and predicted RNase catalytic function in this region. By other research groups RNase activity of RNA polymerase II was reported. We have suggested that this region might be involved in proof reading, if any. By analysis of module organization in transcription repressors, we found that some of them have two or three helix-turn-helix modules and discussed evolutionary process of repressors through module combinations.