Mechanistic investigation of protein translocation on DNA

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The Chemistry of Life Processes Program in the Division of Chemistry is supporting Professor Norbert Reich of University of California Santa Barbara to investigate how cellular proteins locate specific positions on DNA. It is well known that DNA stores genetic information that is transcribed and translated within cells in other biological molecules and that underscores the life of every cell. The "reading and interpretation" of the DNA information require and are modulated by interactions with other molecules in the cell, particularly proteins. The search by proteins of specific locations on DNA is challenging because DNA appears very uniform. This proposal focuses on how the proteins identify specific locations on DNA to bind to and then how they translocate on the DNA to which they are bonded. This work will have a broader impact on scientists' ability to determine how the information stored in DNA is productively interpreted, which is a process common to all cells. It is having further impact on the education of the next generation of scientists, both undergraduate and graduate students, capable of recognizing and addressing scientific issues relevant for human health. Furthermore, Professor Reich and his students actively engage in activities aimed at explaining to broad audiences how science works and what benefits science brings to society.Proteins that act on DNA are responsible for the vast majority of the functions of DNA. The overarching goal of this proposal is to provide a deeper understanding of one such protein, the bacterial DNA adenine methyltransferase (Dam, modifies 5'-GATC-3'). The ability of Dam and related enzymes to carry out multiple cycles of catalysis (processive catalysis) is critical to their biological roles. Yet, current models of processive catalysis are based largely on enzymes faced with entirely different biological challenges and do not account for the characteristics of these enzymes. For example, DNA methyltransferases efficiently modify multiple recognition sites with highly variable intersite distances, and this processivity is modulated by interacting proteins and DNA sequences that flank the target sites. The aims of the research are to investigate the mechanism, regulation, and in vivo importance of processive catalysis by Dam. Several strategies will be pursued to address broadly relevant and unanswered questions of how Dam and other proteins act processively with DNA substrates over intersite distances beyond the ones predicted by conventional models, how some proteins, such as Dam, rely on intra-segment transfer to efficiently move large distances, and what is the mechanism whereby the monomeric Dam modifies both strands of DNA without leaving the DNA.