Michael D. Brenowitz, Ph.D.

Cellular Regulation by Reversible Macromolecular
Assembly and Association Reactions

Biology is a dynamic process. Among the myriad array of reversible association reactions that constitute life, small molecules bind to proteins, proteins self-associate and bind to other proteins and nucleic acids and nucleic acids fold and bind to each other in elaborate processing, signaling and regulatory cascades. What is common to these processes is the physical chemistry that underlies these interactions. For example, electrostatic interactions mediate both the binding of proteins to DNA and the folding of RNA. Proteins that mimic the electrostatic character of DNA may competitively regulate DNA binding by other proteins. Our laboratory seeks answers to a variety of questions related to the structure – function relationships that govern macromolecular function by combining quantitative analysis with innovative approaches. The projects that we seek to pursue going forward are summarized below:

• How does RNA fold? Although RNA is an informational intermediate in the central dogma, much of its biological function requires it to fold into unique three-dimensional structures. However, large RNA molecules often navigate tortuous pathways to achieve their biologically active structure. Our group uses novel kinetics techniques to follow the time evolution of RNA structure with single nucleotide spatial and millisecond time resolution in order to illuminate RNA folding pathways.
• Our interest in RNA structure and folding embraces RNA aptamers, small RNA molecules selected to bind to proteins and cells with high affinity as potential diagnostic tools or therapeutics. We are studying the structure and thermodynamics of aptamer – protein complexes in order to illuminate the principals of aptamer binding and perhaps build biologically efficacious aptamers.
• The longest running programmatic theme of our laboratory is the study of the mechanisms by which proteins recognize and bind specific sequences of DNA. We have turned our attention to proteins involved in epigenetic regulation exploring the biophysics of an epigenetic regulatory methyl-CpG binding protein.
• Our interest in developing better tools with which novel biological questions can be answered is focused on ‘hydroxyl radical footprinting’. A novel solid sate matrix to generate hydroxyl radicals is the enabling technology for a new program in high throughput analysis of macromolecular structure, folding and assembly.