Daniel Barr
B.S. Biochemistry, Arizona State University, 2006
Home Department Chemistry and Biochemistry
Areas of Study Computational Biophysical Chemistry


Background Computer simulations complement experiments by providing detailed, time-resolved information about both the structure and the energetics of the system. I am particularly interested in the coupled protein-folding DNA-binding processes that commonly occur for sequence-specific DNA binding proteins. These processes are currently poorly understood because of the complicated nature of the coupling. One of the chief advantages of computational science over traditional experiments is the ability to decouple the protein-folding and DNA-binding processes in molecular dynamics simulations. These innovative simulations will establish the individual roles of folding and binding in the overall recognition event, quantify the degree of coupling, and identify the specific atomic interactions responsible for the behavior.

I am currently studying the lac repressor protein, a well-documented bacterial system that will provide a paradigm for understanding the binding of sequence-specific DNA-binding proteins. For my research I use large-scale molecular dynamics simulations -- extremely demanding calculations that require high-performance computing. In addition, I am working on the development of new computational methods (e.g. biasing methods and free energy simulation techniques) to advance the understanding of the binding process. Because similar aspects of this molecular recognition have been identified in DNA-binding proteins involved in human disease, this research may also provide critical information for drug design.

lac headpiece bound to its natural operator DNA

lac headpiece bound to non-specific DNA
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Daniel Barr
Arizona State University
Department of Chemistry and Biochemistry
Mail Code 1604
Tempe, AZ 85287

phone: (480) 727-7050
email: daniel.barr
@asu.edu
[Publication] Barr, Daniel A. Synthesis and Characterization of a Model Photosynthetic Antenna. Honors Undergraduate Thesis. April, 2006.