Theoretical Analysis of Protein Search for Targets on DNA Using Discrete-State Stochastic Framework

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Anatoly Kolomeisky of Rice University is supported by an award from the Chemical Theory, Models and Computational Methods Program in the Chemistry Division to develop theoretical approaches to understand how proteins and DNA, the most important molecules in all living systems, interact with each other in supporting fundamental processes of life. Analyzing these processes at the molecular level requires novel theoretical and computational tools that are capable of describing the complexity of living systems. The project involves close collaboration with experimental research groups. High school students, undergraduates and graduate students, and postdoctoral associates participate in the research and receive invaluable training in an important and timely field. The project focuses on developing a fundamental theoretical framework for uncovering microscopic mechanisms of protein search for specific target sites on DNA molecules. The role of various physical and chemical properties of DNA and proteins in these phenomena are tested using a combination of discrete-stochastic models and simulation techniques. The theoretical predictions are tested using single-molecule spectroscopic studies, chemical kinetic experiments and advanced bioinformatics methods. An outreach program developed by Professor Kolomeisky for local high-school students provides the opportunity for them to learn and participate in real scientific work in an academic setting. The broader impacts of this project include a multi-disciplinary training program for young researchers of different levels that will prepare them better for future technological and industrial challenges. In addition, the outreach program promotes advancements in our understanding of cellular processes that may lead to new medical drugs and bio-inspired materials.