Arjan Van Der Vaart of Arizona State University is supported by a CAREER award from the Theoretical and Computational Chemistry program to carry out research on the development of computational methods for simulating conformational binding dynamics of sequence-specific DNA-binding (SSDB) proteins. Molecular dynamics simulations are being carried out to study the coupled DNA binding - protein folding (or unfolding) - of sequence-specific DNA-binding proteins. The studies are focusing on the lac repressor headpiece which partially folds and the Ets-1 transcription factor which partially unfolds upon DNA binding. New analysis methods and biasing algorithms are being developed along with a coarse-grined model to compute transition pathways. The results of these simulations are compared to experiment and specific mutation experiments are then suggested. The aim of the project is to elucidate the key step in the mechanism by which SSDB proteins trigger major cellular events.
The work is having a broad impact on our understanding of important biochemical events. It is having a further impact through the participation of Van Der Vaart in a research immersion program for high school teachers which aims to develop teaching modules for high school students. Van Der Vaart is further broadening the impact of his project by recruiting and mentoring students from under-represented minority groups and involving them in summer undergraduate research projects.
The binding of DNA-binding proteins is often characterized by dramatic conformational changes involving partial protein folding and/or DNA bending or kinking. This project used molecular simulations to rationalize the conformational behavior, to elucidate the triggers for the motion, and to establish the order of events for a number of representative DNA-binding proteins. Intellectual merit: Simulation studies elucidated important aspects of the DNA-binding mechanism of the Ets-1 transcription factor, the lac repressor headpiece, and the E2, Sac7d, and RevErbα proteins. In particular, simulations resolved the allosteric network by which the presence of DNA is transmitted to the site of unfolding in Ets-1. Simulations also explained the DNA bending angle observed in the lac repressor headpiece complex, the DNA binding affinities and selectivity of the E2 protein, and the sequence of binding events for Sac7d and RevErbα. A new, generally applicable analysis method based on the information theory measure of transfer entropy was developed to analyze how allosteric signals are propagated in the system, and a highly efficient method was developed to quantify the energetic cost of DNA deformations by computer simulations. This latter method was used to quantify the flexibility of normal as well as methylated and oxidatively damaged DNA, in order to help assess factors proteins might exploit for selective binding. Broader impacts: Four postdoctoral researchers, five graduate and twenty-one undergraduate students were trained in computational biophysical chemistry as part of this project. A tutorial website for a popular molecular simulation program was developed, and day-long computational workshops for undergraduate students at four different institutions were given. Computational labs were introduced in the undergraduate physical chemistry curriculum to help illustrate and visualize difficult concepts.
