Link between dynamics and function in single and multi-subunit enzymes

Title of dissertation: LINK BETWEEN DYNAMICS AND FUNCTION IN SINGLE AND MULTI-SUBUNIT ENZYMES Jie Chen, Doctor of Philosophy, 2010 Dissertation directed by: Professor Devarajan Thirumalai Biophysics Program Institute for Physical Science and Technology Biopolymers, such as proteins and DNA, are polymers whose three-dimensional conformations define their biological functions. Current emphasis on structures has greatly advanced our understanding of the functions of biopolymers. However, there is a need to understand the deeper link between biopolymer dynamics and function, because in water and under cellular conditions, everything that biopolymers do can be understood in terms of “the jigglings and wigglings of atoms”. These motions arise from thermal noise in the solvent and due to intrinsic motion of the enzymes. In biological systems, the motions are often highly regulated to ensure that cellular processes are executed over the required time scales. For enzymes, which are essentially proteins that catalyze chemical reactions or generate mechanical work, conformational fluctuations are coupled at various stages through interactions with ligands during the catalytic cycle. We have studied two different enzymes, dihydrofolate reductase (DHFR), which catalyzes reduction of dihydrofolate to tetrahydrofolate, and RNA polymerase (RNAP from bacteria and Pol II from yeast), which is responsible for RNA synthesis using DNA as a template. In order to study the link between dynamics and function we have developed new methods and extended a variety of computational techniques. For DHFR, we use both evolutionary imprints (SCA) and structure-based perturbation method (SPM) to extract a network of residues that facilitate the transitions between two distinct conformational states (closed and occluded states). The transition kinetics and pathways connecting the closed and occluded states are described using Brownian dynamics (BD) simulation. We found the sliding motion of Met20 loop across helix 2 is involved in the forward and reverse transitions between the closed and occluded states. We also found that cross-linking M16-G121 inhibits both the forward and the reverse transitions. In addition, we showed the transition states of these transitions are broad and resemble high energy states. For RNAP, we focus on the conformational changes of RNAP and DNA in promoter melting process. Using BD, we show that DNA conformation changes in promoter melting occur in three steps. We also show that internal dynamics of RNAP is relevant to facilitate the bending of DNA. For Pol II, the structural transitions between two initiation conformational states and between initiation state and elongation state are studied using SPM and BD. We determine the structural units that regulate structural transitions and describe the transition kinetics. The combination of three different methods, SCA, SPM and BD, provide results that are in accord with many experiments. Moreover, our description of the detailed structural transitions in these enzymes lead to new insights and testable predictions in these extraordinarily important enzyme functions. Link between dynamics and function in single and multi-subunit enzymes