Topics in protein and RNA folding and dynamics

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Professor Devarajan (Dave) Thirumalai at the University of Texas Austin is supported by an award from the Chemical Theory, Models and Computational Methods Program in the Chemistry Division and the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences. Professor Thirumalai creates novel, theoretical, computational models in order to address outstanding questions in biologically-related research. For example, there are many proteins that do not adopt well-defined structures, these are referred to as Intrinsically Disordered Proteins (IDPs). IDPs behave like synthetic polymers but still control many biological functions. Professor Thirumalai uses computational models to predict the structure and reactions of IDPs with other IDPs as well as of IDPs with RNA (ribonucleic acid). The characteristics of RNA folding and interactions with unstructured proteins are of specific interest. Finally, the physical mechanisms by which molecular-sized motors, transport molecular "cargo" within cells are not well understood. Professor Thirumalai examines how these motors move and make their deliveries. In addition to the potential for broad impact of this research in biotechnology, Professor Thirumalai is devoted to the training of new generations of students in interdisciplinary research.In the last twenty years, it has become increasingly clear that nearly 40% of the proteome consists of the so-called low complexity IDPs, which are involved in a number of still unknown functions. A major goal of Professor Thirumalai's research is to develop reliable models that can quantitatively predict the structural and dynamical properties of IDPs. This first step is needed in order to understand how they interact with RNA and themselves in producing liquid droplets, which are recognized to be important, but whose properties are largely unknown. Another aspect of Professor Thirumalai's research deals with how RNA molecules fold, especially with the focus on the difficult problem of the mechanisms by which metal cations drive their folding. In addition, Thirumalai is keenly interested in uncovering the principles of RNA-RNA interactions. These structures also form droplets by themselves and in interactions with IDPs. Finally, two-headed molecular motors (Myosin, Dynein, and Kinesin) are largely responsible for transport of cargos in cells. They achieve this complex task by walking along actin and microtubules (MTs) in a preferred direction. One of Professor Thirumalai's major goals is to elucidate, using a combination of sophisticated theory and simulations, the structural basis by which the motors coordinate the two heads in a way such that one head steps forward while the other is bound to actin or MTs. Professor Thirumalai uses theoretical ideas to predict the outcomes of experiments, which include the distribution of motor velocities. These results are critically needed in order to redesign motors for synthetic purposes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.