Topics in Protein Folding and Dynamics

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Devarajan Thirumalai of University of Maryland, College Park is funded by the Theoretical and Computational Chemistry program and co-funded by the Molecular Biophysics program of the Division of Molecular and Cellular Biosciences to build on on his prior NSF-supported work. His research provides conceptual frameworks for understanding folding in confined volumes, RNA folding, and chaperonin-mediated folding. The research team is focusing their efforts in three areas. (1) In the first area, the use of model systems and peptides and molecular dynamics to decipher the unfolding action of denaturants is being explored. (2) In the second project, the team is assessing the effects of confinement in nanopores and crowding, while carrying out calculations that probe the thermodynamics and kinetics of protein folding using minimal off-lattice models. (3) Finally, using off-lattice models for the substrate proteins and a coarse-grained description for the GroEL cavity the PI is addressing the question of how the GroEL nanomachine aids in the folding of a large number of structurally unrelated proteins. The work is expected to have a broad impact by contributing to the deciphering of general principles that govern the function of biomolecules.