The ability to visualize the dynamics of protein and RNA molecules and the associated complexes, one at a time using single molecule methods, is dramatically altering our view of their functions and giving us a glimpse of what is possible in terms of redesigning their functions and to target speci?c regions for drug or ligand binding. To realize the full potential of single molecule pulling experiments one has to complement them with computations that not only produce results consistent with measurements but also can make testable predictions. In this computational and theoretical research proposal, with synergistic experimental research collabora- tions, we are advancing new ideas to use mechanical force as a variable, as done in single molecule force spectroscopy (SMFS), to study a set of complex problems of direct relevance to biology. The overarching goal is to push the frontiers of what is achievable using computations in the context of speci?c problems in biophysics, and which in turn will complement experiments. The three speci?c aims are: (1) SMFS for hidden states: Using force as a perturbing agent we propose ways to characterize the dynamics of functionally rele- vant but sparsely populated excited states in proteins. Applications to PDZ domain as well as two structurally similar proteins (PrPC and Doppel ) but with different disease causing mechanisms are intended to illustrate the uses of force in the context of folding and the propensity to aggregate. (2) Nucleosome under tension: The packaging unit of Chromatin is the Nucleosome Core Particle (NCP), a nucleoprotein, contains about 147 base pairs of DNA wound around the highly conserved histone octamer. Understanding the sequence dependence dynamics of the DNA is crucial to deciphering gene expression at the molecular level. Novel com- putational methods are proposed to understand the surprising breakage of symmetry in the NCP dynamics in molecular terms based on the DNA sequence. (3) Using force to monitor Hsp90 assembly: The molecular chaperone Hsp90, a member of the heat shock protein family, has diverse (sometimes) con?icting roles in eukaryotic cellular functions. Spurred by the recent Laser Optical Tweezer pulling experiments we propose ways to systematically study the assembly of Hsp90 containing three independent folding domains. The proposed computational studies conducted in close collaboration with two leading experimentalists will greatly advance our understanding of the dynamics and assembly of large protein complexes. The meth- ods to be developed will signi?cantly in?uence the ?eld, and will be of considerable use in enhancing our understanding of large systems responsible for a variety of diverse cellular functions.
Understanding the diverse behavior of proteins, nucleic acids, and their complexes at the single molecule level holds the key to our ability to design and manipulate their functions. The computational projects are intended to further the scope of single molecule pulling experiments, which are providing a wealth of precise data on large systems of great importance in biology. Our results will be of greatly aid in the design of ligands that can alter the dynamics of speci?c region of proteins and their complexes for use in biomedical applications.
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