CAREER:Multiscale Thermodynamic Tools for Probing the Stability and Function of Natively Unfolded Proteins

Tulane University, New Orleans LA

Investigators

Abstract

ABSTRACT Proposal Title: CAREER: Multi-scale Thermodynamic Tools for Probing the Stability and Function of Natively Unfolded Proteins Principal Investigator: Henry S. Ashbaugh Institution: Tulane University Proposal No: CBET-0746955 Natively unfolded proteins are emerging as an important class of biomacromolecules that carry out necessary biological functions despite their lack of well-defined three-dimensional structures, contrary to traditional ideas linking protein shape and function. As for folded proteins, the propensity for a polypeptide to be an intrinsically disordered coil is encoded in its amino acid sequence. To relate lack of structure to function, natively unfolded proteins must first be identified. To date, sequence based correlations for the prediction of native coil stability have been developed only through empirical database analysis with little fundamental basis. Specific functions for these proteins that have been identified include: ligand / DNA binding, cell signaling, the dispersion of cytoskeletal components, and trans-nuclear membrane transport regulation. Unfortunately, a comprehensive theoretical approach for predicting unfolded protein stability and function has been slow to develop. Intellectual Merit. The PIs propose to develop new simulation strategies for modeling the conformational stability of intrinsically disordered proteins and the function of unfolded nuclear pore associated proteins in regulating trans-nuclear membrane transport based on solute size. Initial simulations will focus on the multiscale modeling of natively unfolded proteins and their conformational stability. Foundational molecular simulations will investigate the solution thermodynamics of component amino acids and probe side chain interactions that destabilize peptide secondary structural elements in favor of unstructured coils. Thermodynamic averages determined from these simulations will be coarse-grained to winnow non-essential degrees-of freedom that diminish computational efficiency, while retaining peptide conformational degrees of-freedom and chemical fidelity using new constraint techniques developed in the PIs lab. These coarse-grained models will provide a deeper thermodynamic and structural understanding of empirical predictors for natively unfolded protein stability. Subsequent simulations will take advantage of the techniques developed herein to model natively unfolded protein function. Specifically, the PIs will investigate interactions between unfolded nuclear pore proteins to discriminate between conflicting mechanisms for size selectivity, virtual gating versus the selective phase model. The modeling efforts will be validated against experiments, and results generated will be used as inputs to continuum transport models developed by our collaborators. Broader Impacts. Beyond unstructured bio-macromolecules, the techniques developed in this proposal are general and constitute a fundamentally new approach towards modeling the properties of polymeric and colloidal materials from the bottom-up. Moreover, the engineering of unstructured polypeptides for emerging applications, like the design of facilitated transport membranes, requires a fundamental understanding of how their stability and polymer coil-like properties depend on amino acid sequence. In an effort to revitalize the academic environment of New Orleans, the PI is initiating a service-learning component in the undergraduate curriculum through the introduction of a new course, "Chemistry and Engineering Science in the Community." In this course, Tulane students interact with local public school students, making presentations on the everyday use of the scientific method to arrive at evidence based explanations. Efforts are also being directed towards recruiting undergraduate participation in research through a freshman seminar series and the Louis Stokes Louisiana Alliance for Minority Participation program at Tulane University. It is hoped through the outreach activities to encourage students from diverse groups to consider lifelong careers in science and engineering, while providing a motivated work force for the local chemical industry effected by Hurricane Katrina.