Stimuli-Responsive Control of Protein-Based Molecular Structure
Abstract
Proteins underlie the broad range of exquisite functions in biology. Proteins and their assemblies define the physical and mechanical properties of cells and tissues, regulate all signaling processes, perform all biosynthetic functions, and are responsible for transducing chemical and electromagnetic energy, among many other roles. The functions of proteins are defined exclusively by the sequences and three-dimensional structures of their polypeptide chains (and associated cofactors). These structures provide active sites capable of catalyzing specific chemical reactions and have surfaces that are complementary to those of other molecules and allow protein-ligand interactions. It is now clear that many native protein functions are regulated by conformational changes in the protein, including those that are modulated by specific stimuli and those that represent thermal fluctuations in the protein structure. Yet, for the approaches now used to develop proteins having novel functions, very few are based on engineering proteins with regulated conformational changes. This gap has its roots in the significant challenges in identifying molecular strategies that can effect defined changes in the motions of protein domains, and in developing syntheses of proteins having the relevant stimuli-responsive dynamic bonding chemistries. These deficiencies in tum define two grand challenges: (1) How does one design reversible covalent chemistries that can be used to regulate the conformations of protein-based structures and (2) How can experimental and computational approaches be combined to design and demonstrate large-scale conformational changes in protein-based structures in response to an applied stimulus. The proposed work will address these grand challenges by combining novel chemistries for regulating conformations in protein-based structures, methods from synthetic biology to prepare protein-based structures having unnatural amino acid residues, analytical methods for characterizing the structures and dynamics of the protein-based structures, and computational methods to both understand stimuli-responsive conformational changes and design structures that undergo such changes. A highly collaborative and multidisciplinary team from Northwestern and University of Chicago will develop new approaches to control the conformational states and dynamics of proteins and protein assemblies using modular, stimuli-responsive chemical switches. The work will begin with the development of chemistries that allow for reversible covalent bonding as well as the methods to incorporate these chemistries into protein structures using codon suppression methods to genetically encode unnatural amino acids into individual proteins or chemical synthesis to create megamolecules by assembling multiple fusion proteins with suitably functionalized covalent linkers. The goal is to use the reversible chemistries to control the conformations of proteins. The project will make extensive use of modeling to design these structures and to identify residues for installation of the reversible chemistries, and will employ a range of sophisticated analytical methods to characterize the structures and dynamics associated with the conformational changes that are regulated by the reversible chemistries. Finally, the proposed work will benefit from a strong and iterative melding of computation, synthesis and characterization to afford protein-based molecules that display structurally well-defined and reversible conformational changes in response to specific stimuli. This work will provide the knowledge base necessary for realizing a broad range of conformationally regulated protein structures. The advances in developing reversible bioorthogonal chemistries, in synthetic biology methods to integrate these chemistries into protein-based structures, md in using these chemistries to control protein conformation will lead to new solutions for many pressing needs in the DoD.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Feb 14, 2019
- Source ID
- W911NF1810200
Entities
People
- Milan Mrksich
Organizations
- Army Contracting Command
- Northwestern University
- United States Army