Identifying Principles of Protein Mechanics by Applying Force and Observing Motion - Identifying Principles of Protein Mechanics by Applying Force and Observing Motion. Concerted internal motions are vital for many aspects of protein function, including substrate binding, control of enzyme activity from remote surface sites (allostery), signal transmission across membranes, and catalytic residue positioning. A complex pattern of amino acid interactions, shaped by evolution, guides these motions, while precluding others. We lack accurate models of such propagation of force and motion through protein interiors, and don’t know the mechanical principles these motions reflect. This leads to stark differences between how nature builds enzymes (as dynamic entities) and how we do so (as solid rocks), as well as between how nature controls protein activity (often allosterically) and how drugs are currently designed (often aimed at out-competing native substrate for access to an active site). I have developed a new experimental approach (EF-X), which uses a strong electric field (EF) to apply specific, controllable patterns of force to proteins (within protein crystals), and short X-ray pulses to make time-lapse, atomic-resolution movies of the resulting motions. I describe how we will use EF-X, alongside complementary computational and experimental methods, to address three key scientific challenges: (1) We ask how concerted motions participate in protein function. Potassium ion channels are ideal model systems for this question, as ion permeation is an important example of a dynamic process, and electric fields are in fact the physiological driving force. Initial results show that we can drive and observe ion permeation and mechanical engagement of the ion channel itself. (2) Rational design of allosteric modulators of protein function needs accurate models of force propagation through proteins. Protein tyrosine phosphatase 1B (PTP-1B) is a diabetes drug target for which allosteric inhibitors are sought. Using PTP-1B as a model, we will apply EF-X to map how force are transmitted from distant surface sites to the active site, both to validate the mechanism of a known allosteric inhibitor, and to discover new modes of allosteric control. (3) Rationally designed catalysts remain much less efficient than natural enzymes. Subsequent directed evolution in the lab has shown that evolution readily improves on computational design. We will ask how the mechanical designs of these rationally designed catalysts differ from their evolved variants and from natural enzymes, and use these reagents to show how we can use nature’s mechanical design principles to improve our capabilities for rational protein engineering. Together, these steps greatly advance our ability to quantitatively assess, understand, and control the mechanical basis of normal and pathological protein function.
