Molecular recognition is one of the most important problems in structural biology. This issue is not just academic, as a clear understanding of the mechanism of recognition will facilitate development of rational design strategies to produce agonistic or antagonistic variants or ligand for clinically important proteins. Although it is clear that the conformational fluctuations (or dynamics) of proteins both affect and are affected by binding, no quantitative, predictive model for the role of dynamics in recognition is available. As a model system, this project investigates the nature and energetics of the native stage conformational ensemble of the SEM5 Sh3 domain from C. elegans.
Our Specific Aims are: 1) experimental characterization of its region stability and dynamics, using NMR-detected hydrogen exchange and 15N relaxation; 2) determining the cooperativity of the conformational fluctuations, by measuring the effects of ALA to GLY mutations at positions showing differential stability in Aim 1; 3) correlating the mutations' effects on stability with those on ligand binding, to provide a quantitative description for the role of fluctuations in the recognition process; and 4) structural thermodynamic analysis of selected mutants to determine the energy of the different states, by solving the mutants' solution structures and modeling their flexible regions to the observed changes in their NOE constraints. These experiments are an essential step toward our long-term goal, a structure-based model for quantitatively describing the role of conformational heterogeneity in molecular recognition.
| Saavedra, Harry G; Wrabl, James O; Anderson, Jeremy A et al. (2018) Dynamic allostery can drive cold adaptation in enzymes. Nature 558:324-328 |
| Chin, Alexander F; Hilser, Vincent J (2017) What's in an Average? An Ensemble View of Phosphorylation Effects. Structure 25:573-575 |
| Li, Jing; White, Jordan T; Saavedra, Harry et al. (2017) Genetically tunable frustration controls allostery in an intrinsically disordered transcription factor. Elife 6: |
| White, Jordan T; Toptygin, Dmitri; Cohen, Randy et al. (2017) Structural Stability of the Coiled-Coil Domain of Tumor Susceptibility Gene (TSG)-101. Biochemistry 56:4646-4655 |
| Hoffmann, Jordan; Wrabl, James O; Hilser, Vincent J (2016) The role of negative selection in protein evolution revealed through the energetics of the native state ensemble. Proteins 84:435-47 |
| Motlagh, Hesam N; Toptygin, Dmitri; Kaiser, Christian M et al. (2016) Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates. Biophys J 110:1280-90 |
| Toptygin, Dmitri; Chin, Alexander F; Hilser, Vincent J (2015) Effect of Diffusion on Resonance Energy Transfer Rate Distributions: Implications for Distance Measurements. J Phys Chem B 119:12603-22 |
| Hilser, Vincent J; Anderson, Jeremy A; Motlagh, Hesam N (2015) Allostery vs. ""allokairy"". Proc Natl Acad Sci U S A 112:11430-1 |
| Choi, Jay H; Laurent, Abigail H; Hilser, Vincent J et al. (2015) Design of protein switches based on an ensemble model of allostery. Nat Commun 6:6968 |
| Martens, Andrew T; Taylor, James; Hilser, Vincent J (2015) Ribosome A and P sites revealed by length analysis of ribosome profiling data. Nucleic Acids Res 43:3680-7 |
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