Understanding how mutations affect protein structure significantly impacts drug discovery, protein engineering, and the interpretation of individual genome sequences. However, the effects of many mutations, whether they are beneficial or deleterious, cannot be understood from static protein structures alone. This problem is especially significant for mutations that are located far away from active sites and interaction surfaces. If these mutations do not have obvious large stability costs and are remote from functional sites, how can they influence protein function? Rather than affecting the average structure defined by traditional X-ray crystallography, this proposal determines how mutations may change the relative population of alternative conformations. However, identifying alternative conformations and measuring their impact on protein function represents an experimental challenge. To address these problems, this project builds on my methodological advances to reveal alternative conformations by room temperature X-ray crystallography and electron density sampling. I will study the protein-protein interactions of ubiquitin (Ub) in S. cerevisiae as a model to understand how perturbing the relative populations of conformations impacts molecular recognition. Ub is an ideal model to study the importance of alternative conformations because: previous studies have indicated that diverse Ub conformations and poly-Ub linkages mediate distinct functional roles;its remarkable sequence and functional conservation suggests that the populations of alternative conformations will be particularly susceptible to mutation;and it is a small protein that can be comprehensively mutated. Moreover, I have generated preliminary high-resolution room temperature X-ray data that complement previous NMR experiments to define its accessible alternative conformations. Despite the central importance of different Ub conformations for the cell, the general principles of how different Ub conformations are recognized and direct the assembly of poly-Ub chains remain to be elucidated. To determine how mutations can affect the assembly of specific poly-Ub chains, I will monitor how alternative side chain conformations of Ub participate in the catalytic mechanism of the E2 Ubc1. To test how mutations afect Ub interactions in vivo, I will measure a unique phenotypic profile for each Ub mutant. The central role of Ub in proteostasis and its sequence conservation suggest that the principles I uncover will be widely applicable across all eukaryotes. By measuring the impact of mutation on the conformational ensemble, this proposal addresses fundamental biophysical models of interaction specificity, the organization of the Ub-interaction network, and the molecular mechanisms of phenotypic change. Predictions of how mutation can change the relative populations of conformations are especially important as increased sequencing efforts provide the genetic basis for rare genetic diseases. This project will improve our knowledge and understanding of the relationship between mutation, alternative conformations, and phenotype.
This proposal describes new methods for measuring and predicting changes in protein conformations caused by mutation. Knowledge of how protein conformations are perturbed by disease-causing mutations, coupled with methods for restoring proper protein conformations would dramatically expand opportunities to treat disease.
| Mavor, David; Barlow, Kyle A; Asarnow, Daniel et al. (2018) Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open 7: |
| Wall, Michael E; Wolff, Alexander M; Fraser, James S (2018) Bringing diffuse X-ray scattering into focus. Curr Opin Struct Biol 50:109-116 |
| Biel, Justin T; Thompson, Michael C; Cunningham, Christian N et al. (2017) Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure 25:739-749.e3 |
| Thomaston, Jessica L; Woldeyes, Rahel A; Nakane, Takanori et al. (2017) XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proc Natl Acad Sci U S A 114:13357-13362 |
| Russi, Silvia; González, Ana; Kenner, Lillian R et al. (2017) Conformational variation of proteins at room temperature is not dominated by radiation damage. J Synchrotron Radiat 24:73-82 |
| Van Benschoten, Andrew H; Liu, Lin; Gonzalez, Ana et al. (2016) Measuring and modeling diffuse scattering in protein X-ray crystallography. Proc Natl Acad Sci U S A 113:4069-74 |
| Mavor, David; Barlow, Kyle; Thompson, Samuel et al. (2016) Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife 5: |
| Cimermancic, Peter; Weinkam, Patrick; Rettenmaier, T Justin et al. (2016) CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol 428:709-719 |
| Keedy, Daniel A; Fraser, James S; van den Bedem, Henry (2015) Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput Biol 11:e1004507 |
| Urzhumtsev, Alexandre; Afonine, Pavel V; Van Benschoten, Andrew H et al. (2015) From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Crystallogr D Biol Crystallogr 71:1668-83 |
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