Protein crystallography and pathogenesis
Developing improved methods for determining crystal structures of proteins and applying these methods to proteins involved in disease.
Crystallography is the primary method for determining the three-dimensional structure of a protein, which provides an essential framework for a detailed understanding of its biochemistry. We focus both on extending the scope and power of the methods used in protein crystallography, and on applying those methods to determine new protein structures. In choosing what to study we focus on proteins involved in pathogenesis and disease, the structures of which can be exploited in the development of new therapies.
We have long been interested in members of the serpin family, most of which undergo an extraordinary conformational change on cleavage by proteases. The structures of two hormone-binding globulins show how they harness this conformational change to deliver thyroxine and cortisol to their sites of action, and recent work has shown how this is modulated physiologically by the effects of temperature. Our structure of angiotensinogen bound to renin indicated that a redox-sensitive disulphide bridge helps to modulate the control of blood pressure. We also have an interest in enzymes mutated in inherited metabolic diseases. The structures we have determined of galactocerebrosidase and iduronate sulphatase are helping to understand how mutations in these enzymes lead to Krabbe disease and Hunter syndrome.
In crystallographic theory, we focus on the understanding of probability distributions relating the structure factors that arise from a diffraction experiment. A detailed understanding of these probability distributions underlies new developments in maximum likelihood methods, which we are implementing in our program Phaser. The current version of Phaser can solve structures by molecular replacement (that is, using the known structures of related proteins), by using the information from single-wavelength anomalous diffraction (SAD), and by a combination of the two. By accounting better for the effects of errors, these new methods can solve structures that evaded earlier approaches.
Chan, W.L., Carrell, R.W., Zhou, A. and Read, R.J. How changes in affinity of corticosteroid-binding globulin modulate free cortisol concentration. J. Clin. Endocrinol. Metab. 98, 3315–3322 (2013).
Deane, J.E., Graham, S.C., Kim, N.N., Stein, P.E., McNair, R., Cachón-González, M.B., Cox, T.M. and Read, R.J. Insights into Krabbe disease from structures of galactocerebrosidase. Proc. Natl. Acad. Sci. USA. 108, 15169–15173 (2011).
Zhou, A., Carrell, R.W., Murphy, M.P., Wei, Z., Yan, Y., Stanley, P.L.D., Stein, P.E., Broughton Pipkin, F. and Read, R.J. A redox switch in angiotensinogen modulates angiotensin release. Nature 468, 108–111 (2010).
Zhou, A.W., Wei, Z., Stanley, P.L.D., Read, R.J., Stein, P.E. and Carrell, R.W. The S-to-R transition of corticosteroid-binding globulin and the mechanism of hormone release. J. Mol. Biol. 380, 244–251 (2008).
Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ & Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nature Methods 12, 127–130 (2015).
DiMaio, F., Terwilliger, T.C., Read, R.J., Wlodawer, A., Oberdorfer, G., Wagner, U., Valkov, E., Alon, A., Fass, D., Axelrod, H.L., Das, D., Vorobiev, S.M., Iwaï, H., Pokkuluri, P.R. and Baker, D. Improving molecular replacement by density- and energy-guided protein structure optimization. Nature 473, 540–543 (2011).
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P.H. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D66, 213–221 (2010).
Qian, B., Raman, S., Das, R., Bradley, P., McCoy, A.J., Read, R.J. and Baker, D. High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259–264 (2007).
McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. and Read, R.J. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007).