Our Goal

The Snell group is engaged in methods development that lead to a deeper understanding of biological structure, function, and mechanism. We are predominantly interested in crystallography with an ever increasing focus on complementary techniques then extend and enhance the understanding of dynamics on top of structure. We have ongoing projects in the enhancement of high-throughput crystallization processes, accurate interpretation of metalloprotein structure, and specific structural projects related to cancer therapy and treatment.

Most recent publications

 

Areas of research

The laboratories research has been in the structure and dynamics of macromolecules and methods to obtain that information. Those methods include the development of crystallization methods and analysis, the use of solution scattering, and work in understanding and effective use of cryo-crystallography. Many of the methods developed have been used for studies of biological structure and mechanism.

Structural publications

Crystallization methods and analysis

We developed analysis and visualization tools to improve the interpretation of crystallization screening data and obtain new biological information. Crystallization is often thought of as a lonely topic, the crystal described being that giving the best diffraction data and that being the extent of any experimental information provided. Crystallization screening experiments are a powerful method of sampling a proteins solubility phase space. By mapping this space with outcome, the driving forces of crystallization can be visualized. Similarly outcomes other than a crystal or no crystal provide landmarks on this phase space. Building on that, laying the chemical screen out in a dendogram and overlaying outcomes shows the biochemical information that comes from crystallization screening, as an example allowing us to define mechanism and key metal ions associated with the otherwise functionally unknown structure. We collaborate closely with the high-throughput crystallization screening center in the institute and managed to use a subset of existing crystallization data to predict those samples that would respond well to crystallization attempts in salts versus those that would respond more favorably in PEG based conditions. Historical data can guide future results. We have also developed methods to make high-throughput become high-output. It is easy to perform high-throughput crystallization experiments but it is harder to perform them efficiently. In this aspect of our laboratories research we have aimed to decrease the steps involved in going from an initial crystallization hit to a diffraction pattern. We defined a means to optimize crystallization conditions using only the chemicals causing the initial hit. A simple drop volume ratio coupled with temperature variation allows the closet space to the nucleation and metastable region in the phase diagram to be traversed. If there is not enough sample to replicate or optimize a hit a novel means to extract and mount the crystal was devised. Very simply, using the transparent properties of the plate observation could occur opposite to the extraction. A capillary can remove the crystal and deposit it into a loop. In situ methods have since superseded this approach.

Publications on crystallization methods and analysis

Studies of biological macromolecules in solution

We made use of complementary techniques to explain the difference between tRNA synthesis in prokaryotes and eukaryotes. Small angle X-ray scattering (SAXS) was a science that told you if your sample was banana, pear or apple shaped – the resolution was poor and the results ambiguous. With the advent of modern detectors, improved beams and the computational power to run mathematically intense algorithms SAXS has changed. The combination of SAXS, crystallography and molecular dynamics was used to explain the differences in eukaryotic and prokaryotic tRNA synthesis, specifically the role of appended domains in eukaryotic systems. In doing so we have established the fidelity of SAXS as a technique and developed high-throughput methods to characterize a sample and determine if there are different oligomeric states in solution and crystal. In doing so we established a quality criteria for SAXS data that distinguishes between data that can be treated routinely by standard software from that needing an expert analysis and finally data that is not usable. This opens up a previously subjective analysis for the use of SAXS by a much wider audience and enables its complementary application.

Solution scattering (SAXS) publications

Exploring cryo-cooling

We developed a physical model of disulfide bond damage from irradiation building on practical studies on cryocooling and using a combination of crystallography, spectroscopy and electron paramagnetic resonance. Our laboratory has been interested in the process of cryocooling and the mitigation of radiation damage. Cryocooling causes a cold wave to flow through the crystal cooling it from the side nearest the cold source to the side furthest from it and establishing a gradient across the crystal. Because this is not a process that goes from outside to inside this means that gradients in d-spacing are continuous along the crystal. A microbeam would see good data in all points but a gradual increase in cell parameters as a function of distance from the cold source. The bam itself heats the sample. This can be considerable taking it from below the point where OH radicals are mobile to above it with bad consequences for structural data. Maintaining an air stream to remove heat has a dramatic effect on this process and is a requirement to minimize beam heating in ambient temperatures. The cooling itself may be reversible with large amounts of cryoprotectant and this also favors annealing approaches. Finally one should be aware that as soon as the first image, disulfide bonds are radicalized. There is some hope however because as well as a damage process there is also a repair one – with sufficient dose rate, the damage can be reduced.

Cryo-crystallography publications

Probing and improving crystal quality (growth in space)

We proved that protein crystals have similar if not better physical characteristics to solid state crystals. Solid state physics has used X-ray techniques to characterize crystals for a long time. During the 1990’s crystals were being grown in space to use the reduced convection properties of freefall to minimize convection over the crystal surface. Applying rocking width measurements to crystals grown in space versus those grown on the earth we found that mosaicity was greatly reduced. Unfortunately mosaicity is a long range affect while resolution depends on short range order. Freefall increased physical quality but not diffraction resolution. Topography and reciprocal space mapping confirmed the result and also pointed the way to a means to exploit long-range order for higher signal to noise, i.e. fine slicing or continuous rotation data collection. This is now possible. Interestingly the physical quality of macromolecular crystals was found to be very similar to that of solid state samples. In the extreme case this would suggest an explicit treatment of diffraction rather than the kinematical approximation used currently.

Crystal quality publications
Other studies
  • Lovelace, JJ, Narayan, K, Chik, JK, Bellamy, HD, Snell, EH, Lindberg, U, Schutt, CE and Borgstahl, GEO. Imaging modulated reflections from a semi-crystalline state of profiling:actin. J. Applied Crystallography 37, 327-330 (2004).
  • Ho JX, Snell EH, Sisk RC, Ruble JR, Carter DC, Owens SM, Gibson WM. Stationary crystal diffraction with a monochromatic convergent X-ray source and application for macromolecular crystal data collection. Acta Crystallogr D Biol Crystallogr. 1998 Mar 1;54(Pt 2):200-14.
  • Chayen NE, Boggon TJ, Cassetta A, Deacon A, Gleichmann T, Habash J, Harrop SJ, Helliwell JR, Nieh YP, Peterson MR, Raftery J, Snell EH, Hädener A, Niemann AC, Siddons DP, Stojanoff V, Thompson AW, Ursby T, Wulff M. Trends and challenges in experimental macromolecular crystallography. Q Rev Biophys. 1996.
  • Bradbrook, G, Deacon, A, Habash, J, Helliwell, JR, Helliwell, M, Nieh, YP, Snell, EH, Trapini, S, Thompson, AW, Campbell, JW, Allinson, NM, Moon, K, Ursby, T, and Wulff, M. Time resolved biological and pertubation chemical crystallography: Laue and monochromatic developments. SPIE 2521, 160-177 (1995).
  • Campbell , JW, deacon, A, Habash, J, Helliwell, JR, McSweeney, S, Quan, H, Raftery, J and Snell, E. Electron density maps of lysozyme calculated using synchrotron Laue data comprising singles and deconvoluted multiples.  Bull. Mater. Sci., 17,1, 1-18 (1994).
  • Cassetta, A, Deacon, A, Emmerich, C, Habash, J, Helliwell, JR, McSweeney, S, Snell, E, Thompson, AW and Weisgerber, S. The emergence of the synchrotron Laue method for rapid data collection from protein crystals. Proc. R. Soc. Lond. A, 177-192 (1993).
Patents

Education

  • John Moores University of Liverpool, UK, Physics, B.Sc. Hons (1st).
  • University of Manchester, UK, Chemistry, Ph.D.
  • NASA Biophysics Laboratory, Marshall Space Flight Center, USA, National Research Council Fellow.