Abstract
Time-resolved macromolecular crystallography is one of several “kinetic crystallography” methods (Bourgeois D, Royant A, Curr Opin Struct Biol 15:538–547, 2005; Bourgeois D, Weik M, Crystallogr Rev 15:87–118, 2009). In kinetic crystallography experiments, genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining structures of intermediate states. In time-resolved experiments in particular, short and intense X-ray pulses are used to probe intermediates in real time and at room temperature, in reactions that are initiated synchronously and rapidly in the crystal. We provide here an overview of time-resolved crystallography as implemented today at the BioCARS beamline 14-ID at the Advanced Photon Source (Graber T et al., J Synchrotron Radiat 18:658–670, 2011), with an overview of future directions and challenges.
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References
Arzt S, Campbell JW, Harding MM, Hao Q, Helliwell JR (1999) LSCALE – the new normalization, scaling and absorption correction program in the Daresbury Laue software suite. J Appl Crystallogr 32:554–562
Bourgeois D, Royant A (2005) Advances in kinetic protein crystallography. Curr Opin Struct Biol 15:538–547
Bourgeois D, Weik M (2009) Kinetic protein crystallography: a tool to watch proteins in action. Crystallogr Rev 15:87–118
Bourgeois D, Wagner U, Wulff M (2000) Towards automated Laue data processing: application to the choice of optimal X-ray spectrum. Acta Crystallogr D56:973–985
Campbell JW (1995) LAUEGEN, an X-windows-based program for the processing of Laue diffraction data. J Appl Crystallogr 28:228–236
Corrie JET, Katayama Y, Reid GP, Anson M, Trentham DR, Sweet RM, Moffat K (1992) The development and application of photosensitive caged compounds to aid time-resolved structure determination of macromolecules [and discussion]. Philos Trans R Soc Lond Ser A 340:233–244
Graber T, Anderson S, Brewer H, Chen Y-S, Cho HS, Dashdorj N, Henning RW, Kosheleva I, Macha G, Meron M et al (2011) BioCARS: a synchrotron resource for time-resolved X-ray science. J Synchrotron Radiat 18:658–670
Haldrup K, Harlang T, Christensen M, Dohn A, van Driel TB, Kjær KS, Harrit N, Vibenholt J, Guerin L, Wulff M et al (2011) Bond shortening (1.4 Å) in the singlet and triplet excited states of [Ir2(dimen)4]2+ in solution determined by time-resolved X-ray scattering. Inorg Chem 50:9329–9336
Haldrup K, Vankó G, Gawelda W, Galler A, Doumy G, March AM, Kanter EP, Bordage A, Dohn A, van Driel TB et al (2012) Guest–host Interactions investigated by time-resolved X-ray spectroscopies and scattering at MHz rates: solvation dynamics and photoinduced spin transition in aqueous Fe(bipy)32+. J Phys Chem A 116:9878–9887
Ihee H, Rajagopal S, Srajer V, Pahl R, Anderson S, Schmidt M, Schotte F, Anfinrud PA, Wulff M, Moffat K (2005) Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. Proc Natl Acad Sci U S A 102:7145–7150
Jung YO, Lee JH, Kim J, Schmidt M, Moffat K, Šrajer V, Ihee H (2013) Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nat Chem 5:212–220
Knapp JE, Pahl R, Srajer V, Royer WE (2006) Allosteric action in real time: time-resolved crystallographic studies of a cooperative dimeric hemoglobin. Proc Natl Acad Sci U S A 103:7649–7654
Kostov KS, Moffat K (2011) Cluster analysis of time-dependent crystallographic data: direct identification of time-independent structural intermediates. Biophys J 100:440–449
Rajagopal S, Schmidt M, Anderson S, Ihee H, Moffat K (2004) Analysis of experimental time-resolved crystallographic data by singular value decomposition. Acta Crystallogr D60:860–871
Rajagopal S, Kostov KS, Moffat K (2004) Analytical trap**: extraction of time-independent structures from time-dependent crystallographic data. J Struct Biol 147:211–222
Rajagopal S, Anderson S, Srajer V, Schmidt M, Pahl R, Moffat K (2005) A structural pathway for signaling in the E46Q mutant of photoactive yellow protein. Structure 13:55–63
Ren Z, Bourgeois D, Helliwell JR, Moffat K, Šrajer V, Stoddard BL (1999) Laue crystallography: coming of age. J Synchrotron Radiat 6:891–917
Ren Z, Chan PWY, Moffat K, Pai EF, Royer WE, Šrajer V, Yang X (2013) Resolution of structural heterogeneity in dynamic crystallography. Acta Crystallogr D69:946–959
Schlichting I, Goody RS (1997) Triggering methods in crystallographic enzyme kinetics. Meth Enzymol 277:467–490
Schmidt M (2008) Structure based kinetics by time-resolved X-ray crystallography. In: Braun M, Gilch P, Zinth W (eds) Ultrashort laser pulses in biology and medicine. Springer, Berlin/Heidelberg, pp 201–241
Schmidt M (2013) Mix and inject: reaction initiation by diffusion for time-resolved macromolecular crystallography. Adv Condens Mat Phys. Article ID 167276
Schmidt M, Rajagopal S, Ren Z, Moffat K (2003) Application of singular value decomposition to the analysis of time-resolved macromolecular X-ray data. Biophys J 84:2112–2129
Schmidt M, Pahl R, Srajer V, Anderson S, Ren Z, Ihee H, Rajagopal S, Moffat K (2004) Protein kinetics: structures of intermediates and reaction mechanism from time-resolved X-ray data. Proc Natl Acad Sci U S A 101:4799–4804
Schmidt M, Ihee H, Pahl R, Srajer V (2005) Protein-ligand interaction probed by time-resolved crystallography. Methods Mol Biol 305:115–154
Schmidt M, Nienhaus K, Pahl R, Krasselt A, Anderson S, Parak F, Nienhaus GU, Srajer V (2005) Ligand migration pathway and protein dynamics in myoglobin: a time-resolved crystallographic study on L29W MbCO. Proc Natl Acad Sci U S A 102:11704–11709
Schmidt M, Graber T, Henning R, Srajer V (2010) Five-dimensional crystallography. Acta Crystallogr A66:198–206
Schotte F, Lim M, Jackson TA, Smirnov AV, Soman J, Olson JS, Phillips GN, Wulff M, Anfinrud PA (2003) Watching a protein as it functions with 150-ps time-resolved X-ray crystallography. Science 300:1944–1947
Schotte F, Cho HS, Kaila VRI, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G et al (2012) Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proc Natl Acad Sci U S A 109:19256–19261
Srajer V, Teng T, Ursby T, Pradervand C, Ren Z, Adachi S, Schildkamp W, Bourgeois D, Wulff M, Moffat K (1996) Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography. Science 274:1726–1729
Srajer V, Crosson S, Schmidt M, Key J, Schotte F, Anderson S, Perman B, Ren Z, Teng TY, Bourgeois D et al (2000) Extraction of accurate structure-factor amplitudes from Laue data: wavelength normalization with wiggler and undulator X-ray sources. J Synchrotron Radiat 7:236–244
Srajer V, Ren Z, Teng TY, Schmidt M, Ursby T, Bourgeois D, Pradervand C, Schildkamp W, Wulff M, Moffat K (2001) Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. Biochemistry 40:13802–13815
Terwilliger TC, Berendzen J (1995) Difference refinement: obtaining differences between two related structures. Acta Crystallogr D51:609–618
Ursby T, Bourgeois D (1997) Improved estimation of structure-factor difference amplitudes from poorly accurate data. Acta Crystallogr A53:564–575
Wöhri AB, Katona G, Johansson LC, Fritz E, Malmerberg E, Andersson M, Vincent J, Eklund M, Cammarata M, Wulff M et al (2010) Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction. Science 328:630–633
Yang X, Ren Z, Kuk J, Moffat K (2011) Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome. Nature 479:428–432
Zhao Y, Schmidt M (2009) New software for the singular value decomposition of time-resolved crystallographic data. J Appl Crystallogr 42:734–740
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Šrajer, V. (2014). Time-Resolved Macromolecular Crystallography in Practice at BioCARS, Advanced Photon Source: From Data Collection to Structures of Intermediates. In: Howard, J., Sparkes, H., Raithby, P., Churakov, A. (eds) The Future of Dynamic Structural Science. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-8550-1_17
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