Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography

Current Opinion in Structural Biology

Volumn 17, Issue 5, 2007, Pages 580-586

  De la Mora Rey, Teresa ^a   Wilmot, Carrie M ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; CRYSTALLIZATION; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; FLUORESCENCE SPECTROSCOPY; INFRARED SPECTROSCOPY; MICROSPECTROPHOTOMETRY; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; RADIATION INJURY; RAMAN SPECTROMETRY; REVIEW; ROENTGEN SPECTROSCOPY; SPECTRUM; ULTRAVIOLET SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; KINETICS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; MULTIENZYME COMPLEXES; MULTIPROTEIN COMPLEXES; PHOTORECEPTORS, MICROBIAL; SPECTROPHOTOMETRY;

EID: 35648929906     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.09.005     Document Type: Review

References (43)

1. Pearson A.R., Mozzarelli A., and Rossi G.L. Microspectrophotometry for structural enzymology. Curr Opin Struct Biol 14 (2004) 656-662. Excellent beginners review on single crystal microspectrophotometry.
2. Klink B.U., Goody R.S., and Scheidig A.J. A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with X-ray diffraction. Biophys J 91 (2006) 981-992
3. Bourgeois D., and Royant A. Advances in kinetic protein crystallography. Curr Opin Struct Biol 15 (2005) 538-547. An inclusive review focused on the techniques used by researchers to analyze kinetic crystallographic experiments.
4. Carey P.R. Raman crystallography and other biochemical applications of Raman microscopy. Annu Rev Phys Chem 57 (2006) 527-554. A comprehensive review that highlights different ways single crystal Raman spectroscopy has been used in the study of biological systems.
5. Enami N., Yoshimura K., Murakami M., Okumura H., Ihara K., and Kouyama T. Crystal structures of archaerhodopsin-1 and -2: common structural motif in archaeal light-driven proton pumps. J Mol Biol 358 (2006) 675-685
6. Padayatti P.S., Sheri A., Totir M.A., Helfand M.S., Carey M.P., Anderson V.E., Carey P.R., Bethel C.R., Bonomo R.A., Buynak J.D., et al. Rational design of a beta-lactamase inhibitor achieved via stabilization of the trans-enamine intermediate: 1.28 a crystal structure of wt SHV-1 complex with a penam sulfone. J Am Chem Soc 128 (2006) 13235-13242
7. Nakamichi H., and Okada T. Local peptide movement in the photoreaction intermediate of rhodopsin. Proc Natl Acad Sci U S A 103 (2006) 12729-12734
8. Carlsson G.H., Nicholls P., Svistunenko D., Berglund G.I., and Hajdu J. Complexes of horseradish peroxidase with formate, acetate, and carbon monoxide. Biochemistry 44 (2005) 635-642
9. Echalier A., Goodhew C.F., Pettigrew G.W., and Fulop V. Activation and catalysis of the di-heme cytochrome c peroxidase from Paracoccus pantotrophus. Structure 14 (2006) 107-117
10. Sukumar N., Chen Z.W., Ferrari D., Merli A., Rossi G.L., Bellamy H.D., Chistoserdov A., Davidson V.L., and Mathews F.S. Crystal structure of an electron transfer complex between aromatic amine dehydrogenase and azurin from Alcaligenes faecalis. Biochemistry 45 (2006) 13500-13510
11. Roujeinikova A., Scrutton N.S., and Leys D. Atomic level insight into the oxidative half-reaction of aromatic amine dehydrogenase. J Biol Chem 281 (2006) 40264-40272
12. Key J., and Moffat K. Crystal structures of deoxy and CO-bound bjFixLH reveal details of ligand recognition and signaling. Biochemistry 44 (2005) 4627-4635
13. Moukhametzianov R., Klare J.P., Efremov R., Baeken C., Goppner A., Labahn J., Engelhard M., Buldt G., and Gordeliy V.I. Development of the signal in sensory rhodopsin and its transfer to the cognate transducer. Nature 440 (2006) 115-119. UV/visible and FTIR spectroscopies confirmed the trapping of two intermediates in phoborhodopsin crystals and enabled comparison of the photocycle kinetics in crystals to that in membrane preparations.
14. Katona G., Snijder A., Gourdon P., Andreasson U., Hansson O., Andreasson L.E., and Neutze R. Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center. Nat Struct Mol Biol 12 (2005) 630-631
15. Nienhaus K., Ostermann A., Nienhaus G.U., Parak F.G., and Schmidt M. Ligand migration and protein fluctuations in myoglobin mutant L29W. Biochemistry 44 (2005) 5095-5105
16. Katona G., Carpentier P., Niviere V., Amara P., Adam V., Ohana J., Tsanov N., and Bourgeois D. Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme. Science 316 (2007) 449-453. Raman spectroscopy confirmed the entrapment of iron(III)-peroxo intermediates in superoxide reductase crystals, which displayed different conformations/interactions within the crystallographic asymmetric unit.
17. Rajagopal S., Anderson S., Srajer V., Schmidt M., Pahl R., and Moffat K. A structural pathway for signaling in the E46Q mutant of photoactive yellow protein. Structure 13 (2005) 55-63. Laue data supplied structural images of the signaling event in the E46Q mutant of PYP. UV/visible spectroscopy allowed the identification of five different intermediates whose structures were used to propose a mechanism for signaling.
18. Padayatti P.S., Helfand M.S., Totir M.A., Carey M.P., Carey P.R., Bonomo R.A., and van den Akker F. High resolution crystal structures of the trans-enamine intermediates formed by sulbactam and clavulanic acid and E166A SHV-1 β-lactamase. J Biol Chem 280 (2005) 34900-34907
19. Totir M.A., Padayatti P.S., Helfand M.S., Carey M.P., Bonomo R.A., Carey P.R., and van den Akker F. Effect of the inhibitor-resistant M69V substitution on the structures and populations of trans-enamine β-lactamase intermediates. Biochemistry 45 (2006) 11895-11904
20. Gall A., Gardiner A.T., Cogdell R.J., and Robert B. Carotenoid stoichiometry in the LH2 crystal: no spectral evidence for the presence of the second molecule in the alpha/beta-apoprotein dimer. FEBS Lett 580 (2006) 3841-3844
21. Pascal A.A., Liu Z., Broess K., van Oort B., van Amerongen H., Wang C., Horton P., Robert B., Chang W., and Ruban A. Molecular basis of photoprotection and control of photosynthetic light-harvesting. Nature 436 (2005) 134-137
22. Sanii L.S., Schill A.W., Moran C.E., and El-Sayed M.A. The protonation-deprotonation kinetics of the protonated Schiff base in bicelle bacteriorhodopsin crystals. Biophys J 89 (2005) 444-451
23. Yeremenko S., van Stokkum I.H., Moffat K., and Hellingwerf K.J. Influence of the crystalline state on photoinduced dynamics of photoactive yellow protein studied by ultraviolet-visible transient absorption spectroscopy. Biophys J 90 (2006) 4224-4235
24. Sanii L.S., and El-Sayed M.A. Partial dehydration of the retinal binding pocket and proof for photochemical deprotonation of the retinal Schiff base in bicelle bacteriorhodopsin crystals. Photochem Photobiol 81 (2005) 1356-1360
25. Baxter R.H., Krausz E., and Norris J.R. Photoactivation of the photosynthetic reaction center of Blastochloris viridis in the crystalline state. J Phys Chem B 110 (2006) 1026-1032
26. Efremov R., Gordeliy V.I., Heberle J., and Buldt G. Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics. Biophys J 91 (2006) 1441-1451
27. Vernede X., Lavault B., Ohana J., Nurizzo D., Joly J., Jacquamet L., Felisaz F., Cipriani F., and Bourgeois D. UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops. Acta Crystallogr D Biol Crystallogr 62 (2006) 253-261
28. Nanao M.H., and Ravelli R.B. Phasing macromolecular structures with UV-induced structural changes. Structure 14 (2006) 791-800. A proposed phasing method that promises to be more effective than using X-ray damage as it introduces more protein specific changes without the need for a synchrotron.
29. Kühnel K., Derat E., Terner J., Shaik S., and Schlichting I. Structure and quantum chemical characterization of chloroperoxidase compound 0, a common reaction intermediate of diverse heme enzymes. Proc Natl Acad Sci U S A 104 (2007) 99-104
30. Dubnovitsky A.P., Ravelli R.B., Popov A.N., and Papageorgiou A.C. Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. Protein Sci 14 (2005) 1498-1507
31. Pearson A.R., Pahl R., Kovaleva E.G., Davidson V.L., and Wilmot C.M. Tracking X-ray-derived redox changes in crystals of a methylamine dehydrogenase/amicyanin complex using single-crystal UV/vis microspectrophotometry. J Synchrotron Radiat 14 (2007) 92-98. The authors devised a general composite data collection strategy that tracked reduction at multiple redox centers to ensure the resulting structures represented the true oxidized intermediates.
32. Beitlich T., Kuhnel K., Schulze-Briese C., Shoeman R.L., and Schlichting I. Cryoradiolytic reduction of crystalline heme proteins: analysis by UV-vis spectroscopy and X-ray crystallography. J Synchrotron Radiat 14 (2007) 11-23
33. McGeehan J.E., Carpentier P., Royant A., Bourgeois D., and Ravelli R.B. X-ray radiation-induced damage in DNA monitored by online Raman. J Synchrotron Radiat 14 (2007) 99-108
34. Noda K., Sato H., Watanabe S., Yokoyama S., and Tashiro H. Efficient characterization for protein crystals using confocal Raman spectroscopy. Appl Spectrosc 61 (2007) 11-18
35. Portuondo-Campa E., Schenkl S., Dolder M., Chergui M., Landau E.M., and Haacke S. Absorption spectroscopy of three-dimensional bacteriorhodopsin crystals at cryogenic temperatures: effects of altered hydration. Acta Crystallogr D Biol Crystallogr 62 (2006) 368-374
36. Garman E.F., and McSweeney S.M. Progress in research into radiation damage in cryo-cooled macromolecular crystals. J Synchrotron Radiat 14 (2007) 1-3
37. Shimizu N., Hirata K., Hasegawa K., Ueno G., and Yamamoto M. Dose dependence of radiation damage for protein crystals studied at various X-ray energies. J Synchrotron Radiat 14 (2007) 4-10
38. Fioravanti E., Vellieux F.M.D., Amara P., Madern D., and Weik M. Specific radiation damage to acidic residues and its relation to their chemical and structural environment. J Synchrotron Radiat 14 (2007) 84-91
39. Southworth-Davies R.J., and Garman E.F. Radioprotectant screening for cryocrystallography. J Synchrotron Radiat 14 (2007) 73-83. Very interesting study analyzing the use of ascorbate, 2,2,6,6-tetramethyl-4-piperidone and reduced dithiothreitol as radioprotectants for thiols and disulfide bond radiation damage, monitored by an on-line UV/vis microspectrophotometer.
40. Garman E.F., and Owen R.L. Cryocooling and radiation damage in macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 62 (2006) 32-47
41. Perrakis A., Cipriani F., Castagna J.C., Claustre L., Burghammer M., Riekel C., and Cusack S. Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13. Acta Crystallogr D Biol Crystallogr 55 (1999) 1765-1770
42. Nanao M.H., Sheldrick G.M., and Ravelli R.B. Improving radiation-damage substructures for RIP. Acta Crystallogr D Biol Crystallogr 61 (2005) 1227-1237
43. Schiltz M., and Bricogne G. Modelling and refining site-specific radiation damage in SAD/MAD phasing. J Synchrotron Radiat 14 (2007) 34-42