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X-ray Scattering for Bio-Molecule Structure Characterization

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Biophysical Techniques in Photosynthesis

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 26))

One of the challenges in photosynthesis research lies in resolving the molecular basis for function with atomic-scale precision across the full time-scale of photosynthetic events. While crystallography provides the most detailed and accurate measurement of molecular structure, structure determination is necessarily confi ned to specifi c crystalline states. Critical issues that can be left unresolved by crystallography include the range, amplitudes, and time-scales of molecular motions, and a determination of how these dynamic events are linked to biological function. Advances in synchrotron X-ray scattering techniques offer new opportunities for characterization of photosynthetic structure and dynamics in non-crystalline media that build upon crystallographic, NMR, and molecular dynamics databases, but are applied to conditions most closely relevant to in-situ function. Recent advances in the application of synchrotron X-ray scattering techniques include the extension to the high-angle, high-resolution domain, where measurements can be routinely made to a spatial resolution of 1 Å or better, and the development of coordinate-based analyses of X-ray scattering data that allows scattering data to be analyzed in terms of detailed coordinate models for structure and dynamics. Promising new directions include application of element specifi c anomalous X-ray scattering and ultrafast time-resolved scattering techniques. This chapter will review recent progress in the application of synchrotron scattering techniques for the in-situ characterization of molecular structure. This work has focused primarily on proof-of-principle and technique development using model compounds and molecular systems. These studies demonstrate opportunities for using in-situ solution diffraction for the resolution of conformational landscapes for photosynthetic complexes in non-crystalline states and for extending these studies to the picosecond time domain using pulsed synchrotron techniques.

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References

  • Adir N, Axelrod HL, Beroza P, Isaacson RA, Rongey S, Okamura MY and Feher G (1996) Co-crystallization and characterization of the photosynthetic reaction center-cytochrome c 2 complex from Rhodobacter sphaeroides. Biochemistry 35: 2535-2547

    Article  CAS  PubMed  Google Scholar 

  • Anfinrud PA and Schotte F (2005) X-ray fingerprinting of chemical intermediates in solution. Science 309: 1192-1193

    Article  CAS  PubMed  Google Scholar 

  • Axelrod HL and Okamura MY (2005) The structure and function of the cytochrome c 2: Reaction center electron transfer complex for Rhodobacter sphaeroides. Photosynth Res 85: 101-114

    Article  CAS  PubMed  Google Scholar 

  • Axelrod HL, Abresch EC, Okamura MY, Yeh AP, Rees DC and Feher G (2002) X-ray structure determination of the cytochrome c 2: Reaction center electron transfer complex from Rhodobacter sphaeroides. J Mol Biol 319: 501-515

    Article  CAS  PubMed  Google Scholar 

  • Badyal YS, Saboungi M-L, Price DL, Shastri SD, Haeffner DR and Soper AK (2000) Electron distribution in water. J Chem Phys 112: 9206-9208

    Article  CAS  Google Scholar 

  • Baxter RHG, Ponomarenko N, Srajer V, Pahl R and Moffat K (2004) Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center. Proc Natl Acad Sci USA 101: 5982-5987

    Article  CAS  PubMed  Google Scholar 

  • Baxter RHG, Seagle B-L, Ponomarenko N and Norris JR (2005) Cryogenic structure of the photosynthetic reaction center of Blastochloris viridis in the light and dark. Acta Crystallogr D61: 605-612

    CAS  Google Scholar 

  • Borgstahl GEO, Williams DR and Getzoff ED (1995) 1.4 Ångström structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold, active site, and chromophore. Biochemistry 34: 6278-6287

    Article  CAS  PubMed  Google Scholar 

  • Breton J (2004) Absence of large-scale displacement of quinone QB in bacterial photosynthetic reaction centers. Biochemistry 43: 3318-3326

    Article  CAS  PubMed  Google Scholar 

  • Bushnell GW, Louie GV and Brayer GD (1990) High-resolution three-dimensional structure of horse heart cytochrome c. J Mol Biol 214: 585-595

    Article  CAS  PubMed  Google Scholar 

  • Cantor CR and Schimmel PR (1980) Biophysical Chemistry, Part II: Techniques for the Study of Biological Structure and Function. W. H. Freeman and Co., San Francisco

    Google Scholar 

  • Chacon P, Diaz JF, Moran F and Andreu JM (2000) Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J Mol Biol 299: 1289-1302

    Article  CAS  PubMed  Google Scholar 

  • Chen LX, Jager WJH, Jennings G, Gosztola DJ, Munkholm A and Hessler JP (2001) Capturing a photoexcited molecular structure through time-domain X-ray absorption fine structure. Science 292: 262-264

    Article  CAS  PubMed  Google Scholar 

  • Chen SH and Bendedouch D (1986) Structure and interactions of proteins in solution studied by small-angle neutron scattering. Meth Enzymol 130: 79-116

    Article  CAS  PubMed  Google Scholar 

  • Cornacchia M, Arthur J, Bane K, Bolton P, Carr R, Decker FJ, Emma P, Galayda J, Hastings J, Hodgson K, Huang Z, Lindau I, Nuhn H-D, Paterson JM, Pellegrini C, Reiche S, Schlarp H, Stohr J, Stupakov G, Walz D and Winick H (2004) Future possibilities of the Linac coherent light source. J Synchrotron Rad 11: 227-238

    Article  CAS  Google Scholar 

  • Das R, Mills TT, Kwok LW, Maskel GS, Millett IS, Doniach S, Finkelstein KD, Herschlag D and Pollack L (2003) Counterion distribution around DNA probed by solution X-ray scattering. Phys Rev Let 90: 188103-1-188103-4

    Article  CAS  Google Scholar 

  • Dimitrijevic NM, Rajh T, Saponjic Z, de la Garza L and Tiede DM (2004) Light-induced charge separation and redox chemistry at the surface of TiO2/host-guest hybrid nanoparticles. J Phys Chem B 108: 9105-9110

    Article  CAS  Google Scholar 

  • Fedorov BA and Denesyuk AI (1978) Large-angle X-ray diffuse scattering, a new method for investigating changes in the conformation of globular proteins in solution. J Appl Cryst 11: 473-477

    Article  CAS  Google Scholar 

  • Fischetti RF, Rodi DJ, Mirza A, Irving TC, Kondrashkina E and Makowski L (2003) High-resolution wide-angle X-ray scattering of protein solutions: Effect of beam dose on protein integrity. J Synchrotron Rad 10: 398-404

    Article  CAS  Google Scholar 

  • Fischetti RF, Rodi DJ, Gore DB and Makowski L (2004) Wide-angle X-ray solution scattering as a probe of ligand-induced conformational changes in proteins. Chem Biol 11: 1431-1443

    Article  CAS  PubMed  Google Scholar 

  • Fraser RDB, MacRae TP and Suzuki E (1978) An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. J Appl Cryst 11: 693-694

    Article  CAS  Google Scholar 

  • Fritzsch G, Koepke J, Diem R, Kuglstatter A and Baciou L (2002) Charge separation induces conformational changes in the photosynthetic reaction centre of purple bacteria. Acta Crystallogr D58: 1660-1663

    CAS  Google Scholar 

  • Giles J (2004) Lasers bend beams for desktop X-ray source. Nature 428: 789

    Google Scholar 

  • Glatter O (1991) Small-angle scattering and light scattering. In: Lindner P and Zemb T (eds) Neutron, X-ray and Light Scattering, pp 33-82. Elsevier Science Publishers B.V., Amsterdam

    Google Scholar 

  • Grishaev A, Wu J, Trewhella J and Bax A (2005) Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. J Am Chem Soc 127: 16621-16628

    Article  CAS  PubMed  Google Scholar 

  • Guinier A and Fournet G (1955) Small Angle Scattering of X-rays. Wiley, New York

    Google Scholar 

  • Hellemans A (1997) X-rays find new ways to shine. Science 277: 1214-1215

    Article  CAS  Google Scholar 

  • Hirai M, Iwase H, Hayakawa T, Miura K and Inoue K (2002) Structural hierarchy of several proteins observed by wide-angle solution scattering. J Synchrotron Rad 9: 202-205

    Article  CAS  Google Scholar 

  • Hirai M, Koizumi M, Hayakawa T, Takahashi H, Abe S, Hirai H, Miura K and Inoue K (2004) Hierarchical map of protein unfolding and refolding at thermal equilibrium revealed by wide-angle X-ray scattering. Biochemistry 43: 9036-9049

    Article  CAS  PubMed  Google Scholar 

  • Hummer G, Schotte F and Anfinrud PA (2004) Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations. Proc Natl Acad Sci USA 101: 15330-15334

    Article  CAS  PubMed  Google Scholar 

  • Ibers JA and Hamilton WC (eds) (1973) International Tables for X-ray Crystallography, Vol IV. Kynoch Press, Birmingham

    Google Scholar 

  • Ihee H, Lobastov VA, Gomez UM, Goodson BM, Srinivasan R, Ruan C-Y and Zewail AH (2001) Direct imaging of transient molecular structures with ultrafast diffraction. Science 291: 458-462

    Article  CAS  PubMed  Google Scholar 

  • Ihee H, Lorenc M, Kim TK, Kong QY, Cammarata M, Lee JH, Bratos S and Wulff M (2005a) Ultrafast X-ray diffraction of transient molecular structures in solution. Science 309: 1223-1227

    Article  CAS  Google Scholar 

  • Ihee H, Rajagopal S, Srajer V, Pahl R, Anderson S, Schmidt M, Schotte F, Anfinrud PA, Wulff M and Moffat K (2005b) Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds. Proc Natl Acad Sci USA 102: 7145-7150

    Article  CAS  Google Scholar 

  • Katona G, Snijder A, Gourdon P, Andreasson J, Hansson O, Andreasson L-E and Neutze R (2005) Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center. Nat Struct Mol Biol 12: 630-631

    Article  CAS  PubMed  Google Scholar 

  • Kim TK, Zuo X, Tiede DM and Ihee H (2004) Exploring fine structures of photoactive yellow protein in solution using wide-angle X-ray scattering. Bull Korean Chem Soc 25: 1676-1680

    Article  CAS  Google Scholar 

  • Kojima M, Timchenko AA, Higo J, Ito K, Kihara H and Takahashi K (2004) Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule. J Appl Cryst 37: 103-109

    Article  CAS  Google Scholar 

  • Londer YY, Pokkuluri P, Tiede DM and Schiffer M (2002) Production and preliminary characterization of a recombinant triheme cytochrome c 7 from Geobacter sulfurreducens in Escherichia coli. Biochim Biophys Acta 1554: 202-211

    Article  CAS  PubMed  Google Scholar 

  • Miao J, Chapman HN, Kirz J, Sayre D and Hodgson KO (2004) Taking X-ray diffraction to the limit: Macromolecular structures from femtosecond X-ray pulses and diffraction microscopy of cells with synchrotron radiation. Annu Rev Biophys Biomol Struct 33: 157-176

    Article  CAS  PubMed  Google Scholar 

  • Miyashita O, Onuchic JN and Okamura MY (2004) Transition state and encounter complex for fast association of cytochrome c 2 with bacterial reaction center. Proc Natl Acad Sci USA 101 (46): 16174-16179

    Article  CAS  PubMed  Google Scholar 

  • Moffat K (2002) The frontiers of time-resolved macromolecular crystallography: Movies and chirped X-ray pulses. Faraday Disc 122: 65-77

    Article  CAS  Google Scholar 

  • Moore PB (1988) On the role of small-angle scattering in biologi-cal research. J Appl Cryst 21: 675-680

    Article  CAS  Google Scholar 

  • Morfin I, Horkay F, Basser PJ, Bley F, Hecht A-M, Rochas C and Geissler E (2004) Adsorption of divalent cations on DNA. Biophys J 87: 2897-2904

    Article  CAS  PubMed  Google Scholar 

  • Nadassy K, Tomas-Oliveira I, Alberts I, Janin J and Wodak SJ (2001) Standard atomic volumes in double-stranded DNA and packing in protein-DNA interfaces. Nucl Acids Res 29: 3362-3376

    Article  CAS  PubMed  Google Scholar 

  • Nina M, Beglov D and Roux B (1997) Atomic radii for continuum electrostatic calculations based on molecular dynamics free energy simulations. J Phys Chem B 101: 5239-5248

    Article  CAS  Google Scholar 

  • Petoukhov MV and Svergun DI (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89: 1237-1250

    Article  CAS  PubMed  Google Scholar 

  • Plech A, Wulff M, Bratos S, Mirloup F, Vuilleumier R, Schotte F and Anfinrud PA (2004) Visualizing chemical reactions in solution by picosecond X-ray diffraction. Phys Rev Let 92: 125505-1-5

    Article  CAS  Google Scholar 

  • Riekel C, Bosecke P, Diat O and Engström P (1996) New opportunities in small-angle X-ray scattering and wide-angle X-ray scattering at a third generation synchrotron radiation source. J Molec Struc 3883: 291-302

    Article  Google Scholar 

  • Saponjic ZV, Dimitrijevic NM, Tiede DM, Goshe A, Zuo X, Chen LX, Barnard AS, Zapol P, Curtiss L and Rajh T (2005) Shaping nanoscale architectures through surface chemistry. Adv Mat 17: 965-972

    Article  CAS  Google Scholar 

  • Seifert S, Winans RE, Tiede DM and Thiyagarajan P (2000) Design and performance of an ASAXS instrument at the Advanced Photon Source. J Appl Cryst 33: 782-784

    Article  CAS  Google Scholar 

  • Stowell MHB, McPhillips TM, Rees DC, Soltis SM, Abresch E and Feher G (1997) Light-induced structural changes in photosynthetic reaction center: Implications for mechanism of electron-proton transfer. Science 276: 812-816

    Article  CAS  PubMed  Google Scholar 

  • Svensson B, Tiede DM and Barry BA (2002) Small-angle X-ray scattering studies of the manganese stabilizing subunit in Photosystem II. J Phys Chem B 106: 8485-8488

    Article  CAS  Google Scholar 

  • Svensson B, Tiede DM, Nelson DR and Barry BA (2004) Structural studies of the manganese-stabilizing subunit in Photosystem II. Biophys J 86: 1807-1812

    Article  CAS  PubMed  Google Scholar 

  • Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Cryst 25: 495-503

    Article  Google Scholar 

  • Svergun DI and Koch MHJ (2003) Small-angle scattering studies of biological macromolecules in solution. Rep Prog Phys 66: 1735-1782

    Article  CAS  Google Scholar 

  • Svergun DI, Feigin LA and Taylor GW (1987) Structure Analysis by Small Angle X-ray and Neutron Scattering, pp 1-335. Plenum Press, New York

    Google Scholar 

  • Svergun DI, Semenyuk AV and Feigin LA (1988) Small-angle scattering data treatment by the regularization method. Acta Crystallogr A 44: 244-250

    Article  Google Scholar 

  • Svergun D, Barberato C and Koch MHJ (1995) CRYSOL — a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Cryst 28: 768-773

    Article  CAS  Google Scholar 

  • Tiede DM and Dutton PL (1993) Electron transfer between bacterial reaction centers and mobile c-type cytochromes. In: Deisenhofer H and Norris JR (eds) The Photosynthetic Reaction Center, pp 257-288. Academic Press, New York

    Google Scholar 

  • Tiede DM, Littrell K, Marone PA, Zhang R and Thiyagarajan P (2000) Solution structure of a biological bimolecular electron transfer complex: Characterization of the photosynthetic reaction center-cytochrome c 2 protein complex by small angle neutron scattering. J Appl Cryst 33: 560-564

    Article  CAS  Google Scholar 

  • Tiede DM, Zhang R and Seifert S (2002) Protein conformations explored by difference high-angle solution X-ray scattering: Oxidation state and temperature dependent changes in cytochrome c. Biochemistry 41: 6605-6614

    Article  CAS  PubMed  Google Scholar 

  • Tiede DM, Zhang R, Chen LX, Yu L and Lindsey JS (2004) Structural characterization of modular supramolecular architectures in solution. J Am Chem Soc 126: 14054-14062

    Article  CAS  PubMed  Google Scholar 

  • Tsai J, Taylor R, Chothia C and Gerstein M (1999) The packing density in proteins: Standard radii and volumes. J Mol Biol 290: 253-266

    Article  CAS  PubMed  Google Scholar 

  • Vaughan PA, Sturdivant JH and Pauling L (1950) The determination of the structures of complex molecules and ions from X-ray diffraction by their solutions: The structures of the groups++. J Am Chem Soc 72: 5477-5486

    Article  CAS  Google Scholar 

  • Vigil D, Gallagher SC, Trewhella J and Garcia AE (2001) Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin. Biophys J 80: 2082-2092

    Article  CAS  PubMed  Google Scholar 

  • Warren BE (1990) X-Ray Diffraction. Dover Publications, New York

    Google Scholar 

  • Williamson JC, Cao J, Ihee H, Frey H and Zewail AH (1997) Clocking transient chemical changes by ultrafast electron diffraction. Nature 386: 159-162

    Article  CAS  Google Scholar 

  • Xiao Y, Cai Z, Wang ZL, Lai B and Chu YS (2005) An X-ray nanodiffraction technique for structural characterization of individual nanomaterials. J Synchrotron Rad 12: 124-128

    Article  CAS  Google Scholar 

  • Zhang R, Marone PA, Thiyagarajan P and Tiede DM (1999) Structure and molecular fluctuations of n-alkyl-β-D-glucopy-ranoside micelles determined by X-ray and neutron scattering. Langmuir 22: 7510-7519

    Article  CAS  Google Scholar 

  • Zhang R, Thiyagarajan P and Tiede DM (2000) Probing protein fine structures by wide angle solution X-ray scattering. J Appl Cryst 33: 565-568

    Article  CAS  Google Scholar 

  • Zhou J, Deyhim A, Krueger S and Gregurick SK (2005) LORES: Low resolution shape program for the calculation of small angle scattering for biological macromolecules in solution. Computer Phys Comm 170: 186-204

    Article  CAS  Google Scholar 

  • Zuo X and Tiede DM (2005) Resolving conflicting crystallo-graphic and NMR models for solution-state DNA with solution X-ray diffraction. J Am Chem Soc 127: 16-17

    Article  CAS  PubMed  Google Scholar 

  • Zuo X, Cui G, Mertz KM, Zhang L, Lewis FD and Tiede DM (2006) X-ray diffraction ‘fingerprinting’ of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proc Natl Acad Sci USA 102: 3534-3539

    Article  CAS  Google Scholar 

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Tiede, D.M., Zuo, X. (2008). X-ray Scattering for Bio-Molecule Structure Characterization. In: Aartsma, T.J., Matysik, J. (eds) Biophysical Techniques in Photosynthesis. Advances in Photosynthesis and Respiration, vol 26. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8250-4_8

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