Hostname: page-component-7c8c6479df-fqc5m Total loading time: 0 Render date: 2024-03-28T15:14:24.887Z Has data issue: false hasContentIssue false

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

Published online by Cambridge University Press:  14 December 2007

Christopher D. Putnam
Affiliation:
Ludwig Institute for Cancer Research, La Jolla, USA
Michal Hammel
Affiliation:
Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Greg L. Hura*
Affiliation:
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
John A. Tainer*
Affiliation:
Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Department of Molecular Biology MB4 and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
*
*G. L. Hura: Tel.: 1 510 486 5378; Fax: 1 510 486 5298; Email: GLHura@lbl.gov
*Correspondence may be addressed to either author: J. A. Tainer: Tel.: 1 858 784 8119; Fax: 1 858 784 2277; Email: jat@scripps.edu

Abstract

Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 Å to 10 Å resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein–nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.

Type
Review Article
Copyright
Copyright © Cambridge University Press 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Akiyama, S., Fujisawa, T., Ishimori, K., Morishima, I. & Aono, S. (2004). Activation mechanisms of transcriptional regulator CooA revealed by small-angle X-ray scattering. Journal of Molecular Biology 341, 651668.CrossRefGoogle ScholarPubMed
Amadei, A., Linssen, A. B. & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins 17, 412425.CrossRefGoogle ScholarPubMed
Andresen, K., Das, R., Park, H. Y., Smith, H., Kwok, L. W., Lamb, J. S., Kirkland, E. J., Herschlag, D., Finkelstein, K. D. & Pollack, L. (2004). Spatial distribution of competing ions around DNA in solution. Physical Review Letters 93, 248103.CrossRefGoogle ScholarPubMed
Apic, G., Gough, J. & Teichmann, S. A. (2001). An insight into domain combinations. Bioinformatics 17, S83S89.CrossRefGoogle ScholarPubMed
Aslam, M., Guthridge, J. M., Hack, B. K., Quigg, R. J., Holers, V. M. & Perkins, S. J. (2003). The extended multidomain solution structures of the complement protein Crry and its chimeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy. Journal of Molecular Biology 329, 525550.CrossRefGoogle ScholarPubMed
Aslam, M. & Perkins, S. J. (2001). Folded-back solution structure of monomeric factor H of human complement by synchrotron X-ray and neutron scattering, analytical ultracentrifugation and constrained molecular modelling. Journal of Molecular Biology 309, 11171138.CrossRefGoogle ScholarPubMed
Bahadur, R. P., Chakrabarti, P., Rodier, F. & Janin, J. (2004). A dissection of specific and non-specific protein-protein interfaces. Journal of Molecular Biology 336, 943955.CrossRefGoogle ScholarPubMed
Bahar, I., Atilgan, A. R. & Erman, B. (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal 80, 505515.Google Scholar
Bahattacharyya, R. P., Remenyi, A., Yeh, B. J. & Lim, W. A. (2006). Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuit. Annual Reviews of Biochemistry 75, 655680.CrossRefGoogle Scholar
Banci, L., Bertini, I., Gray, H. B., Luchinat, C., Reddig, T., Rosato, A. & Turano, P. (1997). Solution structure of oxidized horse heart cytochrome c. Biochemistry 36, 98679877.CrossRefGoogle ScholarPubMed
Barrett, C. P. & Noble, M. E. (2005). Dynamite extended: two new services to simplify protein dynamic analysis. Bioinformatics 21, 31743175.CrossRefGoogle ScholarPubMed
Bax, A. & Grishaev, A. (2005). Weak alignment NMR: a hawk-eyed view of biomolecular structure. Current Opinion in Structural Biology 15, 563570.CrossRefGoogle ScholarPubMed
Bayburt, T. H., Grinkova, Y. V. & Sligar, S. G. (2006). Assembly of single bacteriorhodopsin trimers in bilayer nanodiscs. Archives of Biochemistry and Biophysics 450, 215222.CrossRefGoogle ScholarPubMed
Bergmann, A., Fritz, G. & Glatter, O. (2000). Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA). Journal of Applied Crystallography 33, 12121216.CrossRefGoogle Scholar
Bernado, P., Blanchard, L., Timmins, P., Marion, D., Ruigrok, R. W. & Blackledge, M. (2005). A structural model for unfolded proteins from residual dipolar couplings and small-angle X-ray scattering. Proceedings of the National Academy of Sciences USA 102, 1700217007.CrossRefGoogle ScholarPubMed
Bernado, P., Mylonas, E., Petoukhov, M. V., Blackledge, M. & Svergun, D. I. (2007). Structural characterization of flexible proteins using small-angle X-ray scattering. Journal of the Americal Chemical Society 129, 56565664.CrossRefGoogle ScholarPubMed
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 112, 535542.CrossRefGoogle Scholar
Beuron, F., Flynn, T. C., Ma, J., Kondo, H., Zhang, X. & Freemont, P. S. (2003). Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantized elastic deformation model. Journal of Molecular Biology 327, 619629.CrossRefGoogle Scholar
Bilgin, N., Ehrenberg, M., Ebel, C., Zaccai, G., Sayers, Z., Koch, M. H., Svergun, D. I., Barberato, C., Volkov, V., Nissen, P. & Nyborg, J. (1998). Solution structure of the ternary complex between aminoacyl-tRNA, elongation factor Tu, and guanosine triphosphate. Biochemistry 37, 81638172.CrossRefGoogle ScholarPubMed
Binder, K. & Heerman, D. (1992). Monte Carlo Simulation in Statistical Physics, 2nd edn.Berlin: Springer-Verlag.CrossRefGoogle Scholar
Bjornson, K. P., Blackwell, L. J., Sage, H., Baitinger, C., Allen, D. & Modrich, P. (2003). Assembly and molecular activities of the MutS tetramer. Journal of Biological Chemistry 278, 3466734673.CrossRefGoogle ScholarPubMed
Blow, D. M. & Crick, F. H. C. (1959). The treatment of errors in the isomorphous replacement method. Acta Crystallographica 12, 794802.CrossRefGoogle Scholar
Blundell, T. L. & Johnson, L. N. (1976). Protein Crystallography. London: Academic Press.Google Scholar
Bochtler, M., Hartmann, C., Song, H. K., Bourenkov, G. P., Bartunik, H. D. & Huber, R. (2000). The structures of HslU and the ATP-dependent protease HslU-HslV. Nature 403, 800805.CrossRefGoogle Scholar
Boehm, M. K., Woof, J. M., Kerr, M. A. & Perkins, S. J. (1999). The Fab and Fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling. Journal of Molecular Biology 286, 14211447.CrossRefGoogle ScholarPubMed
Boehr, D. D., McElheny, D., Dyson, H. J. & Wright, P. E. (2006). The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 16381642.CrossRefGoogle ScholarPubMed
Bonvin, A. M. (2006). Flexible protein-protein docking. Current Opinions in Structural Biology 16, 194200.CrossRefGoogle ScholarPubMed
Borgstahl, G. E., Parge, H. E., Hickey, M. J., Johnson, M. J., Boissinot, M., Hallewell, R. A., Lepock, J. R., Cabelli, D. E. & Tainer, J. A. (1996). Human mitochondrial manganese superoxide dismutase polymorphic variant Ile58Thr reduces activity by destabilizing the tetrameric interface. Biochemistry 35, 42874297.CrossRefGoogle ScholarPubMed
Boskovic, J., Rivera-Calzada, A., Maman, J. D., Chacon, P., Willison, K. R., Pearl, L. H. & Llorca, O. (2003). Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. EMBO Journal 22, 58755882.CrossRefGoogle ScholarPubMed
Bourne, Y., Arvai, A. S., Bernstein, S. L., Watson, M. H., Reed, S. I., Endicott, J. E., Noble, M. E., Johnson, L. N. & Tainer, J. A. (1995). Crystal structure of the cell cycle-regulatory protein suc1 reveals a beta-hinge conformational switch. Proceedings of the National Academy of Sciences USA 92, 1023210236.CrossRefGoogle ScholarPubMed
Bourne, Y., Redford, S. M., Steinman, H. M., Lepock, J. R., Tainer, J. A. & Getzoff, E. D. (1996). Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase. Proceedings of the National Academy of Sciences USA 93, 1277412779.CrossRefGoogle ScholarPubMed
Brooks, B. & Karplus, M. (1985). Normal modes for specific motions of macromolecules: applications to the hinge-bending mode of lysozyme. Proceedings of the National Academy of Sciences USA 82, 49954999.CrossRefGoogle Scholar
Brudler, R., Gessner, C. R., Li, S., Tyndall, S., Getzoff, E. D. & Woods, V. L. Jr. (2006). PAS domain allostery and light-induced conformational changes in photoactive yellow protein upon I2 intermediate formation, probed with enhanced hydrogen/deuterium exchange mass spectrometry. Journal of Molecular Biology 363, 148160.CrossRefGoogle ScholarPubMed
Brulet, A., Boue, F. & Cotton, J. P. (1996). About the experimental determination of the persistence length of wormlike chains of polystyrene. Journal of Physics II (France) 6, 855891.Google Scholar
Brunger, A. T. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472475.CrossRefGoogle Scholar
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kuntsleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallographica D54, 905921.Google Scholar
Brunger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458460.CrossRefGoogle ScholarPubMed
Brunner-Popela, J. & Glatter, O. (1997). Small-angle scattering of interacting particles. I. Basic principles of a global evaluation technique. Journal of Applied Crystallography 30, 431442.CrossRefGoogle Scholar
Bu, Z. & Engelman, D. M. (1999). A method for determining transmembrane helix association and orientation in detergent micelles using small angle x-ray scattering. Biophysical Journal 77, 10641073.CrossRefGoogle ScholarPubMed
Buey, R. M., Monterroso, B., Menendez, M., Diakun, G., Chacon, P., Hermoso, J. A. & Diaz, J. F. (2007). Insights into molecular plasticity of choline binding proteins (Pneumococcal surface proteins) by SAXS. Journal of Molecular Biology 365, 411424.CrossRefGoogle ScholarPubMed
Burmeister, W. P. (2000). Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallographica D56, 328341.Google Scholar
Caffrey, M. (2000). A lipid's eye view of membrane protein crystallization in mesophases. Current Opinions in Structural Biology 10, 486497.CrossRefGoogle ScholarPubMed
Calmettes, P., Durand, D., Desmadril, M., Minard, P., Receveur, V. & Smith, J. C. (1994). How random is a highly denatured protein? Biophysical Chemistry 53, 105114.CrossRefGoogle ScholarPubMed
Canady, M. A., Tsuruta, H. & Johnson, J. E. (2001). Analysis of rapid, large-scale protein quaternary structure changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NΩV) maturation. Journal of Molecular Biology 311, 803814.CrossRefGoogle ScholarPubMed
Chacon, P., Diaz, J. F., Moran, F. & Andreu, J. M. (2000). Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. Journal of Molecular Biology 299, 12891302.CrossRefGoogle Scholar
Chacon, P., Moran, F., Diaz, F. J., Pantos, E. & Andreu, J. M. (1998). Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophysical Journal 74, 27602775.CrossRefGoogle ScholarPubMed
Chacon, P., Tama, F. & Wriggers, W. (2003). Mega-dalton biomolecular motion captured from electron microscopy reconstructions. Journal of Molecular Biology 326, 485492.CrossRefGoogle ScholarPubMed
Chacon, P. & Wriggers, W. (2002). Multi-resolution contour-based fitting of macromolecular structures. Journal of Molecular Biology 317, 375384.CrossRefGoogle ScholarPubMed
Chamberlain, A. K., Receveur, V., Spencer, A., Redfield, C. & Dobson, C. M. (2001). Characterization of the structure and dynamics of amyloidogenic variants of human lysozyme by NMR spectroscopy. Protein Science 10, 25252530.CrossRefGoogle ScholarPubMed
Chapados, B. R., Hosfield, D. J., Han, S., Qiu, J., Yelent, B., Shen, B. & Tainer, J. A. (2004). Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116, 3950.CrossRefGoogle ScholarPubMed
Chen, B., Doucleff, M., Wemmer, D. E., De Carlo, S., Huang, H. H., Nogales, E., Hoover, T. R., Kondrashkina, E., Guo, L. & Nixon, B. T. (2007). ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, σ54. Structure 15, 429440.CrossRefGoogle ScholarPubMed
Chen, L., Hodgson, K. O. & Doniach, S. (1996). A lysozyme folding intermediate revealed by solution X-ray scattering. Journal of Molecular Biology 261, 658671.CrossRefGoogle ScholarPubMed
Chen, R., Li, L. & Weng, Z. (2003). ZDOCK: an initial-stage protein-docking algorithm. Proteins 52, 8087.CrossRefGoogle ScholarPubMed
Columbus, L., Lipfert, J., Klock, H., Millett, I., Doniach, S. & Lesley, S. A. (2006). Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination. Protein Science 15, 961975.CrossRefGoogle ScholarPubMed
Corn, J. E., Pease, P. J., Hura, G. L. & Berger, J. M. (2005). Crosstalk between primase subunits can act to regulate primer synthesis in trans. Molecular Cell 20, 391401.CrossRefGoogle ScholarPubMed
Cowtan, K. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Crystallographica D52, 4348.Google Scholar
Cowtan, K. & Main, P. (1998). Miscellaneous algorithms for density modifications. Acta Crystallographica D54, 487493.Google Scholar
Craig, L., Volkmann, N., Arvai, A. S., Pique, M. E., Yeager, M., Egelman, E. H. & Tainer, J. A. (2006). Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Molecular Cell 23, 651662.CrossRefGoogle ScholarPubMed
D'Arcy, A. (1994). Crystallizing proteins – a rational approach? Acta Crystallographica D50, 469471.Google Scholar
Dainese, E., Sabatucci, A., van Zadelhoff, G., Angelucci, C. B., Vachette, P., Veldink, G. A., Agro, A. F. & Maccarrone, M. (2005). Structural stability of soybean lipoxygenase-1 in solution as probed by small angle X-ray scattering. Journal of Molecular Biology 349, 143152.CrossRefGoogle ScholarPubMed
Dauter, Z. (1997). Data collection strategy. Methods in Enzymology 276, 326344.CrossRefGoogle ScholarPubMed
Davies, J. M., Tsuruta, H., May, A. P. & Weis, W. I. (2005). Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-ray scattering. Structure 13, 183195.CrossRefGoogle ScholarPubMed
Delarue, M. & Dumas, P. (2004). On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proceedings of the National Academy of Sciences USA 101, 69576962.CrossRefGoogle ScholarPubMed
Deng, H.-X., Hentai, A., Tainer, J. A., Iqbal, Z., Cayabyab, A., Hung, W.-Y., Getzoff, E. D., Herzfeldt, B., Roos, R. P., Warner, C., Deng, G., Soriano, E., Smyth, C., Parge, H. E., Ahmed, A., Roses, A. D., Hallewell, R. A., Pericak-Vance, M. A. & Siddique, T. (1993). Amyotropic lateral sclerosis and structural defects in Cu,Zn superoxide dismutase. Science 261, 10471051.CrossRefGoogle Scholar
Denisov, I. G., Grinkova, Y. V., Lazarides, A. A. & Sligar, S. G. (2004). Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size. Journal of the American Chemical Society 126, 34773487.CrossRefGoogle ScholarPubMed
dePristo, M. A., de Bakker, P. I. & Blundell, T. L. (2004). Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure 12, 831838.CrossRefGoogle ScholarPubMed
DiDonato, M., Craig, L., Huff, M. E., Thayer, M. M., Cardoso, R. M., Kassmann, C. J., Lo, T. P., Bruns, C. K., Powers, E. T., Kelly, J. W., Getzoff, E. D. & Tainer, J. A. (2003). ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. Journal of Molecular Biology 332, 601615.CrossRefGoogle ScholarPubMed
Diederichs, K., Diez, J., Greller, G., Mueller, C., Breed, J., Schnell, C., Vornrhein, C., Boos, W. & Welte, W. (2000). Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis. EMBO Journal 19, 59515961.CrossRefGoogle ScholarPubMed
Dominguez, C., Bonvin, A. M., Winkler, G. S., van Schaik, F. M., Timmers, H. T. & Boelens, R. (2004). Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure 12, 633644.CrossRefGoogle ScholarPubMed
Doniach, S. (2001). Changes in biomolecular conformation seen by small angle X-ray scattering. Chemical Reviews 101, 17631778.CrossRefGoogle ScholarPubMed
Dore, A. S., Kilkenny, M. L., Jones, S. A., Oliver, A. W., Roe, S. M., Bell, S. D. & Pearl, L. H. (2006). Structure of an archaeal PCNA1-PCNA2-FEN1 complex: elucidating PCNA subunit and client enzyme specificity. Nucleic Acids Research 34, 45154526.CrossRefGoogle ScholarPubMed
Doublie, S. (1997). Preparation of selenometionyl proteins for phase determination. Methods in Enzymology 276, 523530.CrossRefGoogle ScholarPubMed
Drenth, J. (1994). Principles of Protein X-ray Crystallography. New York: Springer-Verlag.CrossRefGoogle Scholar
Drotschmann, K., Aronshtam, A., Fritz, H.-J. & Marinus, M. G. (1998). The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA. Nucleic Acids Research 26, 948953.CrossRefGoogle ScholarPubMed
Dubochet, J., Adrian, M., Chang, J. J., Homo, J. C., Lepault, J., McDowall, A. W. & Schultz, P. (1988). Cryo-electron microscopy of vitrified specimens. Quarterly Reviews in Biophysics 21, 129228.CrossRefGoogle ScholarPubMed
Dyson, H. J. & Wright, P. E. (2005). Intrinsically unstructured proteins and their functions. Nature Reviews of Molecular Cell Biology 6, 197208.CrossRefGoogle ScholarPubMed
Echols, N., Milburn, D. & Gerstein, M. (2003). MolMovDB: analysis and visulation of conformational change and structural flexibility. Nucleic Acids Research 31, 478482.CrossRefGoogle Scholar
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallographica A47, 392400.CrossRefGoogle Scholar
Evans, S. K. & Lundblad, V. (1999). Est1 and Cdc13 as comediators of telomerase access. Science 286, 117120.CrossRefGoogle ScholarPubMed
Fang, X., Littrell, K., Yang, X. J., Henderson, S. J., Siefert, S., Thiyagarajan, P., Pan, T. & Sosnick, T. R. (2000). Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 39, 1110711113.CrossRefGoogle Scholar
Faure, P., Micu, A., Perahia, D., Doucet, J., Smith, J. C. & Benoit, J. P. (1994). Correlated intramolecular motions and diffuse X-ray scattering in lysozyme. Nature Stuctural Biology 1, 124128.Google ScholarPubMed
Ferre-D'Amare, A. R. & Burley, S. K. (1997). Dynamic light scattering in evaluating crystallizability of macromolecules. Methods in Enzymology 276, 157166.CrossRefGoogle ScholarPubMed
Ferreira da Silva, F., Pereira, P. J., Gales, L., Roessle, M., Svergun, D. I., Moradas-Ferreira, P. & Damas, A. M. (2006). The crystal structure and solution structures of glyceraldehyde-3-phosphate dehydrogenase reveal different quaternary structures. Journal of Biological Chemistry 281, 3343333440.CrossRefGoogle ScholarPubMed
Fetler, L., Tauc, P., Herve, G., Moody, M. F. & Vachette, P. (1995). X-ray scattering titration of the quaternary structure transition of aspartate transcarbamylase with a bisubstrate analogue: influence of nucleotide effectors. Journal of Molecular Biology 251, 243255.CrossRefGoogle ScholarPubMed
Filgueira de Azevedo, W. Jr., dos Santos, G. C., dos Santos, D. M., Olivieri, J. R., Canduri, F., Silva, R. G., Basso, L. A., Renard, G., da Fonseca, I. O., Mendes, M. A., Palma, M. S. & Santos, D. S. (2003). Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase. Biochemical and Biophysical Research Communications 309, 923928.CrossRefGoogle ScholarPubMed
Foster, B. A., Coffey, H. A., Morin, M. J. & Rastinejad, F. (1999). Pharmacological rescue of mutant p53 conformation and function. Science 286, 25072510.CrossRefGoogle ScholarPubMed
Fowler, A. G., Foote, A. M., Moody, M. F., Vachette, P., Provencher, S. W., Gabriel, A., Bordas, J. & Koch, M. H. (1983). Stopped-flow solution scattering using synchrotron radiation: apparatus, data collection and data analysis. Journal of Biochemical and Biophysical Methods 7, 317329.CrossRefGoogle ScholarPubMed
Franklin, R. E. & Gosling, R. G. (1953a). Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleate. Nature 172, 156157.CrossRefGoogle ScholarPubMed
Franklin, R. E. & Gosling, R. G. (1953b). Molecular configuration in sodium thymonucleate. Nature 421, 400401.Google Scholar
Fraser, R. D. B., MacRae, T. P. & Suzuki, E. (1978). An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. Journal of Applied Crystallography 11, 693694.CrossRefGoogle Scholar
Fujisawa, T., Uruga, T., Yamaizumi, Z., Inoko, Y., Nishimura, S. & Ueki, T. (1994). The hydration of Ras p21 in solution during GTP hydrolysis based on solution X-ray scattering profile. Journal of Biochemistry (Tokyo) 115, 875880.CrossRefGoogle ScholarPubMed
Furnham, N., Blundell, T. L., DePristo, M. A. & Terwilliger, T. C. (2006). Is one solution good enough? Nature Stuctural Biology 13, 184185.Google ScholarPubMed
Gallagher, S. C., Callaghan, A. J., Zhao, J., Dalton, H. & Trewhella, J. (1999). Global conformational changes control the reactivity of methane monooxygenase. Biochemistry 38, 67526760.CrossRefGoogle ScholarPubMed
Garman, E. F. & Schneider, T. R. (1997). Macromolecular crystallography. Journal of Applied Crystallography 30, 211237.CrossRefGoogle Scholar
Getzoff, E. D., Tainer, J. A. & Olson, A. J. (1986). Recognition and interactions controlling the assemblies of beta barrel domains. Biophysical Journal 49, 191200.CrossRefGoogle ScholarPubMed
Gherardi, E., Sandin, S., Petoukhov, M. V., Finch, J., Youles, M. E., Ofverstedt, L. G., Miguel, R. N., Blundell, T. L., Vande Woude, G. F., Skoglund, U. & Svergun, D. I. (2006). Structural basis of hepatocyte growth factor/scatter factor and MET signalling. Proceedings of the National Academy of Sciences USA 103, 40464051.CrossRefGoogle ScholarPubMed
Giacovazzo, C., Monaco, H. L., Viterbo, D., Scordari, F., Gilli, G., Zanotti, G. & Catti, M. (1992). Fundamentals of Crystallography. Oxford: Oxford University Press.Google Scholar
Gilbert, H. E., Asokan, R., Holers, V. M. & Perkins, S. J. (2006). The 15 SCR flexible extracellular domains of human complement receptor type 2 can mediate multiple ligand and antigen interactions. Journal of Molecular Biology 362, 11321147.CrossRefGoogle ScholarPubMed
Gilbert, H. E., Eaton, J. T., Hannan, J. P., Holers, V. M. & Perkins, S. J. (2005). Solution structure of the complex between CR2 SCR 1–2 and C3d of human complement: an X-ray scattering and sedimentation modeling study. Journal of Molecular Biology 346, 859873.CrossRefGoogle Scholar
Gillmor, S. A., Villasenor, A., Fletterick, R., Sigal, E. & Browner, M. F. (1997). The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity. Nature Stuctural Biology 4, 10031009.CrossRefGoogle Scholar
Glatter, O. (1977). A new method for the evaluation of small angle X-ray scattering data. Journal of Applied Crystallography 10, 415421.CrossRefGoogle Scholar
Glatter, O. (1982). Data treatment. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 120165. London: Academic Press.Google Scholar
Goettig, P., Brandstetter, H., Groll, M., Gohring, W., Konarev, P. V., Svergun, D. I., Huber, R. & Kim, J. S. (2005). X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum. Journal of Biological Chemistry 280, 3338733396.CrossRefGoogle ScholarPubMed
Graille, M., Zhou, C.-Z., Receveur-Brechot, V., Collinet, B., Declerck, N. & van Tileurgh, H. (2005). Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. Journal of Biological Chemistry 280, 1478014789.CrossRefGoogle ScholarPubMed
Grishaev, A., Wu, J., Trewhella, J. & Bax, A. (2005). Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data. Journal of the American Chemical Society 127, 1662116628.CrossRefGoogle ScholarPubMed
Grossmann, J. G., Abraham, Z. H., Adman, E. T., Neu, M., Eady, R. R., Smith, B. E. & Hasnain, S. S. (1993). X-ray scattering using synchrotron radiation shows nitrite reductase from Achromobacter xylosoxidans to be a trimer in solution. Biochemistry 32, 73607366.CrossRefGoogle ScholarPubMed
Guarne, A., Ramon-Maiques, S., Wolff, E. M., Ghirlando, R., Hu, X., Miller, J. H. & Yang, W. (2004). Structure of the MutL C-terminal domain: a model of intact MutL and its roles in mismatch repair. EMBO Journal 23, 41344145.CrossRefGoogle Scholar
Guinier, A. & Fournet, F. (1955). Small Angle Scattering of X-rays. New York: Wiley InterscienceGoogle Scholar
Gutberlet, T., Heinemann, U. & Steiner, M. (2001). Protein crystallography with neutrons – status and perspectives. Acta Crystallographica D57, 349354.Google Scholar
Habel, J. E., Ohren, J. F. & Borgstahl, G. E. O. (2001). Dynamic light-scattering analysis of full-length human RPA14/32 dimer: purification, crystallization and self-association. Acta Crystallographica D57, 254259.Google Scholar
Hamada, D., Higurashi, T., Mayangi, K., Miyata, T., Fukui, T., Iida, T., Honda, T. & Yanagihara, I. (2007). Tetrameric structure of the thermostable direct hemolysin from Vibrio parahaemolyticus revealed by ultracentrifugation, small-angle X-ray scattering and electron microscopy. Journal of Molecular Biology 365, 187195.CrossRefGoogle ScholarPubMed
Hammel, M., Fierobe, H. P., Czjzek, M., Finet, S. & Receveur-Brechot, V. (2004a). Structural insights into the mechanism of formation of cellulosomes probed by small angle X-ray scattering. Journal of Biological Chemistry 279, 5598555994.CrossRefGoogle ScholarPubMed
Hammel, M., Fierobe, H. P., Czjzek, M., Kurkal, V., Smith, J. C., Bayer, E. A., Finet, S. & Receveur-Brechot, V. (2005). Structural basis of cellulosome efficiency explored by small angle X-ray scattering. Journal of Biological Chemistry 280, 3856238568.CrossRefGoogle ScholarPubMed
Hammel, M., Kriechbaum, M., Gries, A., Kostner, G. M., Laggner, P. & Prassl, R. (2002). Solution structure of human and bovine β(2)-glycoprotein I revealed by small-angle X-ray scattering. Journal of Molecular Biology 321, 8597.CrossRefGoogle ScholarPubMed
Hammel, M., Sfyroera, G., Ricklin, D., Magotti, P., Lambris, J. D. & Geisbrecht, B. V. (2007). A structural basis for complement inhibition by Staphylococcus aureus. Nature Immunology 8, 430437.CrossRefGoogle ScholarPubMed
Hammel, M., Walther, M., Prassl, R. & Kuhn, H. (2004b). Structural flexibility of the N-terminal beta-barrel domain of 15-lipoxygenase-1 probed by small angle X-ray scattering. Functional consequences for activity regulation and membrane binding. Journal of Molecular Biology 343, 917929.CrossRefGoogle ScholarPubMed
Hansmann, U. H. E. & Okamoto, Y. (1999). New Monte Carlo algorithms for protein folding. Current Opinions in Structural Biology 9, 177183.CrossRefGoogle ScholarPubMed
Hao, Q. (2001). Phasing from an envelope. Acta Crystallographica D57, 14101414.Google Scholar
Hao, Q. (2006). Macromolecular envelope determination and envelope-based phasing. Acta Crystallographica D62, 909914.Google Scholar
Hao, Q., Dodd, F. E., Grossmann, J. G. & Hasnain, S. S. (1999). Ab initio phasing using molecular envelopes from solution X-ray scattering. Acta Crystallographica D55, 243246.Google Scholar
Head-Gordon, T. & Hura, G. (2002). Water structure from scattering experiments and simulation. Chemical Reviews 102, 26512670.CrossRefGoogle ScholarPubMed
Heifetz, A. & Eisenstein, M. (2003). Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Engineering 16, 179–85.CrossRefGoogle ScholarPubMed
Heller, W. T. (2005). Influence of multiple well-defined conformations on small-angle scattering of proteins in solution. Acta Crystallographica D61, 3344.Google Scholar
Heller, W. T. (2006). ELLSTAT: shape modeling for solution small-angle scattering of proteins and protein complexes with automated statistical characterization. Journal of Applied Crystallography 39, 671675.CrossRefGoogle Scholar
Heller, W. T., Krueger, J. K. & Trewhella, J. (2003). Further insights into calmodulin-myosin light chain kinase interaction from solution scattering and shape restoration. Biochemistry 42, 1057910588.CrossRefGoogle ScholarPubMed
Helliwell, J. R. (1997). Overview of synchrotron radiation and macromolecular crystallography. Methods in Enzymology 276, 203217.CrossRefGoogle ScholarPubMed
Hendrickson, W. A. & Ogata, C. M. (1997). Phase determination from multiwavelength anomalous diffraction measurements. Methods in Enzymology 276, 494523.CrossRefGoogle ScholarPubMed
Hess, M. T., Gupta, R. D. & Kolodner, R. D. (2002). Dominant Saccharomyces cerevisiae msh6 mutations cause increased mispair binding and decreased disassociation from mispairs by Msh2-Msh6 in the absence of ATP. Journal of Biological Chemistry 277, 2554525553.CrossRefGoogle Scholar
Hinsen, K. (1998). Analysis of domain motions by approximate normal mode calculations. Proteins 33, 417429.3.0.CO;2-8>CrossRefGoogle ScholarPubMed
Hinsen, K., Reuter, N., Navaza, J., Stokes, D. L. & Lacapere, J. J. (2005). Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophysical Journal 88, 818827.CrossRefGoogle ScholarPubMed
Hope, H. (1990). Crystallography of biological macromolecules at ultra-low temperature. Annual Reviews of Biophysics and Biophysical Chemistry 19, 107126.CrossRefGoogle ScholarPubMed
Hopfner, K. P., Karcher, A., Craig, L., Woo, T. T., Carney, J. P. & Tainer, J. A. (2001). Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell 105, 473485.CrossRefGoogle ScholarPubMed
Hopfner, K. P., Karcher, A., Shin, D. S., Craig, L., Arthur, L. M., Carney, J. P. & Tainer, J. A. (2000). Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily. Cell 101, 789800.CrossRefGoogle ScholarPubMed
Howlin, B., Butler, S. A., Moss, D. S., Harris, G. W. & Driessen, H. P. C. (1993). TLSANL: TLS parameter-analysis program for segmented anisotropic refinement of macromolecular structures. Journal of Applied Crystallography 26, 622.CrossRefGoogle Scholar
Hubbard, S. R., Hodgson, K. O. & Doniach, S. (1988). Small-angle X-ray scattering investigation of the solution structure of troponin C. Journal of Biological Chemistry 263, 41514158.CrossRefGoogle ScholarPubMed
Hung, L.-W., Wang, I. X., Nikaido, K., Liu, P.-Q., Ames, G. F. & Kim, S.-H. (1998). Crystal structure of the ATP-binding subunit of an ABC transporter. Nature 396, 703707.CrossRefGoogle ScholarPubMed
Jancarik, J., Pufan, R., Hong, C., Kim, S.-H. & Kim, R. (2004). Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins. Acta Crystallographica D60, 16701673.Google Scholar
Jelsch, C., Teeter, M. M., Lamzin, V., Pichon-Pesme, V., Blessing, R. H. & Lecomte, C. (2000). Accurate protein crystallography at ultrahigh resolution: valence electron distribution in crambin. Proceedings of the National Academy of Sciences USA 97, 31713176.CrossRefGoogle ScholarPubMed
Johs, A., Hammel, M., Waldner, I., May, R. P., Laggner, P. & Prassl, R. (2006). Modular structure of solubilized human apolipoprotein B-100. Low resolution model revealed by small angle neutron scattering. Journal of Biological Chemistry 281, 1973219739.CrossRefGoogle ScholarPubMed
Jones, P. M. & George, A. M. (1999). Subunit interactions in ABC transporters: toward a functional architecture. FEMS Microbiology Letters 179, 187202.CrossRefGoogle Scholar
Jones, S. & Thornton, J. M. (1996). Principles of protein-protein interactions. Proceedings of the National Academy of Sciences USA 93, 1320.CrossRefGoogle ScholarPubMed
Kamata, K., Mitsuya, M., Nishimura, T., Eiki, J. & Nagata, Y. (2004). Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase. Structure 12, 429438.CrossRefGoogle ScholarPubMed
Karplus, M. & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Stuctural Biology 9, 646652.CrossRefGoogle ScholarPubMed
Karpowich, N., Martsinkevich, O., Millen, L., Yuan, Y.-R., Dia, P. L., MacVey, K., Thomas, P. J. & Hunt, J. F. (2001). Crystal structure of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter. Structure 9, 571586.CrossRefGoogle ScholarPubMed
Ke, H. (1997). Overview of isomorphous replacement phasing. Methods in Enzymology 276, 448461.CrossRefGoogle ScholarPubMed
Keskin, O., Ma, B. & Nussinov, R. (2005). Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. Journal of Molecular Biology 345, 12811294.CrossRefGoogle ScholarPubMed
Kidera, A. & Go, N. (1990). Refinement of protein dynamic structure: normal mode refinement. Proceedings of the National Academy of Sciences USA 87, 37183722.CrossRefGoogle ScholarPubMed
Kleywegt, G. J. & Jones, T. A. (1997). Model building and refinement practice. Methods in Enzymology 277, 208230.CrossRefGoogle ScholarPubMed
Knablein, J., Neuefeind, T., Schneider, F., Bergner, A., Messerschmidt, A., Lowe, J., Steipe, B. & Huber, R. (1997). Ta6Br(2+)12, a tool for phase determination of large biological assemblies by X-ray crystallography. Journal of Molecular Biology 270, 17.CrossRefGoogle ScholarPubMed
Ko, T. P., Robinson, H., Gao, Y. G., Cheng, C. H., DeVries, A. L. & Wang, A. H. (2003). The refined crystal structure of an eel type III antifreeze protein RD1 at 0·62 Å resolution reveals structural microheterogeneity of protein and solvation. Biophysical Journal 84, 12281237.CrossRefGoogle ScholarPubMed
Koch, M. H., Vachette, P. & Svergun, D. I. (2003). Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Quarterly Reviews of Biophysics 36, 147227.CrossRefGoogle ScholarPubMed
Kollman, J. M. & Quispe, J. (2005). The 17 A structure of the 420 kDa lobster clottable protein by single particle reconstruction from cryoelectron micrographs. Journal of Structural Biology 151, 306314.CrossRefGoogle ScholarPubMed
Konarev, P. V., Petoukhov, M. V. & Svergun, D. I. (2001). MASSHA – a graphics system for rigid-body modeling of macromolecular complexes against solution scattering data. Journal of Applied Crystallography 34, 527532.CrossRefGoogle Scholar
Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J. & Svergun, D. I. (2003). PRIMUS: a Windows PC-based system for small-angle scattering data analysis. Journal of Applied Crystallography 36, 12771282.CrossRefGoogle Scholar
Kong, Y., Ming, D., Wu, Y., Stoops, J. K., Zhou, Z. H. & Ma, J. (2003). Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model. Journal of Molecular Biology 330, 129135.CrossRefGoogle ScholarPubMed
Kontopidis, G., Wu, S. Y., Zheleva, D. I., Taylor, P., McInnes, C., Lane, D. P., Fischer, P. M. & Walkinshaw, M. D. (2005). Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design. Proceedings of the National Academy of Sciences USA 102, 18711876.CrossRefGoogle ScholarPubMed
Korzhnev, D. M., Billeter, M., Arseniev, A. S. & Orekhov, V. Y. (2001). NMR studies of Brownian tumbling and internal motions in proteins. Progress Nuclear Magnetic Resonance Spectroscopy 38, 197266.CrossRefGoogle Scholar
Kosinski, J., Steindorf, L., Bujnicki, J. M., Giron-Monzon, L. & Friedhoff, P. (2005). Analysis of the quaternary structure of the MutL C-terminal domain. Journal of Molecular Biology 351, 895909.CrossRefGoogle ScholarPubMed
Kozak, M. (2005). Direct comparison of the crystal and solution structure of glucose/xylose isomerase from Streptomyces rubiginosus. Protein Peptide Letters 12, 547550.CrossRefGoogle ScholarPubMed
Kozin, M. B. & Svergun, D. I. (2001). Automated matching of high- and low-resolution structural models. Journal of Applied Crystallography 34, 3341.CrossRefGoogle Scholar
Kozin, M. B., Volkov, V. V. & Svergun, D. I. (1997). ASSA, a program for three-dimensional rendering in solution scattering from biopolymers. Journal of Applied Crystallography 30, 811815.CrossRefGoogle Scholar
Kratky, O. & Porod, G. (1949). Roetgenuntersuchung Geloester Fadenmolekuele. Recueil des Travaux Chimiques des Pays-Bas 68, 11061122.CrossRefGoogle Scholar
Krebs, A., Durchschlag, H. & Zipper, P. (2004). Small angle X-ray scattering studies and modeling of Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin. Biophysical Journal 87, 11731185.CrossRefGoogle ScholarPubMed
Krebs, W. G., Alexandrov, V., WIlson, C. A., Echols, N., Yu, H. & Gerstein, M. (2002). Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48, 682695.CrossRefGoogle Scholar
Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992). The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. Journal of Molecular Biology 228, 1322.CrossRefGoogle ScholarPubMed
Kuwamoto, S., Akiyama, S. & Fujisawa, T. (2004). Radiation damage to a protein solution, detected by synchrotron X-ray small-angle scattering: dose-related considerations and suppression by cryoprotectants. Journal of Synchrotron Radiation 11, 462468.CrossRefGoogle ScholarPubMed
Kwok, L. W., Shcherbakova, I., Lamb, J. S., Park, H. Y., Andresen, K., Smith, H., Brenowitz, M. & Pollack, L. (2006). Concordant exploration of the kinetics of RNA folding from global and local perspectives. Journal of Molecular Biology 355, 282293.CrossRefGoogle ScholarPubMed
Lamers, M. H., Georgescu, R. E., Lee, S. G., O'Donnell, M. & Kuriyan, J. (2006). Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III. Cell 126, 881892.CrossRefGoogle ScholarPubMed
Lamers, M. H., Georgijevic, D., Lebbink, J. H., Winterwerp, H. H. K., Agianian, B., de Wind, N. & Sixma, T. K. (2004). ATP increases the affinity between MutS ATPase domains: Implications for ATP hydrolysis and conformational changes. Journal of Biological Chemistry 279, 4387943885.CrossRefGoogle ScholarPubMed
Lamers, M. H., Perrakis, A., Enzlin, J. H., Winterwerp, H. H., de Wind, N. & Sixma, T. K. (2000). The crystal structure of the DNA mismatch repair protein MutS binding to a G×T mismatch. Nature 407, 711717.CrossRefGoogle Scholar
Lattman, E. E. (1989). Rapid calculation of the solution scattering profile from a macromolecule of known structure. Proteins 5, 149155.CrossRefGoogle ScholarPubMed
Leach, A. R. (2001). Exploring conformational space using simulation methods. In Molecular Modelling: Principles and Applications (ed. Hall, P.), pp. 457508. Harlow: Pearson Education.Google Scholar
Lee, K. K., Gan, L., Tsuruta, H., Hendrix, R. W., Duda, R. L. & Johnson, J. E. (2004). Evidence that a local refolding event triggers maturation of HK97 bacteriophage capsid. Journal of Molecular Biology 340, 419433.CrossRefGoogle ScholarPubMed
Lei, M., Zavodszky, M. I., Kuhn, L. A. & Thorpe, M. F. (2004). Sampling protein conformations and pathways. Journal of Computational Chemistry 25, 11331148.CrossRefGoogle ScholarPubMed
Levitt, M., Sander, C. & Stern, P. S. (1985). Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease, and lysozyme. Journal of Molecular Biology 181, 423447.CrossRefGoogle Scholar
Levy, Y. & Becker, O. M. (2002). Conformational polymorphism of wild-type and mutant prion proteins: energy landscape analysis. Proteins 47, 458468.CrossRefGoogle ScholarPubMed
Li, L., Chen, R. & Weng, Z. (2003). RDOCK: refinement of rigid-body protein docking predictions. Proteins 53, 693707.CrossRefGoogle ScholarPubMed
Li, X., Keskin, O., Ma, B., Nussinov, R. & Liang, J. (1985). Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that preorganize in the unbound states: implications for docking. Journal of Molecular Biology 334, 781795.Google Scholar
Lindahl, E. & Delarue, M. (2005). Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimiziation. Nucleic Acids Research 33, 44964506.CrossRefGoogle Scholar
Lipfert, J., Columbus, L., Chu, V. B. & Doniach, S. (2007a). Analysis of small-angle X-ray scattering data of protein-detergent complexes by singular value decomposition. Journal of Applied Crystallography 40, 15.CrossRefGoogle Scholar
Lipfert, J., Das, R., Chu, V. B., Kudaravalli, M., Boyd, N., Herschlag, D. & Doniach, S. (2007b). Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology 365, 13931406.CrossRefGoogle ScholarPubMed
Lipfert, J. & Doniach, S. (2007). Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annual Review of Biophysics and Biomolecular Structure 36, 307327.CrossRefGoogle ScholarPubMed
Liu, Q., Weaver, A. J., Xiang, T., Thiel, D. J. & Hao, Q. (2003). Low-resolution molecular replacement using a six-dimensional search. Acta Crystallographica D59, 10161019.Google Scholar
Locher, K. P., Lee, A. T. & Rees, D. C. (2002). The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 296, 10911098.CrossRefGoogle Scholar
Losonczi, J. A., Andrec, M., Fischer, M. W. & Prestegard, J. H. (1999). Order matrix analysis of residual dipolar couplings using singular value decomposition. Journal of Magnetic Resonance 138, 334342.CrossRefGoogle ScholarPubMed
Lucic, V., Forster, F. & Baumeister, W. (2005). Structural studies by electron tomography: from cells to molecules. Annual Reviews in Biochemistry 74, 833865.CrossRefGoogle ScholarPubMed
Lunde, C. S., Rouhani, S., Facciotti, M. T. & Glaeser, R. M. (2006). Membrane-protein stability in a phospholipid-based crystallization medium. Journal of Structural Biology 154, 223231.CrossRefGoogle Scholar
Ma, B., Elkayam, T., Wolfson, H. & Nussinov, R. (2003). Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proceedings of the National Academy of Sciences USA 100, 57725777.CrossRefGoogle ScholarPubMed
MacKerell, A. D. Jr., Bashford, D., Bellott, M., Dunbrack, R. L. Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Mischnick, S., Ngo, T., Nguygen, D. T., Prodhom, B., Reiher, W. E. III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Staub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. & Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102, 35863616.CrossRefGoogle ScholarPubMed
Maiorov, V. & Abagyan, R. (1997). A new method for modeling large-scale rearrangements of protein domains. Proteins 27, 410424.3.0.CO;2-G>CrossRefGoogle ScholarPubMed
Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi, V., Mitchell, J. C., Nelson, F., Tsigelny, I. & Ten Eyck, L. F. (2001). Protein docking using continuum electrostatics and geometric fit. Protein Engineering 14, 105113.CrossRefGoogle ScholarPubMed
Marino, M., Zou, P., Svergun, D., Garcia, P., Edlich, C., Simon, B., Wilmanns, M., Muhle-Goll, C. & Mayans, O. (2006). The Ig doublet Z1Z2: a model system for the hybrid analysis of conformational dynamics in Ig tandems from titin. Structure 14, 14371447.CrossRefGoogle Scholar
Matthews, B. W. (1968). Solvent content of protein crystals. Journal of Molecular Biology 33, 491497.CrossRefGoogle ScholarPubMed
Mattinen, M. L., Paakkonen, K., Ikonen, T., Craven, J., Drakenberg, T., Serimaa, R., Waltho, J. & Annila, A. (2002). Quaternary structure built from subunits combining NMR and small-angle X-ray scattering data. Biophysical Journal 83, 11771183.CrossRefGoogle ScholarPubMed
McMurray, C. T. & Tainer, J. A. (2003). Cancer, cadmium and genome integrity. Nature Genetics 34, 239241.CrossRefGoogle ScholarPubMed
Meinhold, L. & Smith, J. C. (2007). Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins Structure Function and Bioinformatics 66, 941953.CrossRefGoogle ScholarPubMed
Mendenhall, M. D. & Hodge, A. F. (1998). Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbial Molecular Biology Reviews 62, 11911243.CrossRefGoogle ScholarPubMed
Mendillo, M. L., Mazur, D. J. & Kolodner, R. D. (2005). Analysis of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 complexes with DNA using a reversible DNA end-blocking system. Journal of Biological Chemistry 280, 2224522257.CrossRefGoogle ScholarPubMed
Mendillo, M. L., Putnam, C. D. & Kolodner, R. D. (2007). Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo. Journal of Biological Chemistry 282, 1634516354.CrossRefGoogle Scholar
Merzel, F. & Smith, J. C. (2002a). Is the first hydration shell of lysozyme of higher density than bulk water? Proceedings of the National Academy of Sciences USA 99, 53785383.CrossRefGoogle ScholarPubMed
Merzel, F. & Smith, J. C. (2002b). SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallographica D58, 242249.Google Scholar
Metropolis, N., Rosenbluth, A., Rosenbluth, M., Teller, A. & Teller, E. (1953). Equation of state calculations by fast computing machines. Journal of Chemical Physics 21, 10871092.CrossRefGoogle Scholar
Miake-Lye, R. C., Doniach, S. & Hodgson, K. O. (1983). Anomalous x-ray scattering from terbium-labeled parvalbumin in solution. Biophysical Journal 41, 287292.CrossRefGoogle ScholarPubMed
Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks, C. L. 3rd, Ban, N. & Frank, J. (2005). Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438, 318324.CrossRefGoogle Scholar
Mizuguchi, K., Kidera, A. & Go, N. (1994). Collective motions in proteins investigated by X-ray diffuse scattering. Proteins 18, 3448.CrossRefGoogle ScholarPubMed
Montange, R. K. & Batey, R. T. (2006). Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441, 11721175.CrossRefGoogle ScholarPubMed
Moore, P. B. (1980). Small-angle scattering. Information content and error analysis. Journal of Applied Crystallography 13, 168175.CrossRefGoogle Scholar
Mueller, J. J., Hansen, S. & Puerschel, H. V. (1996). The use of small-angle scattering and the maximum-entropy method for shape-model determination from distance-distribution functions. Journal of Applied Crystallography 29, 547554.CrossRefGoogle Scholar
Muller, K., Laggner, P., Glatter, O. & Kostner, G. (1978). The structure of human-plasma low-density lipoprotein B. An X-ray small-angle scattering study. European Journal of Biochemistry 82, 7390.CrossRefGoogle ScholarPubMed
Mustard, D. & Ritchie, D. W. (2005). Docking essential dynamics eigenstructures. Proteins 60, 269274.CrossRefGoogle ScholarPubMed
Mylonas, F. & Svergun, D. I. (2007). Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. Journal of Applied Crystallography 40, s245s249.CrossRefGoogle Scholar
Nagar, B., Hantschel, O., Seeliger, M., Davies, J. M., Weis, W. I., Superti-Furga, G. & Kuriyan, J. (2006). Organization of the SH3-SH2 unit in active and inactive forms of the c-Abl tyrosine kinase. Molecular Cell 21, 787798.CrossRefGoogle ScholarPubMed
Nagar, B., Hantschel, O., Young, M. A., Scheffzek, K., Veach, D., Bornmann, W., Clarkson, B., Superti-Furga, G. & Kuriyan, J. (2003). Structural basis of the autoinhibition of c-Abl tyrosine kinase. Cell 112, 859871.CrossRefGoogle ScholarPubMed
Nath, A., Atkins, W. M. & Sligar, S. G. (2007). Applications of phospholipid bilayer nanodiscs in the study of membranes and membrane proteins. Biochemistry 46, 20592069.CrossRefGoogle Scholar
Navaza, J. (2001). Implementation of molecular replacement in AMoRe. Acta Crystallographica D57, 13671372.Google Scholar
Navaza, J., Lepault, J., Rey, F. A., Alvarez-Rua, C. & Borge, J. (2002). On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta Crystallographica D58, 18201825.Google Scholar
Nemeth-Pongracz, V., Barabas, O., Fuxreiter, M., Simon, I., Pichova, I., Rumlova, M., Zabranska, H., Svergun, D., Petoukhov, M., Harmat, V., Klement, E., Hunyadi-Gulyas, E., Medzihradszky, K. F., Konya, E. & Vertessy, B. G. (2007). Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins. Nucleic Acids Research 35, 495505.CrossRefGoogle ScholarPubMed
Nilsson, L., Clore, G. M., Gronenbom, A. M., Brunger, A. T. & Karplus, M. (1986). Structural refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton restrains: application to 5′d(C-G-T-A-C-G)2. Journal of Molecular Biology 188, 455475.CrossRefGoogle Scholar
Nowak, E., Panjikar, S., Konarev, P., Svergun, D. I. & Tucker, P. A. (2006a). The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis. Journal of Biological Chemistry 281, 96599666.CrossRefGoogle ScholarPubMed
Nowak, E., Panjikar, S., Morth, J. P., Jordanova, R., Svergun, D. I. & Tucker, P. A. (2006b). Structural and functional aspects of the sensor histidine kinase PrrB from Mycobacterium tuberculosis. Structure 14, 275285.CrossRefGoogle ScholarPubMed
Obmolova, G., Ban, C., Hsieh, P. & Yang, W. (2000). Crystal structure of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407, 703710.CrossRefGoogle ScholarPubMed
Ockwell, D. M., Hough, M., Grossmann, J. G., Hasnain, S. S. & Hao, Q. (2000). Implementation of cluster analysis for ab initio phasing using the molecular envelope from solution X-ray scattering. Acta Crystallographica D56, 10021006.Google Scholar
Palma, P. N., Krippahl, L., Wampler, J. E. & Moura, J. J. (2000). BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 39, 372384.3.0.CO;2-Q>CrossRefGoogle Scholar
Parge, H. E., Arvai, A. S., Murtari, D. J., Reed, S. I. & Tainer, J. A. (1993). Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control. Science 262, 387395.CrossRefGoogle ScholarPubMed
Parsiegla, G., Reverbel-Leroy, C., Tardif, C., Belaich, J. P., Driguez, H. & Haser, R. (2000). Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action. Biochemistry 39, 1123811246.CrossRefGoogle ScholarPubMed
Pascal, J. M., O’Brien, P. J., Tomkinson, A. E. & Ellenberger, T. (2004). Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473478.CrossRefGoogle ScholarPubMed
Pascal, J. M., Tsodikov, O. V., Hura, G. L., Song, W., Cotner, E. A., Classen, S., Tomkinson, A. E., Tainer, J. A. & Ellenberger, T. (2006). A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Molecular Cell 24, 279291.CrossRefGoogle ScholarPubMed
Pennock, E., Buckley, K. & Lundblad, V. (2001). Cdc13 delivers separate complexes to the telomere for end protection and replication. Cell 104, 387396.CrossRefGoogle Scholar
Perez, J., Vachette, P., Russo, D., Desmadril, M. & Durand, D. (2001). Heat-induced unfolding of neocarzinostatin, a small all-beta protein investigated by small-angle X-ray scattering. Journal of Molecular Biology 308, 721743.CrossRefGoogle ScholarPubMed
Perkins, S. J. (2001). X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modeling fits. Biophysical Chemistry 93, 129139.CrossRefGoogle ScholarPubMed
Perrakis, A., Morris, R. M. & Lamzin, V. S. (1999). Automated protein model building combined with iterative structure refinement. Nature Stuctural Biology 6, 458463.CrossRefGoogle ScholarPubMed
Perry, J. J., Fan, L. & Tainer, J. A. (2007). Developing master keys to brain pathology, cancer, and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair. Neuroscience 145, 12801299.CrossRefGoogle ScholarPubMed
Perry, J. J., Yannone, S. M., Holden, L. G., Hitomi, C., Asaithamby, A., Han, S., Cooper, P. K., Chen, D. J. & Tainer, J. A. (2006). WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nature Strucutral and Molecular Biology 13, 414422.CrossRefGoogle ScholarPubMed
Perutz, M. F., Bolton, W., Diamond, R., Muirhead, H. & Watson, H. C. (1964). Structure of haemoglobin. An X-ray examination of reduced horse haemoglobin. Nature 203, 687690.CrossRefGoogle ScholarPubMed
Petoukhov, M. V., Eady, N. A., Brown, K. A. & Svergun, D. I. (2002). Addition of missing loops and domains to protein models by X-ray solution scattering. Biophysical Journal 83, 31133125.CrossRefGoogle ScholarPubMed
Petoukhov, M. V., Monie, T. P., Allain, F. H., Matthews, S., Curry, S. & Svergun, D. I. (2006). Conformation of polypyrimidine tract binding protein in solution. Structure 14, 10211027.CrossRefGoogle ScholarPubMed
Petoukhov, M. V. & Svergun, D. I. (2005). Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophysical Journal 89, 12371250.CrossRefGoogle ScholarPubMed
Petoukhov, M. V. & Svergun, D. I. (2006). Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. European Biophysical Journal 35, 567576.CrossRefGoogle ScholarPubMed
Petoukhov, M. V., Svergun, D. I., Konarev, P. V., Ravasio, S., van den Heuvel, R. H., Curti, B. & Vanoni, M. A. (2003). Quaternary structure of Azospirillum brasilense NADPH-dependent glutamate synthase in solution as revealed by synchrotron radiation x-ray scattering. Journal of Biological Chemistry 278, 2993329939.CrossRefGoogle ScholarPubMed
Petrova, T. & Podjarny, A. (2004). Protein crystallography at subatomic resolution. Reports on Progress in Physics 67, 15651605.CrossRefGoogle Scholar
Pilz, I. (1982). Proteins. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 239293. London: Academic Press.Google Scholar
Pioletti, M., Findeisen, F., Hura, G. L. & Minor, D. L. J. (2006). Three-dimensional structure of KChIP1-Kv4.3 T1 complex reveals a cross-shaped octamer. Nature Strucutral and Molecular Biology 13, 987995.CrossRefGoogle ScholarPubMed
Porod, G. (1951). X-ray small angle scattering of close packed colloidal systems. Kolloid Zeitschrift 124, 83114.CrossRefGoogle Scholar
Porod, G. (1982). General Theory. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 1751. London: Academic Press.Google Scholar
Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. (1992). Numerical Recipes in C, Second Edition. New York, NY: Cambridge University PressGoogle Scholar
Provencher, S. W. & Glockner, J. (1983). Analysis of the components present in kinetics (or titration) curves. Journal of Biochemical and Biophysical Methods 7, 331334.CrossRefGoogle ScholarPubMed
Putnam, C. D., Clancy, S. B., Tsuruta, H., Gonzalez, S., Wetmur, J. G. & Tainer, J. A. (2001). Structure and mechanism of the RuvB Holliday junction branch migration motor. Journal of Molecular Biology 311, 297310.CrossRefGoogle ScholarPubMed
Putnam, C. D., Shroyer, M. J., Lundquist, A. J., Mol, C. D., Arvai, A. S., Mosbaugh, D. W. & Tainer, J. A. (1999). Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. Journal of Molecular Biology 287, 331346.CrossRefGoogle ScholarPubMed
Putnam, C. D. & Tainer, J. A. (2005). Protein mimicry of DNA and pathway regulation. DNA Repair 4, 14101420.CrossRefGoogle ScholarPubMed
Qazi, O., Bolgiano, B., Crane, D., Svergun, D. I., Konarev, P. V., Yao, Z. P., Robinson, C. V., Brown, K. A. & Fairweather, N. (2007). The HC fragment of tetanus toxin forms stable, concentration-dependent dimers via an intermolecular disulphide bond. Journal of Molecular Biology 365, 123134.CrossRefGoogle Scholar
Rajamani, D., Thiel, S., Vajda, S. & Camacho, C. J. (2004). Anchor residues in protein-protein interactions. Proceedings of the National Academy of Sciences USA 101, 1128711292.CrossRefGoogle ScholarPubMed
Rallison, J. M. & Harding, S. E. (1985). Excluded volume for pairs of triaxial ellipsoids at dominant Brownian motion. Journal of Colloid Interface Science 103, 284289.CrossRefGoogle Scholar
Ravelli, R. B. & McSweeney, S. M. (2000). The ‘fingerprint’ that X-rays can leave on structures. Structure Fold Design 8, 315328.CrossRefGoogle ScholarPubMed
Redecke, L., Bergen, M., Clos, J., Konarev, P. V., Svergun, D. I., Fittschen, U. E., Broekaert, J. A., Bruns, O., Georgieva, D., Mandelkow, E., Genov, N. & Betzel, C. (2007). Structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. Journal of Structural Biology 157, 308320.CrossRefGoogle ScholarPubMed
Rejto, P. A. & Freer, S. T. (1996). Protein conformational substrates from X-ray crystallography. Progress in Biophysical and Molecular Biology 66, 167196.CrossRefGoogle Scholar
Rodier, F., Bahadur, R. P., Chakrabarti, P. & Janin, J. (2005). Hydration of protein-protein interfaces. Proteins 60, 3645.CrossRefGoogle ScholarPubMed
Roseman, A. M. (2000). Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallographica D56, 13321340.Google Scholar
Rosenberg, O. S., Deindl, S., Sung, R. J., Nairn, A. C. & Kuriyan, J. (2005). Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme. Cell 123, 849860.CrossRefGoogle ScholarPubMed
Rossmann, M. G. (1995). Ab initio phase determination and phase extension using non-crystallographic symmetry. Current Opinions in Structural Biology 5, 650655.CrossRefGoogle ScholarPubMed
Rossmann, M. G. (2000). Fitting atomic models into electron-microscopy maps. Acta Crystallographica D56, 13411349.Google Scholar
Rouiller, I., DeLaBarre, B., May, A. P., Weis, W. I., Brunger, A. T., Milligan, R. A. & Wilson-Kubalek, E. M. (2002). Conformational changes of the multifunctional p97 AAA ATPase during its ATPase cycle. Nature Structural Biology 9, 950957.CrossRefGoogle ScholarPubMed
Sakurai, S., Kitano, K., Yamaguchi, H., Hamada, K., Okada, K., Fukuda, K., Uchida, M., Ohtsuka, E., Morioka, H. & Hakoshima, T. (2005). Structural basis for recruitment of human flap endonuclease 1 to PCNA. EMBO Journal 34, 683693.CrossRefGoogle Scholar
Sanishvili, R., Volz, K. W., Westbrook, E. M. & Margoliash, E. (1995). The low ionic strength crystal structure of horse cytochrome c at 2·1 Å resolution and comparison with its high ionic strength counterpart. Structure 3, 707716.CrossRefGoogle ScholarPubMed
Scheres, S. H. G., H. Valle, M., Herman, G. T., Eggermont, P. P., Frank, J. & Carazo, J. M. (2007). Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nature Methods 4, 2729.CrossRefGoogle ScholarPubMed
Schlick, T. (2001). Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work. Structure 9, R4553.CrossRefGoogle ScholarPubMed
Schnecke, V., Swanson, C. A., Getzoff, E. D., Tainer, J. A. & Kuhn, L. A. (1998). Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 33, 7487.3.0.CO;2-L>CrossRefGoogle ScholarPubMed
Schomaker, V. & Trueblood, K. (1968). On rigid body motion of molecules in crystals. Acta Crystallographica B24, 6376.CrossRefGoogle Scholar
Semenyuk, A. V. & Svergun, D. I. (1991). GNOM – a program package for small-angle scattering data processing. Journal of Applied Crystallography 24, 537540.CrossRefGoogle Scholar
Shannon, C. E. & Moore, W. (1949). The Mathematical Theory of Communication. Urbana, IL: University of Illinois Press.Google Scholar
Sheldrick, G. M. & Schneider, T. R. (1997). SHELXL: high-resolution refinement. Methods in Enzymology 277, 319343.CrossRefGoogle ScholarPubMed
Shell, S. S., Putnam, C. D. & Kolodner, R. D. (2007). The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA. Molecular Cell 26, 565578.CrossRefGoogle Scholar
Shin, D. S., Pellegrini, L., Daniels, D. S., Yelent, B., Craig, L., Bates, D., Yu, D. S., Shivji, M. K., Hitomi, C., Arvai, A. S., Volkmann, N., Tsuruta, H., Blundell, T. L., Venkitaraman, A. R. & Tainer, J. A. (2003). Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO Journal. 22, 45664576.CrossRefGoogle ScholarPubMed
Sim, G. A. (1959). The distribution of phase angles for structrues containing heavy atoms. II. A modification of the normal heavy atom method for non-centrosymmetric structures. Acta Crystallographica 12, 813815.CrossRefGoogle Scholar
Smith, G. R., Sternberg, M. J. & Bates, P. A. (2005). The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. Journal of Molecular Biology 347, 10771101.CrossRefGoogle ScholarPubMed
Smith, K. F., Harrison, R. A. & Perkins, S. J. (1990). Structural comparisons of the native and reactive-centre-cleaved forms of alpha 1-antitrypsin by neutron- and X-ray scattering in solution. Biochemical Journal 267, 203212.CrossRefGoogle ScholarPubMed
Smith, P. E., van Schaik, R. C., Szyperski, T., Wuthrich, K. & van Gunsteren, W. F. (1995). Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. Journal of Molecular Biology 246, 356365.CrossRefGoogle ScholarPubMed
Sokolova, A. V., Volkov, V. V. & Svergun, D. I. (2003a). Database for rapid protein classification based on small-angle X-ray scattering data. Crystallography Reports 48, 10271033.CrossRefGoogle Scholar
Sokolova, A. V., Volkov, V. V. & Svergun, D. I. (2003b). Prototype of a database for rapid protein classification based on solution scattering data. Journal of Applied Crystallography 36, 865868.CrossRefGoogle Scholar
Sondermann, H., Nagar, B., Bar-Sagi, D. & Kuriyan, J. (2005). Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless. Proceedings of the National Academy of Sciences USA 102, 1663216637.CrossRefGoogle ScholarPubMed
Sousa, M. C., Trame, C. B., Tsuruta, H., Wilbanks, S. M., Reddy, V. S. & McKay, D. B. (2000). Crystal and solution structures of an HslUV protease-chaperone complex. Cell 103, 633643.CrossRefGoogle ScholarPubMed
Stuhrmann, H. B. (1973). Comparison of the three basic scattering functions of myoglobin in solution with those from the known structure in crystalline state. Journal of Molecular Biology 77, 363369.CrossRefGoogle ScholarPubMed
Stuhrmann, H. B. (1981). Anomalous small angle scattering. Quarterly Reviews in Biophysics 14, 433460.CrossRefGoogle ScholarPubMed
Stuhrmann, H. B. (1982). Contrast variation. In Small Angle X-ray Scattering (ed. Glatter, O. and Kratky, O.), pp. 197213. London: Academic Press.Google Scholar
Stuhrmann, H. B., Haas, J., Ibel, K., Wolf, B., Koch, M. H., Parfait, R. & Crichton, R. R. (1976). New low resolution model for 50S subunit of Escherichia coli ribosomes. Proceedings of the National Academy of Sciences USA 73, 2379–83.CrossRefGoogle ScholarPubMed
Stuhrmann, H. B., Tardieu, A., Mateu, L., Sardet, C., Luzzati, V., Aggerbeck, L. & Scanu, A. M. (1975). Neutron scattering study of human serum low density lipoprotein. Proceedings of the National Academy of Sciences USA 72, 22702273.CrossRefGoogle ScholarPubMed
Suhre, K., Navaza, J. & Sanejouand, Y. H. (2006). NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallographica D62, 10981100.Google Scholar
Suhre, K. & Sanejouand, Y. H. (2004). ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research 32, W610614.CrossRefGoogle ScholarPubMed
Sun, Z., Reid, K. B. & Perkins, S. J. (2004). The dimeric and trimeric solution structures of the multidomain complement protein properdin by X-ray scattering, analytical ultracentrifugation and constrained modeling. Journal of Molecular Biology 343, 13271343.CrossRefGoogle Scholar
Svergun, D. (1992). Determination of the regularization parameter in indirect-transform methods using perceptual criteria. Journal of Applied Crystallography 25, 495503.CrossRefGoogle Scholar
Svergun, D., Baraberato, C. & Koch, M. H. (1995). CRYSOL – a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. Journal of Applied Crystallography 28, 768773.CrossRefGoogle Scholar
Svergun, D. I. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophysical Journal 76, 28792886.CrossRefGoogle ScholarPubMed
Svergun, D. I. (2007). Small-angle scattering studies of macromolecular solutions. Journal of Applied Crystallography 40, s10s17.CrossRefGoogle Scholar
Svergun, D. I., Burkhardt, N., Pedersen, J. S., Koch, M. H., Volkov, V. V., Kozin, M. B., Meerwink, W., Stuhrmann, H. B., Diedrich, G. & Nierhaus, K. H. (1997a). Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. I. Invariants and validation of electron microscopy models. Journal of Molecular Biology 271, 588601.CrossRefGoogle ScholarPubMed
Svergun, D. I., Burkhardt, N., Pedersen, J. S., Koch, M. H., Volkov, V. V., Kozin, M. B., Meerwink, W., Stuhrmann, H. B., Diedrich, G. & Nierhaus, K. H. (1997b). Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. II. A model of the ribosome and its RNA at 3·5 nm resolution. Journal of Molecular Biology 271, 602618.CrossRefGoogle Scholar
Svergun, D. I., Petoukhov, M. V. & Koch, M. H. (2001a). Determination of domain structure of proteins from X-ray solution scattering. Biophysical Journal 80, 29462953.CrossRefGoogle ScholarPubMed
Svergun, D. I., Petoukhov, M. V. & Koch, M. H. (2001b). Determination of domain structure of proteins from X-ray solution scattering. Biophysical Journal 76, 28792886.CrossRefGoogle Scholar
Svergun, D. I., Petoukhov, M. V., Koch, M. H. J. & Koenig, S. (2000). Crystal versus solution structures of thiamine diphosphate-dependent enzymes. Journal of Biological Chemistry 275, 297302.CrossRefGoogle ScholarPubMed
Svergun, D. I. & Stuhrmann, H. B. (1991). New developments in direct shape determination from small-angle scattering. 1. Theory and model calculations. Acta Crystallographica A47, 736744.CrossRefGoogle Scholar
Svergun, D. I., Volkov, V. V., Kozin, M. B. & Stuhrmann, H. B. (1996). New developments in direct shape determination from small-angle scattering. 2. Uniqueness. Acta Crystallographica A52, 419426.CrossRefGoogle Scholar
Tai, K. (2004). Conformational sampling for the impatient. Biophysical Chemistry 107, 213220.CrossRefGoogle ScholarPubMed
Takahashi, Y., Nishikawa, Y. & Fujisawa, T. (2003). Evaluation of three algorithms for ab initio determination of three dimensional shapes from one dimensional solvent scattering profiles. Journal of Applied Crystallography 36, 546550.CrossRefGoogle Scholar
Tama, F., Miyashita, O. & Brooks, C. L. 3rd (2004). Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. Journal of Molecular Biology 337, 985999.CrossRefGoogle ScholarPubMed
Tama, F. & Sanejouand, Y. H. (2001). Conformational change of proteins arising from normal mode analysis. Protein Engineering 14, 16.CrossRefGoogle Scholar
Tama, F., Wriggers, W. & Brooks, C. L. 3rd (2002). Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. Journal of Molecular Biology 321, 297305.CrossRefGoogle ScholarPubMed
Taylor, A., Dunne, M., Bennington, S., Ansell, S., Gardner, I., Norreys, P., Broome, T., Findlay, D. & Nelmes, R. (2007). A route to the brightest possible neutron source? Science 317, 10921095.CrossRefGoogle Scholar
Terwilliger, T. C. (2003). Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallographica D59, 3844.Google Scholar
Tidow, H., Melero, R., Mylonas, E., Freund, S. M. V., Grossmann, J. G., Carazo, J. M., Svergun, D. I., Valle, M. & Fersht, A. R. (2007). Quaternary structures of tumor suppressor p53 and a specific p53-DNA complex. Proceedings of the National Academy of Sciences USA 104, 1232412329.CrossRefGoogle Scholar
Tiede, D. M., Zhang, R. & 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, 66056614.CrossRefGoogle ScholarPubMed
Tiede, D. M. & Zuo, X. (2007). X-ray scattering for bio-molecule structure characterization. In Biophysical Techniques in Photosynthesis II (ed. Aartsma, T. J. and Matysik, J.). Springer.Google Scholar
Tirion, M. M. (1996). Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Physical Review Letters 77, 19051908.CrossRefGoogle ScholarPubMed
Tjioe, E. & Heller, W. T. (2007). ORNL_SAS: software for calculation of small-angle scattering intensities of proteins and protein complexes. Journal of Applied Crystallography 40, 782785.CrossRefGoogle Scholar
Trikha, J., Theil, E. C. & Allewell, N. M. (1995). High resolution structure of amphibian red-cell L-ferritin: potential roles for structural plasticity and solvation in function. Journal of Molecular Biology 248, 949967.CrossRefGoogle ScholarPubMed
Tsutakawa, S. E., Hura, G. L., Frankel, K. A., Cooper, P. K. & Tainer, J. A. (2007). Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography. Journal of Structural Biology 158, 214223.CrossRefGoogle ScholarPubMed
Tung, C. S., Walsh, D. A. & Trewhella, J. (2002). A structural model of the catalytic subunit-regulatory subunit dimeric complex of the cAMP-dependent protein kinase. Journal of Biological Chemistry 277, 1242312431.CrossRefGoogle ScholarPubMed
Urzhumtsev, A. G. & Podjarny, A. (1995). On the solution of the molecular-replacement problem at very low resolution: application to large complexes. Acta Crystallographica D51, 888895.Google Scholar
Uzawa, T., Kimura, T., Ishimori, K., Morishima, I., Matsui, T., Ikeda-Saito, M., Takahashi, S., Akiyama, S. & Fujisawa, T. (2006). Time-resolved small-angle X-ray scattering investigation of the folding dynamics of heme oxygenase: implication of the scaling relationship for the submillisecond intermediates of protein folding. Journal of Molecular Biology 357, 9971008.CrossRefGoogle ScholarPubMed
Vachette, P. & Svergun, D. (2000). Small-angle X-ray scattering by solutions of biological macromolecules: neutron and synchrotron radiation for condensed studies. In Structure and Dynamics of Biomolecules (ed. Fanchon, E., Geissler, E., Hodeau, J. L., Regnard, J. E. and Timmins, P. A.), pp. 199237. Oxford: Oxford University Press.Google Scholar
Valdar, W. S. & Thornton, J. M. (2001a). Conservation helps to identify biologically relevant crystal contacts. Journal of Molecular Biology 313, 399416.CrossRefGoogle ScholarPubMed
Valdar, W. S. & Thornton, J. M. (2001b). Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 42, 108124.3.0.CO;2-O>CrossRefGoogle ScholarPubMed
van Aalten, D. M., Conn, D. A., de Groot, B. L., Berendsen, H. J., Findlay, J. B. & Amadei, A. (1997). Protein dynamics derived from clusters of crystal structures. Biophysical Journal 73, 28912896.CrossRefGoogle ScholarPubMed
Vellieux, F. M. D. & Read, R. J. (1997). Non-crystallographic symmetry averaging in phase refinement and extension. Methods in Enzymology 277, 1853.CrossRefGoogle Scholar
Vestergaard, B. & Hansen, S. (2006). Application of Bayesian analysis to indirect Fourier transformation in small-angle scattering. Journal of Applied Crystallography 39, 797804.CrossRefGoogle Scholar
Vestergaard, B., Sanyal, S., Roessle, M., Mora, L., Buckingham, R. H., Kastrup, J. S., Gajhede, M., Svergun, D. I. & Ehrenberg, M. (2005). The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Molecular Cell 20, 929938.CrossRefGoogle ScholarPubMed
Volkmann, N. & Hanein, D. (1999). Quantitative fitting of atomic models into observed densities derived by electron microscopy. Journal of Structural Biology 125, 176184.CrossRefGoogle ScholarPubMed
Volkmann, N. & Hanein, D. (2003). Docking of atomic models into reconstructions from electron microscopy. Methods Enzymol 374, 204225.CrossRefGoogle ScholarPubMed
Volkov, V. V. & Svergun, D. I. (2003). Uniqueness of ab initio shape determination in small-angle scattering. Journal of Applied Crystallography 36, 860864.CrossRefGoogle Scholar
von Ossowski, I., Eaton, J. T., Czjzek, M., Perkins, S. J., Frandsen, T. P., Schulein, M., Panine, P., Henrissat, B. & Receveur-Brechot, V. (2005). Protein disorder: conformational distribution of the flexible linker in a chimeric double cellulase. Biophysical Journal 88, 28232832.CrossRefGoogle Scholar
Vucetic, S., Brown, C. J., Dunker, A. K. & Obradovic, Z. (2003). Flavors of protein disorder. Proteins 52, 573584.CrossRefGoogle ScholarPubMed
Wall, M. E., Clarage, J. B. & Phillips, G. N. (1997a). Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5, 15991612.CrossRefGoogle ScholarPubMed
Wall, M. E., Ealick, S. E. & Gruner, S. M. (1997b). Three-dimensional diffuse X-ray scattering from crystals of Staphylococcal nuclease. Proceedings of the National Academy of Sciences USA 94, 61806184.CrossRefGoogle ScholarPubMed
Wall, M. E., Gallagher, S. C. & Trewhella, J. (2000). Large-scale shape changes in proteins and macromolecular complexes. Annual Review of Physcial Chemistry 51, 355380.CrossRefGoogle ScholarPubMed
Walther, D., Cohen, F. E. & Doniach, S. (2000). Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules. Journal of Applied Crystallography 33, 350363.CrossRefGoogle Scholar
Weber, P. C. (1997). Overview of protein crystallization methods. Methods in Enzymology 276, 1322.CrossRefGoogle ScholarPubMed
Weeks, C. M., Blessing, R. H., Miller, R., Mungee, R., Potter, S. A., Rappleye, J., Smith, G. D., Xu, H. & Furey, W. (2002). Toward automated protein structure determination: BnP, the SnB-PHASES interface. Zeitschrift fur Kristallographie 217, 686693.Google Scholar
Williams, R. S., Chasman, D. I., Hau, D. D., Hui, B., Lau, A. Y. & Glover, J. N. (2003). Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. Journal of Biological Chemistry 278, 5300753016.CrossRefGoogle ScholarPubMed
Willis, B. T. M. & Pryor, A. W. (1975). Thermal Vibrations in Crystallography. London: Cambridge University Press.Google Scholar
Wilson, A. J. C. (1942). Determination of absolute from relative X-ray intensity data. Nature 150, 152.CrossRefGoogle Scholar
Wilson, M. A. & Brunger, A. T. (2000). The 1·0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity. Journal of Molecular Biology 301, 12371256.CrossRefGoogle Scholar
Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001). Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallographica D57, 122133.Google Scholar
Winn, M. D., Murshudov, G. N. & Papiz, M. Z. (2003). Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods in Enzymology 374, 300321.CrossRefGoogle ScholarPubMed
Wriggers, W. & Chacon, P. (2001). Modeling tricks and fitting techniques for multiresolution structures. Structure 9, 779788.CrossRefGoogle ScholarPubMed
Wriggers, W., Milligan, R. A. & McCammon, J. A. (1999). Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. Journal of Structural Biology 125, 185195.CrossRefGoogle ScholarPubMed
Wu, L. & Hickson, I. D. (2006). DNA helicases required for homologous recombination and repair of damaged replication forks. Annual Review of Genetics 40, 279306.CrossRefGoogle ScholarPubMed
Yamagata, A. & Tainer, J. A. (2007). Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO Journal 26, 878890.CrossRefGoogle ScholarPubMed
Yeats, T. O. (1997). Detecting and overcoming crystal twinning. Methods in Enzymology 276, 344358.CrossRefGoogle Scholar
Yuan, Y.-R., Blecker, S., Martsinkevich, O., Millen, Y., Thomas, P. J. & Hunt, J. F. (2001). The crystal structure of the MJ0796 ATP-binding cassette: implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter. Journal of Biological Chemistry 276, 3231332321.CrossRefGoogle ScholarPubMed
Yuzawa, S., Yokochi, M., Hatanaka, H., Ogura, K., Kataoka, M., Miura, K., Mandiyan, V., Schlessinger, J. & Inagaki, F. (2001). Solution structure of Grb2 reveals extensive flexibility necessary for target recognition. Journal of Molecular Biology 306, 527537.CrossRefGoogle ScholarPubMed
Zegerman, P. & Diffley, J. F. X. (2007). Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature 445, 281285.CrossRefGoogle ScholarPubMed
Zhang, K. Y. J., Cowtan, K. & Main, P. (1997). Combining constraints for electron density modification. Methods in Enzymology 277, 5364.CrossRefGoogle ScholarPubMed
Zhang, R., Thiyagarajan, P. & Tiede, D. M. (2000a). Probing protein fine structures by wide angle solution X-ray scattering. Journal of Applied Crystallography 33, 565568.CrossRefGoogle Scholar
Zhang, X., Shaw, A., Bates, P. A., Newman, R. H., Bowen, B., Orlova, E., Gorman, M. A., Kondo, H., Dokurno, P. & Lally, J. (2000b). Structure of the AAA ATPase p97. Molecular Cell 6, 14731484.CrossRefGoogle ScholarPubMed
Zhao, J., Hoye, E., Boylan, S., Walsh, D. A. & Trewhella, J. (1998). Quaternary structure of a catalytic subunit-regulatory subunit dimeric complex and the holoenzyme of the cAMP-dependent protein kinase by neutron contrast variation. Journal of Biological Chemistry 273, 3044830459.CrossRefGoogle ScholarPubMed
Zheng, Y., Doerschuk, P. C. & Johnson, J. E. (1995). Determination of three-dimensional low-resolution viral structure from solution X-ray scattering. Biophysical Journal 69, 619639.CrossRefGoogle ScholarPubMed
Zipper, P. & Durschschlag, H. (2003). Modeling of protein solution structures. Journal of Applied Crystallography 36, 509514.CrossRefGoogle Scholar
Zuker, M., Mathews, D. H. & Turner, D. H. (1999). Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology. Dordrecht: Kluwer Academic Publishers.Google Scholar
Zulauf, M. & D'Arcy, A. (1992). Light scattering of proteins as a criterion for crystallization. Journal of Crystal Growth 122, 102106.CrossRefGoogle Scholar