International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 19.3, pp. 436-437   | 1 | 2 |

Section 19.3.3.4.1. Studies of proteins in solution that complement high-resolution structures

H. Tsurutaa and J. E. Johnsonb*

aSSRL/SLAC & Department of Chemistry, Stanford University, PO Box 4349, MS69, Stanford, California 94309-0210, USA, and bDepartment of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
Correspondence e-mail:  jackj@scripps.edu

19.3.3.4.1. Studies of proteins in solution that complement high-resolution structures

| top | pdf |

Recent advances in solution scattering data interpretation have made it possible to determine three-dimensional structures at resolutions comparable to those of electron microscopy. In some cases, low-resolution structures were derived from solution X-ray scattering independent of a structural model obtained by other structural techniques. Svergun et al. (1994)[link] derived a 15 Å-resolution model of 50S ribosome using the spherical harmonics method. The low-resolution structures of the dimeric and tetrameric forms of pyruvate decarboxylase were obtained by the same method from X-ray solution scattering data (König et al., 1992[link]) before the crystal structure was published. The X-ray structure, at a comparable resolution, was in close agreement with the solution scattering result. The same enzyme obtained from different organisms has also been modelled with solution scattering data.

Calcium-binding proteins have been extensively studied by solution X-ray scattering. These data first demonstrated the large conformation change of calmodulin promoted by binding Ca2+ (Seaton et al., 1985[link]). Comparison of the solution scattering curve calculated for the crystal structure of calmodulin with the experimental scattering curve showed that crystal-packing forces substantially altered the solution conformation of the protein (Heidorn & Trewhella, 1988[link]). Kataoka et al. (1989)[link] reported the first glimpse of the conformational change of calmodulin induced by melittin, a model peptide for target enzymes. These early studies led to a number of important solution scattering studies on the protein–protein interaction in Ca2+-regulated molecular switching, including the troponin system in muscle contraction. Krueger et al. (1997)[link] recently took a combined approach to X-ray and neutron small-angle scattering by using contrast variation to obtain the first structural model of calmodulin complexed with an enzymatically active truncation mutant of skeletal muscle myosin light chain kinase.

A series of structural studies on 70 kDa heat-shock cognate protein, a molecular chaperone, combined crystallography and X-ray solution scattering. It was not possible to crystallize the whole protein, but the crystal structure of the ATPase domain was solved. ATP binding induces a conformational change in the protein, resulting in the release of a bound peptide. Wilbanks et al. (1995)[link] constructed a low-resolution model of the whole molecule from solution X-ray scattering data, based on the ATPase domain crystal structure. Solution X-ray scattering was recently used to screen a point-mutated version of the protein, which retains the ATP-induced conformational change, contributing to the interpretation of the role of specific residues in the molecular chaperone mechanism (Sousa & McKay, 1998[link]).

Solution scattering complemented high-resolution NMR structural studies in the investigation of titin (connectin), a giant muscle protein (Improta et al., 1998[link]). The high-resolution structures were determined for two immunoglobulin-like fragments of the I-band region of titin. Two ellipsoids that simulate the molecular envelopes of the two fragments were then used to model solution X-ray scattering data in order to determine the relative position of the two fragments. The resulting structural model suggests that the motions around the interdomain-connecting regions are restricted and that titin behaves as a row of beads connected by rigid hinges. A similar approach was taken for EGF domains in coagulation factor X (Sunnerhagen et al., 1996[link]).

There is a long list of large proteins or protein complexes whose solution X-ray scattering studies have made important contributions in structural biology. One study demonstrated that the quaternary structure of an allosteric enzyme, E. coli aspartate transcarbamoylase, in the R (relaxed) state is significantly different from that observed in the R-state crystal, suggesting that a crystal lattice could deform functional quaternary structure (Svergun, Barberato et al., 1997[link]). A. vinelandii nitrogenase, the key enzyme in nitrogen fixation, is composed of two proteins: Fe protein and MoFe protein, which were crystallized separately. Grossman et al. (1997)[link] determined a low-resolution structure of the complex of Fe and MoFe proteins stabilized by ADP–AlF4−, a nucleotide triphosphate analogue, solely from solution X-ray scattering data. This was later confirmed by a crystallographic study of the same complex (Schindelin et al., 1997[link]). A more advanced approach was used to construct the three-dimensional structure of E. coli F1 ATPase, which consists of four different soluble subunits in the form of α3β3[epsilon]δ (Svergun, Konrad et al., 1998[link]). Two smaller subunits, [epsilon] and δ, were disordered in the crystal structure, while NMR provided solution structures for these subunits. Solution scattering was used to construct the three-dimensional structure of the F1 ATPase structure that incorporates all the subunits. The program CRYSOL was used to calculate individual scattering amplitudes by approximating high-resolution structures with sums of spherical harmonics. Then individual amplitudes were combined, according to the relative positions of all subunits, while the subunits were moved with respect to each other to fit the experimental scattering amplitudes obtained for the whole complex. The programs ASSA and ALM22INT were used to construct the most plausible model for the complex. A 32 Å-resolution structure of M. Sextra V1 ATPase was determined ab initio using the spherical harmonics method (Svergun, Aldag et al., 1998[link]). Here, a three-fold molecular symmetry in the A3B3 part, which resembles α3β3 in F1 ATPase, reduced the number of parameters. The model structure of V1 ATPase has a 110 Å-long stalk region, corresponding to the total mass of the CDEFG3 part of the complex that connects V1 to the V0 domain embedded in the membrane.

X-ray scattering amplitudes have recently been used in the correction of the contrast-transfer function in cryo-electron microscopy in an attempt to improve the fidelity of reconstructed electron-microscope models (Thuman-Commike et al., 1999[link]). A low-resolution structure model derived from solution X-ray scattering and electron microscopy was used to obtain initial phases for determining the crystal structure of E. coli ClpP, a molecular chaperone (Wang et al., 1997[link]).

References

First citationGrossman, J. G., Hasnain, S. S., Yousafzai, F. K., Smith, B. E. & Eady, R. R. (1997). The first glimpse of a complex of nitrogenase component proteins by solution X-ray scattering: conformation of the electron transfer transition state complex of Klebsiella pneumonia nitrogenase. J. Mol. Biol. 266, 642–648.Google Scholar
First citationHeidorn, D. B. & Trewhella, J. (1988). Comparison of the crystal and solution structures of calmodulin and troponin C. Biochemistry, 27, 909–915.Google Scholar
First citationImprota, S., Krueger, J. K., Gautel, M., Atkinson, R. A., Lefevre, J. F., Moulton, S., Trewhella, J. & Pastore, A. (1998). The assembly of immunoglobulin-like modules in titin: implications for muscle elasticity. J Mol. Biol. 284, 761–777.Google Scholar
First citationKataoka, M., Head, J. F., Seaton, B. A. & Engelman, D. M. (1989). Melittin binding causes a large calcium-dependent conformational change in calmodulin. Proc. Natl Acad. Sci. USA, 86, 6944–6948.Google Scholar
First citationKrueger, J. K., Glah, G. A., Rokop, S. E., Zhi, G., Stull, J. T. & Trewhella, J. (1997). Structures of calmodulin and a functional myosin light chain kinase in the activated complex: a neutron scattering study. Biochemistry, 36, 6017–6023.Google Scholar
First citationKönig, S., Svergun, D., Koch, M. H. J., Höbner, G. & Schellenberger, A. (1992). Synchrotron radiation solution X-ray scattering study of the pH dependence of the quaternary structure of yeast pyruvate decarboxylase. Biochemistry, 31, 8726–8731.Google Scholar
First citationSchindelin, H., Kisker, C., Schlessman, J. L., Howard, J. B. & Rees, D. C. (1997). Structure of ADP. AIF-4-stabilized nitrogenase complex and its implications for signal transduction. Nature (London), 387, 370–376.Google Scholar
First citationSeaton, B. A., Head, J. F., Engelman, D. M. & Richards, F. M. (1985). Calcium-induced increase in the radius of gyration and maximum dimension of calmodulin measured by small-angle X-ray scattering. Biochemistry, 24, 6740–6743.Google Scholar
First citationSousa, M. C. & McKay, D. B. (1998). The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change. Biochemistry, 37, 15392–15399.Google Scholar
First citationSunnerhagen, M., Olah, G. A., Stenflo, J., Forsen, S., Drakenberg, T. & Trewhella, J. (1996). The relative orientation of Gla and EGF domains in coagulation factor X is altered by Ca-2+ binding to the first EGF domain. A combined NMR–small angle X-ray scattering study. Biochemistry, 35, 11547–11559.Google Scholar
First citationSvergun, D. I., Aldag, I., Sieck, T., Altendorf, K., Koch, M. H. J., Kane, D. J., Kozin, M. B. & Grueber, G. (1998). A model of the quaternary structure of the Escherichia coli F1 ATPase from X-ray solution scattering and evidence for structural changes in the Delta subunit during ATP hydrolysis. Biophys. J. 75, 2212–2219. Google Scholar
First citationSvergun, D. I., Barberato, C., Koch, M. H. J., Fetler, L. & Vachette, P. (1997). Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins Struct. Funct. Genet. 27, 110–117.Google Scholar
First citationSvergun, D. I., Koch, M. H. & Serdyuk, I. N. (1994). Structural model of the 50 S subunit of Escherichia coli ribosomes from solution scattering. I. X-ray synchrotron radiation study. J. Mol. Biol. 240, 66–77.Google Scholar
First citationSvergun, D. I., Konrad, S., Huss, M., Koch, M. H. J., Wieczorek, H., Altendorf, K., Volkov, V. V. & Grueber, G. (1998). Quaternary structure of V1 and F1 ATPase: significance of structural homologies and diversities. Biochemistry, 37, 17659–17663. Google Scholar
First citationThuman-Commike, P. A., Tsuruta, H., Greene, B., Prevelige, P. E., King, J. & Chiu, W. (1999). Solution X-ray scattering based estimation of electron cryomicroscopy imaging parameters for reconstruction of virus particles. Biophys. J. 76, 2249–2261.Google Scholar
First citationWang, J., Harting, J. A. & Flanagan, J. M. (1997). The structure of ClpP at 2.3 Å resolution suggests a model for ATP-dependent proteolysis. Cell, 91, 447–456.Google Scholar
First citationWilbanks, S. M., Chen, L., Tsuruta, H., Hodgson, K. O. & McKay, D. B. (1995). Solution small-angle X-ray scattering study of the molecular chaperone Hsc70 and its subfragments. Biochemistry, 34, 12095–12106.Google Scholar








































to end of page
to top of page