Advances in structure analysis using small-angle scattering in solution

Current Opinion in Structural Biology

Volumn 12, Issue 5, 2002, Pages 654-660

  Svergun, Dmitri I ^a,b   Koch, Michel H J ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b SHUBNIKOV INSTITUTE OF CRYSTALLOGRAPHY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; LIGAND BINDING; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR SIZE; NEUTRON SCATTERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FOLDING; QUANTITATIVE ANALYSIS; RELIABILITY; REVIEW; STRUCTURE ANALYSIS; X RAY;

EID: 0036816606     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00363-9     Document Type: Review

References (68)

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2. Stuhrmann HB: Ein neues verfahren zur bestimmung der oberflaechenform und der inneren struktur von geloesten globularen proteinen aus roentgenkleinwinkelmessungen. Zeitschr Physik Chem Neue Folge 1970, 72:177-198. [Title translation: A new procedure for determination of shape and internal structure of dissolved globular proteins from small-angle X-ray scattering.].
3. Svergun D.I., Stuhrmann H.B. New developments in direct shape determination from small-angle scattering 1. Theory and model calculations. Acta Crystallogr. A47:1991;736-744.
4. Svergun D.I., Volkov V.V., Kozin M.B., Stuhrmann H.B., Barberato C., Koch M.H.J. Shape determination from solution scattering of biopolymers. J Appl Crystallogr. 30:1997;798-802.
5. Svergun D.I., Volkov V.V., Kozin M.B., Stuhrmann H.B. New developments in direct shape determination from small-angle scattering 2. Uniqueness. Acta Crystallogr. A52:1996;419-426.
6. Chacon P., Moran F., Diaz J.F., Pantos E., Andreu J.M. Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J. 74:1998;2760-2775.
7. Chacon P., Diaz J.F., Moran F., Andreu J.M. Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J Mol Biol. 299:2000;1289-1302.
8. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 76:1999;2879-2886.
9. Svergun D.I., Nierhaus K.H. A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome. J Biol Chem. 275:2000;14432-14439. The first application of simulated annealing to the analysis of contrast variation data from a multicomponent macromolecular complex. The data comprised 42 X-ray and neutron solution scattering curves from reconstituted E. coli ribosomes, in which the protein and rRNA moieties in the subunits were either protonated or deuterated in all possible combinations. The search volume, defined by a cryo-electron microscopic model of the ribosome, is divided into almost 8000 densely packed 0.5 nm radius spheres. Each sphere is assigned to solvent, protein or rRNA moieties to simultaneously fit all the scattering curves. The resulting 3 nm resolution model represents the volumes occupied by the rRNA and protein moieties in the entire ribosome. The protein-rRNA map predicted from SAS is in remarkably good agreement with the later high-resolution crystallographic models of ribosomal subunits from other species.
10. Walther D., Cohen F.E., Doniach S. Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules. J Appl Crystallogr. 33:2000;350-363.
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12. Kozin M.B., Svergun D.I. Automated matching of high- and low-resolution structural models. J Appl Crystallogr. 34:2001;33-41.
13. max. During simulated annealing, a randomly chosen DR is moved to a point 0.38 nm (typical distance between adjacent residues) away from another randomly selected DR. The final model is constrained to be locally 'chain compatible' (in particular, each DR should have two neighbours at a distance of 0.38 nm). The efficiency of the method is illustrated by the reconstruction of several proteins, with known and unknown crystal structure, from experimental scattering data. The method substantially improves the resolution and reliability of models compared to ab initio shape determination.
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18. Svergun D.I., Richard S., Koch M.H.J., Sayers Z., Kuprin S., Zaccai G. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci USA. 95:1998;2267-2272.
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20. Kozin M.B., Svergun D.I. A software system for automated and interactive rigid body modeling of solution scattering data. J Appl Crystallogr. 33:2000;775-777.
21. Konarev P.V., Petoukhov M.V., Svergun D.I. MASSHA-a graphic system for rigid body modelling of macromolecular complexes against solution scattering data. J Appl Crystallogr. 34:2001;527-532. The Wintel-based program MASSHA for three-dimensional rendering and rigid-body refinement is similar to the UNIX-based program ASSA [20]. It allows the display and manipulation of high-resolution atomic structures and low-resolution models represented as smooth envelopes or ensembles of beads. The program is coupled with computational modules for advanced modelling, such as the alignment of different types of models by invoking the program SUPCOMB [12]. MASSHA provides both interactive and automated refinement to position subunits in a heterodimeric complex (general case) and in a homodimeric complex with a twofold symmetry axis.
22. 2 tetramer differs from that of the protein with full occupancy (two Mo atoms per molecule). This is consistent with the existence of MoFe protein molecules that contain only one occupied FeMo cofactor site and have 50% lower specific activity. The restored shape of a complex between the MoFe protein lacking one of the cofactors and the Fe protein points to a 1:1 stoichiometry and suggests that the Fe protein interacts with the FeMo cofactor-binding α subunit of the MoFe protein. The authors conclude that the conformation of the α subunit or the αβ subunit pair that lacks the FeMo cofactor is altered and that the change is recognised by the Fe protein.
23. 1 ATPase.
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28. Scott D.J., Grossmann J.G., Tame J.R., Byron O., Wilson K.S., Otto B.R. Low resolution solution structure of the apo form of Escherichia coli haemoglobin protease Hbp. J Mol Biol. 315:2002;1179-1187.
29. Funari S.S., Rapp G., Perbandt M., Dierks K., Vallazza M., Betzel C., Erdmann V.A., Svergun D.I. Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering. J Biol Chem. 275:2000;31283-31288.
30. Svergun D.I., Petoukhov M.V., Koch M.H.J., Koenig S. Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J Biol Chem. 275:2000;297-302. A systematic study of differences between the quaternary crystal and solution structures of the thiamine-diphosphate-dependent enzymes. The X-ray scattering data collected from five multisubunit enzymes in the crystallization buffers are compared with the curves computed from the available crystallographic structures. For all enzymes, except the very compact pyruvate decarboxylase from Z. mobilis, differences are observed between the experimental and calculated profiles. The changes in the relative position of the subunits in solution are determined by rigid-body refinement. For pyruvate oxidase from L. plantarum and transketolase from S. cerevisiae, which have tight intersubunit contacts in the crystal, relatively small modifications of the quaternary structure, with a root mean square displacement (rmsd) of about 0.25 nm, suffice to fit the experimental data. For the enzymes with looser contacts (the native and activated forms of yeast pyruvate decarboxylase), modifications of the crystallographic models with rmsd up to 1.5 nm are required. The magnitude of the distortions induced by the crystal environment is thus correlated with the interfacial area between subunits.
31. Sousa M.C., Trame C.B., Tsuruta H., Wilbanks S.M., Reddy V.S., McKay D.B. Crystal and solution structures of an HslUV protease-chaperone complex. Cell. 103:2000;633-643. This paper presents and validates the crystal structure of a 'prokaryotic proteasome' - HslUV from H. influenzae composed of the HslV protease and the HslU ATPase - at 0.34 nm resolution. Two hexameric ATP-binding rings of HslU bind to opposite sides of the HslV protease, whereas the HslU intermediate domains extend outward from the complex. The scattering calculated from the crystallographic model gives a good fit to the experimental X-ray SAS data recorded from solutions under conditions in which the complex is assembled and active. The fit can further be improved by adding structural fragments from the crystallographic model of HslU (about 50 residues missing in the current model). It is interesting that the scattering computed from the earlier atomic model of E. coli HslUV in the crystal (showing a different arrangement of subunits) fails to fit the SAS pattern.
32. Svergun D.I., Barberato C., Koch M.H.J., Fetler L., Vachette P. Large differences are observed between the crystal and solution quaternary structures of allosteric aspartate transcarbamylase in the R state. Proteins. 27:1997;110-117.
33. Fetler L., Vachette P. The allosteric activator Mg-ATP modifies the quaternary structure of the R-state of E. coli aspartate transcarbamylase without altering the T↔R equilibrium. J Mol Biol. 309:2001;817-832. The quaternary structure of the R-state of E. coli ATCase, a paradigm of allosteric enzymes, has previously been shown to display large differences between the solution and the crystal forms [32]. This paper demonstrates that Mg•ATP, an allosteric activator, modifies this quaternary structure into a more expanded conformation, which is modelled using rigid-body movements. Interestingly, Mg•ATP binding does not alter the T↔R equilibrium. Beyond rigid-body modelling, these results, together with previous studies, shed new light on the molecular mechanisms behind the regulatory properties of ATCase.
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37. Tung C.S., Walsh D.A., Trewhella J. A structural model of the catalytic subunit-regulatory subunit dimeric complex of the cAMP-dependent protein kinase. J Biol Chem. 277:2002;12423-12431. An excellent example of detailed model building constrained by low-resolution SAS data. Previous neutron scattering analysis of selectively deuterated complexes (reviewed in [16]) yielded a model of the quaternary structure of the protein kinase holoenzyme. The docking of homology models of the subunits was constrained by the dimensions and positions of the ellipsoids in the neutron-derived model, and by mutagenesis data. The 'best fit' model of the heterodimer was further refined using molecular dynamics and energy minimisation to establish the sidechain packing at the heterodimer interface. The calculations using the two different homology models predicted similar interfaces. The resulting model provides an explanation for the stability of both the nondissociated protein kinase and its dissociated subunits in aqueous solutions.
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