Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Aug;89(2):1237-50.
doi: 10.1529/biophysj.105.064154. Epub 2005 May 27.

Global rigid body modeling of macromolecular complexes against small-angle scattering data

Maxim V Petoukhov  1 , Dmitri I Svergun
Affiliations

Global rigid body modeling of macromolecular complexes against small-angle scattering data

Maxim V Petoukhov et al. Biophys J. 2005 Aug.

Abstract

New methods to automatically build models of macromolecular complexes from high-resolution structures or homology models of their subunits or domains against x-ray or neutron small-angle scattering data are presented. Depending on the complexity of the object, different approaches are employed for the global search of the optimum configuration of subunits fitting the experimental data. An exhaustive grid search is used for hetero- and homodimeric particles and for symmetric oligomers formed by identical subunits. For the assemblies or multidomain proteins containing more then one subunit/domain per asymmetric unit, heuristic algorithms based on simulated annealing are used. Fast computational algorithms based on spherical harmonics representation of scattering amplitudes are employed. The methods allow one to construct interconnected models without steric clashes, to account for the particle symmetry and to incorporate information from other methods, on distances between specific residues or nucleotides. For multidomain proteins, addition of missing linkers between the domains is possible. Simultaneous fitting of multiple scattering patterns from subcomplexes or deletion mutants is incorporated. The efficiency of the methods is illustrated by their application to complexes of different types in several simulated and practical examples. Limitations and possible ambiguity of rigid body modeling are discussed and simplified docking criteria are provided to rank multiple models. The methods described are implemented in publicly available computer programs running on major hardware platforms.

PubMed Disclaimer

Figures

FIGURE 1
FIGURE 1
A quasiuniform grid of angular directions generated for 11th Fibonacci number (145 directions) (A) and the schemes of the two grid-search modeling approaches: DIMFOM modeling of heterodimers (B) and GLOBSYMM modeling of symmetric oligomers (C).
FIGURE 2
FIGURE 2
Validation of the rigid body modeling techniques on a simulated tRNA-GTS complex. (A) Models of the complex. (Top row) Initial model of the dimer (orange and gray) superimposed with the model reconstructed by SASREF using the distance restraint as described in the text. The restored model fits the curves of the dimeric tRNA and the entire complex using one tRNA (in blue) and one GTS monomer (in red) in the asymmetric part. (Middle row) An incorrect arrangement obtained by SASREF without the distance restraint. (Bottom row) Superposition of the model of monomeric GTS-tRNA complex built by BUNCH with the initial monomer. Fixed domain of GTS, DR linker, and the moving domain are shown in green, red, and magenta, respectively. The right panel is rotated by 90° about the vertical axis. (B) Scattering patterns of the dimeric complex, 1; dimeric tRNA, 2; and monomeric complex, 3. The simulated data are denoted by open circles, triangles, and squares; the fits obtained by SASREF with contacts restraint and by BUNCH are displayed as red dashed lines; and those from the in the middle model as blue solid lines.
FIGURE 3
FIGURE 3
Results of grid-search rigid body modeling of F1 ATPase using DIMFOM (A) and of tetrameric ZmPDC using GLOBSYMM (B). (Left panel) Structural models. The crystal structures and the results of the modeling are shown on the left and the right columns, respectively. The δɛ substructure of F1 ATPase and the monomer of ZmPDC are displayed in dark shading. The bottom views in A and B are rotated by 90° about the horizontal axis. (Right panel) Scattering curves. Dots denote experimental data; open triangles and solid lines are, respectively, theoretical scattering curves computed from crystal structures and fits from the rigid body models. The corresponding reduced residuals of the fits, i.e., individual terms in Eq. 3, are given in the insets.
FIGURE 4
FIGURE 4
Results of rigid body modeling of Hc (A), BTK (B), and GST-DHFR (C) using simulated annealing. (Left panel) X-ray scattering patterns. The experimental data in A–C are displayed as symbols, and the fits from the reconstructed models are shown as solid lines. In A, 1 and 2 stands for 150- and 100-kDa constructs, respectively; in B, the full-length BTK, PH–SH3–SH2, and SH3–SH2 constructs are denoted as 1, 2, and 3. (Right panel) Structural models. (A) Assembly of Hc structural units reconstructed from the SAXS data of 100- and 150-kDa fragments by SASREF. A low-resolution model previously reconstructed using envelope functions (36) is displayed in gray. The first, second, and the third subunits are displayed as red, green, and magenta Cα-traces, respectively. (B) Domain structure of BTK restored by simultaneous multiple data sets fitting using BUNCH. PH, SH3, SH2, kinase domain, and flexible DR linkers are shown in red, green, cyan, magenta, and blue, respectively. The earlier published model obtained by subsequent fitting (37) is displayed as yellow beads. (C) Dimeric GST-DHFR fusion protein. Crystallographic GST dimer is displayed in green, the two DHFR monomers and the linkers positioned by BUNCH using P2 symmetry are shown in blue and red. Yellow beads represent the two DHFR domains of the fusion protein reconstructed ab initio in the previous work (27). The bottom views in A–C are rotated by 90° about the horizontal axis.
FIGURE 5
FIGURE 5
Screening of the multiple models provided by rigid body refinement methods. (A) Models of ZmPDC generated by GLOBSYMM. (Left panel, first row) Crystal structure of ZmPDC; (second row) the best GLOBSYMM model; (third row) the model with the highest CC; and (fourth row) the model with a poor correlation criterion. The four subunits of ZmPDC are shown in different colors, the models in middle column are rotated by 90° about the horizontal axis, those in right column are further rotated by 90° about the vertical axis. (Right panel) Experimental data (black dots) from ZmPDC and the fits from the above models (plotted as red, blue, green, and magenta lines, respectively). The reduced residuals are given in the inset using the same colors. (B) Modeling of chymotrypsin-eglin complex using SASREF. (Left panel, left column) Crystallographic model of the complex; (middle column) the model with Ncnt = 31 and CC = 0.40; and (right column) the model with Ncnt = 40 and CC = 0.31. Chromatin and eglin molecules are displayed in blue and red, respectively. Bottom view is rotated by 90° about the horizontal axis. (Right panel) Simulated data of the complex (dots), and fits from SASREF models in the middle and the right columns (blue and red solid lines, respectively).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Gerstein, M., A. Edwards, C. H. Arrowsmith, and G. T. Montelione. 2003. Structural genomics: current progress. Science. 299:1663. - PubMed
    1. Sali, A., R. Glaeser, T. Earnest, and W. Baumeister. 2003. From words to literature in structural proteomics. Nature. 422:216–225. - PubMed
    1. Aloy, P., B. Bottcher, H. Ceulemans, C. Leutwein, C. Mellwig, S. Fischer, A. C. Gavin, P. Bork, G. Superti-Furga, L. Serrano, and R. B. Russell. 2004. Structure-based assembly of protein complexes in yeast. Science. 303:2026–2029. - PubMed
    1. Feigin, L. A., and D. I. Svergun. 1987. Structure analysis by small-angle x-ray and neutron scattering. Plenum Press, New York.
    1. Svergun, D. I., and M. H. J. Koch. 2003. Small angle scattering studies of biological macromolecules in solution. Rep. Prog. Phys. 66:1735–1782.

Publication types

Substances

LinkOut - more resources