Structural NMR of protein oligomers using hybrid methods - PubMed (original) (raw)

Review

Structural NMR of protein oligomers using hybrid methods

Xu Wang et al. J Struct Biol. 2011 Mar.

Abstract

Solving structures of native oligomeric protein complexes using traditional high-resolution NMR techniques remains challenging. However, increased utilization of computational platforms, and integration of information from less traditional NMR techniques with data from other complementary biophysical methods, promises to extend the boundary of NMR-applicable targets. This article reviews several of the techniques capable of providing less traditional and complementary structural information. In particular, the use of orientational constraints coming from residual dipolar couplings and residual chemical shift anisotropy offsets are shown to simplify the construction of models for oligomeric complexes, especially in cases of weak homo-dimers. Combining this orientational information with interaction site information supplied by computation, chemical shift perturbation, paramagnetic surface perturbation, cross-saturation and mass spectrometry allows high resolution models of the complexes to be constructed with relative ease. Non-NMR techniques, such as mass spectrometry, EPR and small angle X-ray scattering, are also expected to play increasingly important roles by offering alternative methods of probing the overall shape of the complex. Computational platforms capable of integrating information from multiple sources in the modeling process are also discussed in the article. And finally a new, detailed example on the determination of a chemokine tetramer structure will be used to illustrate how a non-traditional approach to oligomeric structure determination works in practice.

Copyright © 2010 Elsevier Inc. All rights reserved.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Steps of the grid search used to produce dimer models of Sr360 & SeR13. (a) Place monomer in the alignment tensor frame. (b) Create 2nd monomer by rotating the structure 180 degrees around one of the principal axes. (c) Translate the 2nd monomer in the plane perpendicular to the rotation axis. Discard models that have monomers too far apart or too close. (d) Perform energy minimization and MD to relax the interface and create better complementarity. (e) Evaluate the model based on experimental/simulated RDC correlation, RP score and VDW energy. Adapted from (Wang et al., 2008).

Figure 2

Figure 2

Correlation between experimental RDCs for both the wild type and E66S CCL5 and those calculated from the CCL5 dimer structure (PDB accession code 1U4L).

Figure 3

Figure 3

Orientation of the alignment tensor principal axes and the symmetry axis of the dimer. The symmetry axis is shown in gold; the Sxx axis of the tensor is shown in red; the Syy axis is shown in blue and the Szz axis is shown in green. The angle between the symmetry axis and the Sxx axis is 11 degrees.

Figure 4

Figure 4

Experimental scattering curve for wild type CCL5 and the calculated scattering curves for the MCP-1 tetramer, the IP-10 tetramer, and a tretramer based on RDC and SAXS data. q is the magnitude of the momentum transfer vector, 4πsin(θ)/λ, where 2θ is the scattering angle and λ is the X-ray wavelength.

Figure 5

Figure 5

Steps in the grid search used in constructing the tetramer models of CCL5. (a) Place one dimeric unit in the alignment tensor frame. (b) Create 2nd dimer by rotating the structure 180 degrees around the dimeric symmetry axis. (c) Translate the 2nd dimer in the plane perpendicular to the rotation axis. Discard models that have the dimers too far apart or too close. (d) Perform energy minimization and MD to relax the interface and create better complementarity. (e) Evaluate the model based agreement between theoretical and experimental scattering curve and residue pairing score.

Figure 6

Figure 6

A) Contour plot of the scattering curve fitting χ values for models generated by the grid search. The four locations on the grid that produced better fitting models are 3×12, 54×45, 4×43, 61×18. B) Contour plot of the residue-pairing score of the models generated by the grid search.

Figure 7

Figure 7

Two models of the tetramer whose scattering profile showed good agreement with the experimental scattering curve of wild type CCL5. Model A is from grid 3×12 and model B is from grid 4×43.

Figure 8

Figure 8

Comparison of the grid search models with the ab initio shape generated from the scattering curve. The tetramer model A superimposed onto the dummy atom model calculated from the scattering curve (green spheres).

Figure 9

Figure 9

Comparison of the tetrameric interface of CXCL12 (PDB accession code 3HP3, upper panel) and Model A of the CCL5 tetramer model found by grid search.

Similar articles

Cited by

References

    1. Al-Hashimi HM, Bolon PJ, Prestegard JH. Molecular symmetry as an aid to geometry determination in ligand protein complexes. J Magn Reson. 2000a;142:153–8. - PubMed
    1. Al-Hashimi HM, Valafar H, Terrell M, Zartler ER, Eidsness MK, Prestegard JH. Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. Journal of Magnetic Resonance. 2000b;143:402–406. - PubMed
    1. Alber F, Dokudovskaya S, Veenhoff LM, Zhang WZ, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A. Determining the architectures of macromolecular assemblies. Nature. 2007;450:683–694. - PubMed
    1. Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, Berger EA. CC CKRS: A RANTES, MIP-1 alpha, MIP-1 beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science. 1996;272:1955–1958. - PubMed
    1. Andre I, Strauss CEM, Kaplan DB, Bradley P, Baker D. Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:16148–16152. - PMC - PubMed

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources