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WIREs Comput Mol Sci
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Low‐resolution structural approaches to study biomolecular assemblies

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Abstract The delineation of the intricate network of biomolecular interactions is currently the focus of intense scientific effort. However, a complete understanding of these processes can be achieved only from three‐dimensional structures of these interactions. High‐resolution structural biology techniques, X‐ray crystallography, and nuclear magnetic resonance (NMR) are still far from being of general application, thus highlighting the need for alternative methodologies that incorporate low‐resolution structural information to model biomolecular assemblies. This overview describes the main sources of low‐resolution data, i.e., NMR, cryo‐electron microscopy, small angle X‐ray scattering, and mass spectrometry, and examples are provided on how these data have been integrated into computational procedures. Special emphasis is given to the exploitation of the synergy of several low‐resolution data obtained from different methods. Despite low‐affinity complexes are a highly relevant family of biomolecular assemblies, their study is complicated by the presence of multiple species in solution. Examples are presented of how data measured for these complexes have been analyzed to obtain structurally valuable information. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 283‐297 DOI: 10.1002/wcms.15 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics

Conformational changes in a SecM‐stalled ribosome by cryoEM. Atomic Escherichia coli ribosome model refined using the electronic density for the 50S (left panel) and 30S (right panel) units. The phosphate backbone of the rRNA is shown colored according to the RMSD between the atomic models fitted into the cryoEM reconstructions of the SecM‐stalled and the stalled prestate ribosome complexes. See Ref 52 for details. Figure (Reprinted with permission from Ref 52. Copyright 2006 Cell Press.)

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Both experimental and calculated values of R2/R1 for the lmwPTP. Experimental R2/R1 values at different concentrations are shown with their error bars: (b) and (g) 0.17 mM (pink); (c) and (h) 0.34 mM (green); (d) and (i) 0.66 mM (orange); (e) and (j) 1.24 mM (cyan). Calculated R2/R1values are for the monomer–dimer model (b‐e, red) and the monomer–dimer–tetramer model (g‐j, dark blue). Residuals for each value are shown in panels a and f, respectively. Contributions to the residuals from experimental data at different concentrations follow the same color code as in panels b–e (bottom figure). Surface representation of the crystallographic dimer of lmwPTP with residues 21, 59, 60, 61, 70, 71, and 72 highlighted in red and residue 39 highlighted in yellow. The clustering of residues suggests a tetramerization interface. (Reprinted with permission from Ref 78. Copyright 2003 American Chemical Society.)

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Insights into lmwPTP oligomerization by SAXS. Crystallographic structures of the (a) monomeric (1pnt; red) and (b) dimeric (1c0e; green) species of lmwPTP. Changes of (c) Rg and (d) Dmax with the total concentration of lmwPTP obtained from the SAXS dataset. The red and green lines correspond to the expected values for the monomer and the dimer computed from the structures depicted in (a) and (b). (e) SAXS curves measured for lmwPTP ranging concentrations from 0.056 to 0.61 mM. No intensity scaling was performed on the curves. (f) SAXS profiles obtained for the monomer (red line) and dimer (green line) using the chemiometrics approach described in the text. Only the first five curves were used for the analysis. These curves are in perfect agreement with the 3D structures of the monomer, and the dimer as can be observed by the excellent fit obtained with the program CRYSOL (black dashed line). See Ref. 79 for details. (Reprinted with permission from Ref 77. Copyright 2009 American Chemical Society.)

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Intermolecular paramagnetic relaxation enhancement (PRE) profiles observed between 15N‐labeled wild‐type HPr and EDTA‐Mn2+‐conjugated (a) E5C‐HPr, (b) E32C‐HPr, and (c) E25C‐HPr. PREs in E25C‐HPr are negligible and not used for structure calculations (see original study). The three‐dimensional structure in (a) displays the location of the three conjugation sites (E5C, E25C, and E32C) and of Ser‐46, whose mutation to Aspartic acid significantly reduced HPr self‐association. Three groups of residues that experience large intermolecular PREs are colored in red (group 1, residues 15–17), green (group 2, residue 41), and blue (group 3, residues 46–49). A fourth group, comprising residues 7, 67, and 85, displaying small PRE effects only with paramagnetically labeled E32CHPr, is colored in yellow (b). (right panels) Ensemble representation for the self‐associated state using four structures. (top) Weighted atomic probability density map showing the distribution of 15N‐labeled HPr relative to paramagnetically labeled HPr (gray transparent surface and ribbon, with the location of the E5C and E32C sites indicated in magenta; bottom) Weighted atomic probability density map showing the distribution of the paramagnetically labeled HPr molecule relative to the 15N‐labeled HPr molecule (gray surface and ribbon, with the four groups of residues that experience large intermolecular PREs colored in red, green, blue, and yellow using the same color scheme as in left panels. Figure (Reprinted with permission from Ref 75. Copyright 2008 American Chemical Society.)

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Plots of linearly changing residual dipolar couplings (RDCs) in CD2AP‐SH3‐C: Ubiquitin complex with respect to population of the bound state. The fully bound values (open circles) represent the values determined by the optimization procedure. The remaining values (full circles) are experimental values. Five sites are shown for each RDC type [(a–d) for 13C‐15N‐SH3, (e) for 15N‐Ubiquitin]. Resulting structures of the complex obtained from refinement using RDCbound and CS data are displayed, SH3 (red) and Ubiquitin (blue). Figure (Reprinted with permission from Ref 74. Copyright 2009 Oxford University Press.)

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Summary of the exosome subcomplexes and steps taken to build the three‐dimensional (3D) model by MS. Dotted lines indicate the subset of proteins the interactions of which are unknown at each step. (a) Perturbation in solution was used to generate dimeric and trimeric complexes confirmed by MS/MS. (b) Overlap of these complexes is used to derive their subunit interactions. (c) The loss of Mtr3 and Rrp43 orientates the Mtr3:Rrp42 dimer within the ring. (d,e) Solution‐phase loss of Rrp43, Mtr3, and Csl4 is used to locate Csl4 and Rrp4. (f) Analysis of subcomplexes containing Dis3 positions this protein in contact with Rrp45, Rrp41, and Rrp42. These data are used to build the 3D topological model of the exosome displayed in the center of the figure. Figure (Reprinted with permission from Ref 68. Copyright 2006 Nature Publishing Group.)

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