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Cited by 246

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Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. distance restraints from paramagnetic relaxation and calculation of an ensemble of structures

Gillespie, Joel R., Shortle, David·1997·Journal of Molecular Biology
DOI 10.1006/jmbi.1997.0953
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Figures

Figure 1 A, RMSD (C a distances) as a function of distance bounds on d R , in A ˚ , (i.e. the allowed variation in d R without an energy penalty). At each value of bounds, ten structures were calculated and their C a -C a distances were compared to the average C a -C a distances for ten structures calculated assuming t c 4 ns with 5A ˚ bounds. For bounds of 5 A ˚ and above, there was no restraint violation within a set of ten calculated structures. At shorter distances, the average number of restraint violations were: 1 2 for the 4 A ˚ bounds; 39 9 for the 3 A ˚ bounds; and 116 7 for the 2 A ˚ bounds. B, Average radius of gyration R g for ten calculated structures as a function of distance bounds, in A ˚ .
Figure 1 A, RMSD (C a distances) as a function of distance bounds on d R , in A ˚ , (i.e. the allowed variation in d R without an energy penalty). At each value of bounds, ten structures were calculated and their C a -C a distances were compared to the average C a -C a distances for ten structures calculated assuming t c 4 ns with 5A ˚ bounds. For bounds of 5 A ˚ and above, there was no restraint violation within a set of ten calculated structures. At shorter distances, the average number of restraint violations were: 1 2 for the 4 A ˚ bounds; 39 9 for the 3 A ˚ bounds; and 116 7 for the 2 A ˚ bounds. B, Average radius of gyration R g for ten calculated structures as a function of distance bounds, in A ˚ .CC-BY-NC-ND · From the PDF
Figure 2 A, A plot of the relationship between a distance restraint d R derived from a measured value of R 2 (indicated above each curve) and the rotational correlation time t c (ns). B, Average radius of gyration R g , the standard deviation, for ten structures of 131 as a function of correlation time t c used to calcu-
Figure 2 A, A plot of the relationship between a distance restraint d R derived from a measured value of R 2 (indicated above each curve) and the rotational correlation time t c (ns). B, Average radius of gyration R g , the standard deviation, for ten structures of 131 as a function of correlation time t c used to calcu-CC-BY-NC-ND · From the PDF
Image 3
CC-BY-NC-ND · From the PDF
Image 4
CC-BY-NC-ND · From the PDF
Figure 5 Ensemble of five virtual C a traces corresponding to 131 structures calculated with all paramagnetic relaxation enhancement restraints ( t c , 4 ns; 5 A ˚ bounds) plus 42 NOE restraints. Residue 44, dark blue; segment 4555, gold/orange; segment 56-67, red; segment 68-77, gold/orange; segment 78-89, bright yellow; segment 90-98, dark green; segment 99-108, slate blue; segment 109-121, yellow-green; segment 122-136, light gray-blue; segment 137-139, dark green; residue 140, red. Drawn with the RasMol software (Sayle, 1995). A, Perspective from above, demonstrating the overall U-shape, with the chain termini at the opening of the U and the hydrophilic 78-89 segment forming the bottom. B, Perspective from below and slightly behind the bottom of the U-shape.
Figure 5 Ensemble of five virtual C a traces corresponding to 131 structures calculated with all paramagnetic relaxation enhancement restraints ( t c , 4 ns; 5 A ˚ bounds) plus 42 NOE restraints. Residue 44, dark blue; segment 4555, gold/orange; segment 56-67, red; segment 68-77, gold/orange; segment 78-89, bright yellow; segment 90-98, dark green; segment 99-108, slate blue; segment 109-121, yellow-green; segment 122-136, light gray-blue; segment 137-139, dark green; residue 140, red. Drawn with the RasMol software (Sayle, 1995). A, Perspective from above, demonstrating the overall U-shape, with the chain termini at the opening of the U and the hydrophilic 78-89 segment forming the bottom. B, Perspective from below and slightly behind the bottom of the U-shape.CC-BY-NC-ND · From the PDF
Figure 6 (a,b) ( legend on page 178)
Figure 6 (a,b) ( legend on page 178)CC-BY-NC-ND · From the PDF
Figure 6 Ensemble of five virtual C a traces of the same 131 structures as shown in Figure 5, but broken into three segments and with slightly different coloring schemes. Drawn with the RasMol software (Sayle, 1995). A, Residues 44 to 77. Residue 44, dark blue; segment 45-55, gold/orange; segment 56-67 ( a 1), red; segment 68-70, salmon/pink; segment 71-76 ( b 4), yellow/gold; residue 77, bright red. B, Residues 71 to 94. Residue 71, dark blue; segment 72-77 ( b 4), gold/orange; segment 78-89 (hydrophilic loop), bright yellow; segment 90-93 ( b 5), green; residue 94, bright red. C, Residues 90 to 140. Residue 90, dark blue; segment 91-94 ( b 5), green; segment 95-98, yellow; segment 99-108 ( a 2), dark gray; segment 109-116 ( b 6*), gold/orange; segment 117-121, pale yellow-green; segment 123-136 ( a 3), light grayblue; segment 137-139, green; residue 140, bright red.
Figure 6 Ensemble of five virtual C a traces of the same 131 structures as shown in Figure 5, but broken into three segments and with slightly different coloring schemes. Drawn with the RasMol software (Sayle, 1995). A, Residues 44 to 77. Residue 44, dark blue; segment 45-55, gold/orange; segment 56-67 ( a 1), red; segment 68-70, salmon/pink; segment 71-76 ( b 4), yellow/gold; residue 77, bright red. B, Residues 71 to 94. Residue 71, dark blue; segment 72-77 ( b 4), gold/orange; segment 78-89 (hydrophilic loop), bright yellow; segment 90-93 ( b 5), green; residue 94, bright red. C, Residues 90 to 140. Residue 90, dark blue; segment 91-94 ( b 5), green; segment 95-98, yellow; segment 99-108 ( a 2), dark gray; segment 109-116 ( b 6*), gold/orange; segment 117-121, pale yellow-green; segment 123-136 ( a 3), light grayblue; segment 137-139, green; residue 140, bright red.CC-BY-NC-ND · From the PDF
Figure 7 Superpositioning of residues 56 to 140 of folded, wild-type staphylococcal nuclease (wide C a trace) with respect to an ensemble of five structures calculated for 131 (narrow C a traces). The three alpha helices are shaded in red. The three beta strands are yellow ( b 4), yellow green ( b 5) and orange ( b 6*). Drawn with the RasMol software (Sayle, 1995).
Figure 7 Superpositioning of residues 56 to 140 of folded, wild-type staphylococcal nuclease (wide C a trace) with respect to an ensemble of five structures calculated for 131 (narrow C a traces). The three alpha helices are shaded in red. The three beta strands are yellow ( b 4), yellow green ( b 5) and orange ( b 6*). Drawn with the RasMol software (Sayle, 1995).CC-BY-NC-ND · From the PDF

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Citations

Cites

Research works printed but not linked: 21

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  16. Schmidt, 1984, Distance measurements in spin-labeled lysozyme, Biochemistry, 23, 4261, 10.1021/bi00313a038 · DOI
  17. Shortle, 1996, The denatured state (the other half of the folding equation) and its role in protein stability, FASEB J., 10, 27, 10.1096/fasebj.10.1.8566543 · DOI · Paper page
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  19. Wang, 1995, The equilibrium folding pathway of staphylococcal nuclease, Identification of the most stable chain-chain interactions by NMR and CD spectroscopy, Biochemistry, 34, 15895, 10.1021/bi00049a004 · DOI
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  21. Zhang, 1997, Triple-resonance NOESY-based experiments with improved spectral resolution, J. Mol. Biol.

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Metadata

Authors
Gillespie, J. R., & Shortle, D.
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
1997-04
Volume
268
Issue
1
Pages
170-184
ISSN
0022-2836
DOI
10.1006/jmbi.1997.0953
Cited by
246
References
1
Language
en
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