1LE1
NMR Structure of Tryptophan Zipper 2: A stable, Monomeric Beta-Hairpin with a Type I' Turn
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 3mM trpzip2 | 92% H2O, 8% D2O, pH 5.5, 0.1mM DSS | 0 | 5.5 | ambient | 288 | |
2 | DQF-COSY | 3mM trpzip2 | 92% H2O, 8% D2O, pH 5.5, 0.1mM DSS | 0 | 5.5 | ambient | 288 | |
3 | 2D TOCSY | 3mM trpzip2 | 92% H2O, 8% D2O, pH 5.5, 0.1mM DSS | 0 | 5.5 | ambient | 288 | |
4 | 2D ROESY | 3mM trpzip2 | 92% H2O, 8% D2O, pH 5.5, 0.1mM DSS | 0 | 5.5 | ambient | 288 | |
5 | 2D COSY-35 | 0 | 5.5 | ambient | 288 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
NMR Refinement | ||
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Method | Details | Software |
Hybrid distance geometry/simulated annealing using the program DGII, followed by molecular dynamics using the program AMBER, in conjunction not only with distance and dihedral angle restraints, but also 1H chemical shift-based restraints. | Structures are based on a total of 80 (including 26 intra-residue, 15 sequential, 6 medium-range, and 33 long-range) NOE-derived distance restraints, 15 dihedral angle restraints, and 1H chemical shift restraints for 39 carbon-bound 1H resonances; (chemical shift restraints were not imposed for the terminal residues, or for side chains exhibiting evidence of rotational averaging). The ensemble agrees well with the experimental restraints with no distance or dihedral angle violations greater than 0.10 angstrom or 5 deg, respectively, and an average rmsd of only 0.087 ppm between observed and calculated chemical shifts. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 76 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Additional NMR Experimental Information | |
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Details | The structure of trpzip2 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle restraints were derived from analysis of NOESY, ROESY, DQF-COSY, and COSY-35 data. Chi-1 rotamers and stereospecific assignments for beta-methylene groups were based on combined analysis of 3JHaHb and local ROEs, suggesting that all four Trp residues adopt a chi1 of -60 deg. Quantitative analysis of the 1H chemical shifts, however, revealed that the frequencies of the Hb and He3 resonances of Trp4 and Trp11 were inconsistent with a -60 deg chi1 value, and indicated that the side chains for these tryptophans actually reside primarily in the 180 deg chi1 rotamer (Skelton et al., manuscript in preparation). The current coordinates result from refinement with the Sander module of AMBER (v6.0), and included not only NOE-derived distance restraints and dihedral angle restraints, but also 1H chemical shift-based restraints. Thus, the resulting updated coordinates differ from the previous ones in the side chain orientations of Trp4 and Trp11. However, the rest of the structure is similar with a backbone rmsd between the average coordinates of the two ensembles of 0.69 angstrom(res.2-11). The two strands are highly twisted, as described previously, however there is a slight difference in the relative position of the turn with respect to the strands. The key difference, however, is that each pair of cross-strand tryptophan rings now shows edge-to-face packing against one another. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.5 | Bruker |
2 | data analysis | Felix | 98.0 | Molecular Simulations, Inc. |
3 | structure solution | DGII | 98.0 | Molecular Simulations, Inc. |
4 | refinement | Amber | 6.0 | Case and Kollman |