SOLUTION NMR Experimental Data

Experimental Details
Sample Conditions
Sample Contents2mM trpzip4
Solvent92% H2O, 8% D2O, pH 6.0, 0.1mM DSS
Ionic Strength0
Temperature (K)288
Experiment(s):2D NOESY, DQF-COSY, 2D-ROESY, 2D-TOCSY
Spectrometer Information
Manufacturer Model Field Strength
Bruker DRX 600.0
Bruker DRX 500.0
NMR Refinement
Method 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.
Details Structures are based on a total of 130 (including 29 intra-residue, 30 sequential, 20 medium-range, and 51 long-range) NOE-derived distance restraints, 22 dihedral angle restraints, and 1H chemical shift restraints for 46 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 0.106 ppm between observed and calculated chemical shifts.
NMR Ensemble Information
Conformer Selection Criteria structures with the least restraint violations
Conformers Calculated Total Number 64
Conformers Submitted Total Number 20
Representative Model Choice Rationale
1 closest to the average
Additional NMR Experimental Information
1 The structure of trpzip4 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 Trp5 and Trp14 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 Trp5 and Trp14. However, the rest of the structure is similar with a backbone rmsd between the average coordinates of the two ensembles of 0.72 angstrom(res.43-54). 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. This sort of packing is observed for all tryptophan zipper peptides, regardless of turn type.
Computation: NMR Software
# Classification Software Name Author
1 refinement AMBER 6.0 Case and Kollman
2 structure solution DGII 98.0 Molecular Simulations, Inc.
3 data analysis FELIX 98.0 Molecular Simulations, Inc.
4 collection XWINNMR 2.5 Bruker