1LE1

NMR Structure of Tryptophan Zipper 2: A stable, Monomeric Beta-Hairpin with a Type I' Turn

SOLUTION NMR

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NMR Experiment
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
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500

NMR Refinement
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
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

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
#	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