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Solution Structure of Switch Arc, a Mutant with 3(10) Helices Replacing a Wild-Type Beta-Ribbon
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
4 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)
90% H2O/10% D2O
20mM phosphate
4.8
ambient
303
2
3D_15N-separated_NOESY
4 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)
90% H2O/10% D2O
20mM phosphate
4.8
ambient
303
3
HNHA
4 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)
90% H2O/10% D2O
20mM phosphate
4.8
ambient
303
4
HNHB
4 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)
90% H2O/10% D2O
20mM phosphate
4.8
ambient
303
5
HSQCs (hydrogen exchange)
5 mM uniform 15N-labelled Arc repressor NL11/LN12 (Switch Arc)
100% D2O
20 mM phosphate, 150 mM KCl
4.67
ambient
303
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX
500
NMR Refinement
Method
Details
Software
simulated annealing
Experimentally derived restraints included 810 nOe distance restraints per monomer, along with 3 hydrogen bond restraints, 31 phi-angle restraints and 3 chi1-angle restraints, for a total of 847 restraints per monomer spanning residues 5-53. Structure calculations were performed using a simulated annealing protocol designed for symmetric dimers (M. Nilges, Proteins Struct. Funct. Gen, 17, 297 (1993)). As starting points for the calculation, 28 structures were generated in which the conformation of the N-terminal region (residues 1-13) was random, and that of the remainder of the protein restrained to be similar to wild-type Arc. The use of completely random starting structures led to extremely poor convergence rates, but those calculations which did converge yielded structures similar to those obtained from calculations using non-random starting structures. Each semi-random starting structure was then annealed to a model structure using the distance, angle and hydrogen bond restraints mentioned above. Two "seed" restraints, Arg 40 HE-Phe 45 HD and Trp 14 HE3-Tyr 38 HE, were described as unambiguously intermolecular. In the wild-type Arc structure, the difference between the intra and intermolecular distances for these atoms is >10 A. Use of the seed restraints improved convergence but again did not alter the qualitative nature of the results. All other NOE distance restraints were described ambiguously using sum potentials. Hydrogen-bond restraints in alpha-helices were described as intramonomer. In the conformational search phase of the calculations, non-bonded interactions were computed only between C-alpha atoms with a van der Waals term of 0.1. 13 of 28 calculated structures were accepted with no angle violations >5 degrees and no more than two nOe violations >0.35 A. These comprise the ensemble submitted here.