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NMR assignment and structure of a peptide derived from the membrane proximal external region of HIV-1 gp41 in DPC
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H COSY 0.5 mM MPERp, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM [U-99% 2H] DPC, 2 mM HEPES, 0.1 mM DSS 90% H2O/10% D2O 2 7.0 ambient 298 2 2D 1H-1H TOCSY 0.5 mM MPERp, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM [U-99% 2H] DPC, 2 mM HEPES, 0.1 mM DSS 90% H2O/10% D2O 2 7.0 ambient 298 3 2D 1H-1H NOESY 0.5 mM MPERp, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM [U-99% 2H] DPC, 2 mM HEPES, 0.1 mM DSS 90% H2O/10% D2O 2 7.0 ambient 298 4 2D 1H-13C HSQC aliphatic 0.5 mM MPERp, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM [U-99% 2H] DPC, 2 mM HEPES, 0.1 mM DSS 90% H2O/10% D2O 2 7.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software torsion angle dynamics, molecular dynamics TopSpin
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 100 Conformers Submitted Total Number 20 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 processing TopSpin Bruker Biospin 3 chemical shift assignment Sparky Goddard 4 structure solution CYANA Guntert, Mumenthaler and Wuthrich 5 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 6 refinement CYANA