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The peptide PaAMP1B3 is an analog derived from the PaAMP1. The sequence of the ribosomal protein of Pyrobaculum aerophylum was used as template for rational design, using the Joker algorithm.
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H TOCSY 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O 90% H2O/10% D2O acid 4.3 1 atm 298 Bruker AVANCE III 500 2 2D 1H-1H NOESY 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O 90% H2O/10% D2O acid 4.3 1 atm 298 Bruker AVANCE III 500 3 2D 1H-13C HSQC 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O 90% H2O/10% D2O acid 4.3 1 atm 298 Bruker AVANCE III 500 4 2D 1H-15N HMQC 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O 90% H2O/10% D2O acid 4.3 1 atm 298 Bruker AVANCE III 500
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 500
NMR Refinement Method Details Software simulated annealing X-PLOR NIH
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment NMRView Johnson, One Moon Scientific 2 structure calculation X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 3 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 6 geometry optimization TALOS Cornilescu, Delaglio and Bax