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Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H TOCSY 5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate 90% H2O/10% D2O 7 ambient 298 2 2D 1H-1H NOESY 5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate 90% H2O/10% D2O 7 ambient 298 3 2D 1H-13C HSQC 5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate 90% H2O/10% D2O 7 ambient 298 4 2D 1H-15N sfHMQC 5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate 90% H2O/10% D2O 7 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 500
NMR Refinement Method Details Software simulated annealing In the final step was performed refinement in water 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 structure solution X-PLOR NIH 2.28 Schwieters, Kuszewski, Tjandra and Clore 2 refinement X-PLOR NIH 2.28 Schwieters, Kuszewski, Tjandra and Clore 3 processing NMRDraw Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 5 data analysis NMRView Johnson, One Moon Scientific 6 geometry optimization TALOS Cornilescu, Delaglio and Bax 7 data analysis TALOS Cornilescu, Delaglio and Bax 8 data analysis QUEEN Nabuurs, Spronk, Krieger, Maassen, Vriend and Vuister 9 data analysis ProcheckNMR Laskowski and MacArthur 10 data analysis MOLMOL Koradi, Billeter and Wuthrich