Experiment: 2K9B

Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	2.0 mM dd k, 400 mM [U-2H] DPCd38	400mM DPCd38/H2O		6.0	ambient	318
2	2D 1H-1H NOESY	2.0 mM dd k, 400 mM [U-2H] DPCd38	400mM DPCd38/H2O		6.0	ambient	318

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
simulated annealing	NOE INTENSITIES WERE CONVERTED INTO SEMI-QUANTITATIVE DISTANCE RESTRAINS. THE UPPER LIMITS OF THE DISTANCES RESTRAINS THUS OBTAINED WERE 2.8, 3.4 AND 5.0 A (STRONG, MEDIUM, AND WEAK NOES RESPECTIVELY). STRUCTURE CALCULATIONS WERE PERFORMED USING THE XPLOR-NIH SOFTWARE, VERSION 2.17.0 (SCHWIETERS ET AL., 2003). STARTING WITH THE EXTENDED STRUCTURE, 500 STRUCTURES WERE GENERATED USING A SIMULATED ANNEALING PROTOCOL. THIS WAS FOLLOWED BY 20000 STEPS OF SIMULATED ANNEALING AT 1000 K AND A SUBSEQUENT DECREASE IN TEMPERATURE IN 15000 STEPS IN THE FIRST SLOW-COOL ANNEALING STAGE.	TopSpin

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	500
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	2.0	Bruker Biospin
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	chemical shift assignment	NMRView		Johnson, One Moon Scientific
4	data analysis	NMRView		Johnson, One Moon Scientific
5	peak picking	NMRView		Johnson, One Moon Scientific
6	geometry optimization	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
7	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
8	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
9	data analysis	ProcheckNMR		Laskowski and MacArthur
10	data analysis	MOLMOL		Koradi, Billeter and Wuthrich