8S4L | pdb_00008s4l

NMR structure of orfamide A in micellar DPC solution


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1.9 mM orfamide A, 111.9 mM [U-2H] DPC90% H2O/10% D2O26 (buffer only) mM7.41 atm310Bruker AVANCE II 700
22D 1H-1H TOCSY1.9 mM orfamide A, 111.9 mM [U-2H] DPC90% H2O/10% D2O26 (buffer only) mM7.41 atm310Bruker AVANCE II 700
32D 1H-1H COSY1.9 mM orfamide A, 111.9 mM [U-2H] DPC90% H2O/10% D2O26 (buffer only) mM7.41 atm310Bruker AVANCE II 700
42D 1H-13C HSQC1.9 mM orfamide A, 111.9 mM [U-2H] DPC90% H2O/10% D2O26 (buffer only) mM7.41 atm310Bruker AVANCE II 700
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE II700
NMR Refinement
MethodDetailsSoftware
molecular dynamicsThe lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a single peptide molecule with an explicit dodecylphosphocholine (DPC) micelle. The representative peptide conformation of the trajectory (=refined structure) was selected using cluster analysis. Solvent model: TIP3PAmber
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number11
Representative Model1 (closest to the average)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementAmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2data analysisAmberToolsCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3processingTopSpinBruker Biospin
4collectionTopSpinBruker Biospin
5peak pickingCcpNmr AnalysisVuister et al.
6structure calculationCNSBrunger, Adams, Clore, Gros, Nilges and Read
8chemical shift assignmentCcpNmr AnalysisVuister et al.