SOLUTION NMR

NMR Experiment
Experiment Type Sample Contents Ionic Strength Solvent pH Pressure Temprature (K)
1 2D NOESY 1.82 mM tanniamide, 102.2 mM [U-2H] DPC, 90% H2O/10% D2O 26 (buffer only) 90% H2O/10% D2O 7.4 1 310
2 2D TOCSY 1.82 mM tanniamide, 102.2 mM [U-2H] DPC, 90% H2O/10% D2O 26 (buffer only) 90% H2O/10% D2O 7.4 1 310
3 2D COSY 1.82 mM tanniamide, 102.2 mM [U-2H] DPC, 90% H2O/10% D2O 26 (buffer only) 90% H2O/10% D2O 7.4 1 310
4 2D 1H-13 HSQC 1.82 mM tanniamide, 102.2 mM [U-2H] DPC, 90% H2O/10% D2O 26 (buffer only) 90% H2O/10% D2O 7.4 1 310
NMR Spectrometer Information
Spectrometer Manufacturer Model Field Strength
1 Bruker AVANCE II 700
NMR Refinement
Method Details Software
molecular dynamics The 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: TIP3P. Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1). Side-chain outlier values for the 2TL4 residue are the results of the depsi bond. 1
NMR Ensemble Information
Conformer Selection Criteria structures with the lowest energy
Conformers Calculated Total Number 100
Conformers Submitted Total Number 11
Representative Model 1 (closest to the average)
Computation: NMR Software
# Classification Version Software Name Author
1 refinement ? Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2 data analysis ? AmberTools Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3 processing 3.x TopSpin Bruker Biospin
4 collection 3.x TopSpin Bruker Biospin
5 peak picking ? CcpNmr Analysis Vuister et al. (CCPN)
6 structure calculation ? CNS Brunger, Adams, Clore, Gros, Nilges and Read
7 chemical shift assignment ? CcpNmr Analysis CCPN