8Q1L
NMR structure of arthrofactin A in micellar DPC solution
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.3 mM NA arthrofactin A, 142.8 mM [U-2H] DPC | 90% H2O/10% D2O | 26 (buffer only) mM | 7.4 | 1 atm | 310 | Bruker AVANCE II 700 |
2 | 2D 1H-1H TOCSY | 1.3 mM NA arthrofactin A, 142.8 mM [U-2H] DPC | 90% H2O/10% D2O | 26 (buffer only) mM | 7.4 | 1 atm | 310 | Bruker AVANCE II 700 |
3 | 2D 1H-1H COSY | 1.3 mM NA arthrofactin A, 142.8 mM [U-2H] DPC | 90% H2O/10% D2O | 26 (buffer only) mM | 7.4 | 1 atm | 310 | Bruker AVANCE II 700 |
4 | 2D 1H-13C HSQC | 1.3 mM NA arthrofactin A, 142.8 mM [U-2H] DPC | 90% H2O/10% D2O | 26 (buffer only) mM | 7.4 | 1 atm | 310 | Bruker AVANCE II 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE II | 700 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | The lowest energy NMR structure issued from CNS was refined in an unrestrained AMBER molecular dynamics simulation (agains 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, #1) 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. | Amber |
NMR Ensemble Information | |
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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 | ||||
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# | 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 | TopSpin | 3.x | Bruker Biospin |
4 | collection | TopSpin | 3.x | Bruker Biospin |
5 | peak picking | CcpNmr Analysis | Vuister et al. | |
6 | structure calculation | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
8 | chemical shift assignment | CcpNmr Analysis | Vuister et al. |