Solution structure of Exenatide (exendin-4) in 30-vol% trifluoroethanol using CS-Rosetta
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-13C HSQC | 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS | 60 % H2O/30%Trifluoroethanol/10 % D2O | 20 mM | 5.35 | 1 atm | 315 | Bruker AVANCE III 600 |
| 2 | 2D 1H-15N HSQC | 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS | 60 % H2O/30%Trifluoroethanol/10 % D2O | 20 mM | 5.35 | 1 atm | 315 | Bruker AVANCE III 600 |
| 3 | 2D 1H-13C HSQC TOCSY | 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS | 60 % H2O/30%Trifluoroethanol/10 % D2O | 20 mM | 5.35 | 1 atm | 315 | Bruker AVANCE III 600 |
| 4 | 2D 1H-15N HSQC TOCSY | 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS | 60 % H2O/30%Trifluoroethanol/10 % D2O | 20 mM | 5.35 | 1 atm | 315 | Bruker AVANCE III 600 |
| 5 | 2D 1H-13C HMBC (carbonyl selective) | 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS | 60 % H2O/30%Trifluoroethanol/10 % D2O | 20 mM | 5.35 | 1 atm | 315 | Bruker AVANCE III 600 |
| 6 | 1D 13C APT | 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS | 60 % H2O/30%Trifluoroethanol/10 % D2O | 20 mM | 5.35 | 1 atm | 315 | Bruker AVANCE III 600 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | CS-ROSETTA | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 3000 |
| Conformers Submitted Total Number | 5 |
| Representative Model | 1 (medoid) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | NMRFAM-SPARKY | Lee W, Tonelli M, Markley JL | |
| 2 | structure calculation | CS-ROSETTA | Shen, Vernon, Baker and Bax Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples" Oliver F. Lange; Paolo Rossi; Nikolaos G. Sgourakis; Yifan Song; Hsiau-Wei Lee; James M. Aramini; Asli Ertekin; Rong Xiao; Thomas B. Acton; Gaetano T. Montelione; David Baker; Proceedings of the National Academy of Sciences 109(27) 10873-10878 (2012) doi: 10.1073/pnas.1203013109 "De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds," Yang Shen; Philip N. Bryan; Yanan He; John Orban; David Baker; Ad Bax; Protein Science 19, 349-356 (2010) doi: 10.1002/pro.303 "De novo protein structure generation from incomplete chemical shift assignments," Yang Shen; Robert Vernon; David Baker; Ad Bax; J. Biomol. NMR 43, 63-78 (2009) doi: 10.1007/s10858-008-9288-5 "Consistent blind protein structure generation from NMR chemical shift data," Yang Shen; Oliver Lange; Frank Delaglio; Paolo Rossi; James M. Aramini; Gaohua Liu; Alexander Eletsky; Yibing Wu; Kiran K. Singarapu; Alexander Lemak; Alexandr Ignatchenko; Cheryl H. Arrowsmith; Thomas Szyperski; Gaetano T. Montelione; David Baker; Ad Bax; Proceedings of the National Academy of Sciences 105(12) 4685-4690 (2008) doi: 10.1073/pnas.0800256105 | |
| 3 | refinement | Rosetta | Firas Khatib 1, Seth Cooper, Michael D Tyka, Kefan Xu, Ilya Makedon, Zoran Popovic, David Baker, Foldit Players - Algorithm discovery by protein folding game players. Jack B. Maguire Hugh K. Haddox Devin Strickland Samer F. Halabiya Brian Coventry Jermel R. Griffin Surya V. S. R. K Pulavarti Matthew Cummins David F Thieker Eric Klavins Thomas Szyperski Frank DiMaio David Baker Brian Kuhlman - Perturbing the energy landscape for improved packing during computational protein design | |
