Experiment: 7MLL

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