Experiment: 2JQ3

Structure and Dynamics of Human Apolipoprotein C-III

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	CBCA(CO)NH	0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS	92% H2O/8% D2O	0.3	5.0	ambient	315.7
2	HNCACB	0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS	92% H2O/8% D2O	0.3	5.0	ambient	315.7
3	HNCO	0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS	92% H2O/8% D2O	0.3	5.0	ambient	315.7
4	HNHA	0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS	92% H2O/8% D2O	0.3	5.0	ambient	315.7
5	15N NOESY HSQC	0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS	92% H2O/8% D2O	0.3	5.0	ambient	315.7
6	15N HSQC NOESY HSQC	0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS	92% H2O/8% D2O	0.3	5.0	ambient	315.7

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	800

NMR Refinement
Method	Details	Software
simulated annealing, torsion angle dynamics	Simulated annealing using IVM algorithm available within XPLOR-NIH (2.10) followed by energy minimization. IVM dynamics (XPLOR-NIH) with restraining terms: noe, cdih, jcoup, rdc and 7 positional restraints (appr. one CA atom per helix near the middle of each helix).	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	50
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	peak picking	XEASY		Bartels et al.
3	backbone torsion angles from chemical shifts	TALOS		Cornilescu, Delaglio and Bax
4	restr. md caclulations	X-PLOR NIH	2.10	Schwieters, Kuszewski, Tjandra and Clore
5	monte carlo simulation to fit helical structures to experimental rdc's	Monte_Carlo_script		S.Wijmenga (unpublished)
6	program for positioning helices on the micelle	Protein Constructor		under development)
7	caclulations of hydropobic moment directions	Protein Constructor		under development)
8	inverse kinematic for junction of helices, rdc simulation	Protein Constructor		under development)