1P5A | pdb_00001p5a

Conformational Mapping of the N-terminal Peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier Transform Infrared Spectroscopy


INFRARED SPECTROSCOPY
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
113C-isotope enhanced FTIRTHIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527,528,529,530,531,532,533,534,538,539.94 mM SDS (sodium dodecyl sulfate) in deuterated PBS (phosphate buffered saline), where PBS is 120 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO40.2717.4ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1Mattson FTIRResearch Series
NMR Refinement
MethodDetailsSoftware
molecular dynamicsThe system of more than 16,000 atoms (peptide, SDS micelle, water, sodium counterions) was simulated for 2.5 nanoseconds at a constant pressure P=1 atm and constant temperature T=303.15 K.Winfirst
NMR Ensemble Information
Conformer Selection Criteriastructures with acceptable covalent geometry
Conformers Calculated Total Number20
Conformers Submitted Total Number19
Representative Model1 (closest to the average)
Additional NMR Experimental Information
DetailsThe coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information. Peptide concentration was 47 micromolar. Peptide/SDS ratio was 1/200. FTIR spectra were averaged over 256 scans at a gain of 4 and a resolution of 2 cm-1
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1data analysisWinfirstFTIR curve fitting softwareKauppine et al.
2refinementCHARMMc28b2Brooks et al.