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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
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
13C-isotope enhanced FTIR
THIS 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 Na2HPO4
0.271
7.4
ambient
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Mattson FTIR
Research Series
NMR Refinement
Method
Details
Software
molecular dynamics
The 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 Criteria
structures with acceptable covalent geometry
Conformers Calculated Total Number
20
Conformers Submitted Total Number
19
Representative Model
1 (closest to the average)
Additional NMR Experimental Information
Details
The 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