1P5A
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 | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Mattson FTIR | Research Series |
NMR Refinement | ||
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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 | |
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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 | |
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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 |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | Winfirst | FTIR curve fitting software | Kauppine et al. |
2 | refinement | CHARMM | c28b2 | Brooks et al. |