1p5a
From Proteopedia
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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
Overview
The N-terminal domain of HIV-1 glycoprotein 41,000 (gp41) participates in, viral fusion processes. Here, we use physical and computational, methodologies to examine the secondary structure of a peptide based on the, N terminus (FP; residues 1-23) in aqueous and detergent environments., (12)C-Fourier transform infrared (FTIR) spectroscopy indicated greater, alpha-helix for FP in lipid-detergent sodium dodecyl sulfate (SDS) and, aqueous phosphate-buffered saline (PBS) than in only PBS. (12)C-FTIR, spectra also showed disordered FP conformations in these two environments, along with substantial beta-structure for FP alone in PBS. In experiments, that map conformations to specific residues, isotope-enhanced FTIR, spectroscopy was performed using FP peptides labeled with (13)C-carbonyl., (13)C-FTIR results on FP in SDS at low peptide loading indicated, alpha-helix (residues 5 to 16) and disordered conformations (residues, 1-4). Because earlier (13)C-FTIR analysis of FP in lipid bilayers, demonstrated alpha-helix for residues 1-16 at low peptide loading, the FP, structure in SDS micelles only approximates that found for FP with, membranes. Molecular dynamics simulations of FP in an explicit SDS micelle, indicate that the fraying of the first three to four residues may be due, to the FP helix moving to one end of the micelle. In PBS alone, however, electron microscopy of FP showed large fibrils, while (13)C-FTIR spectra, demonstrated antiparallel beta-sheet for FP (residues 1-12), analogous to, that reported for amyloid peptides. Because FP and amyloid peptides each, exhibit plaque formation, alpha-helix to beta-sheet interconversion, and, membrane fusion activity, amyloid and N-terminal gp41 peptides may belong, to the same superfamily of proteins.
About this Structure
1P5A is a Single protein structure of sequence from [1] with NH2 as ligand. Full crystallographic information is available from OCA.
Reference
Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy., Gordon LM, Mobley PW, Lee W, Eskandari S, Kaznessis YN, Sherman MA, Waring AJ, Protein Sci. 2004 Apr;13(4):1012-30. PMID:15044732
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