Local helix content in an alanine-rich peptide as determined by the complete set of 3JHNα coupling constants

Abstract

Alanine-rich peptides serve as models for exploring the factors that control helix structure in peptides and proteins. Scalar C alpha H-NH couplings (3JHN alpha) are an extremely useful measure of local helix content; however, the large alanine content in these peptides leads to significant signal overlap in the C alpha H region of 1H 2D NMR spectra. Quantitative determination of all possible 3JHN alpha values is, therefore, very challenging. Szyperski and co-workers [(1992) J. Magn. Reson. 99, 552-560] have recently developed a method for determining 3JHN alpha from NOESY spectra. Because 3JHN alpha may be determined from 2D peaks outside of the C alpha H region, there is a much greater likelihood of identifying resolved resonances and measuring the associated coupling constants. It is demonstrated here that 3JHN alpha can be obtained for every residue in the helical peptide Ac-(AAAAK)3A-NH2. The resulting 3JHN alpha profile clearly identifies a helical structure in the middle of the peptide and further suggests that the respective helix termini unfold via distinct pathways.

An NMR Investigation of the Conformational Effect of Nitroxide Spin Labels on Ala-Rich Helical Peptides

“…However, the unlabeled peptides follow the same general pattern as the labeled peptides and 3K0, with more negative shifts observed at the Nterminus and center of the peptide and a decrease in conformational shift for the C-terminal four residues. These results are consistent with previous observations by NMR (16) and ESR (4) which report the most helical structure to be toward the center of the peptide. Aside from the large upfield conformational shifts of the Cys residues, there do not appear to be any distinct local perturbations, but rather a global loss of helicity resulting from the introduction of Cys into the sequence, which is consistent with the general shape of the CD curve and the 222 nm/208 nm ratios for the 3K8u and 3K12u peptides.…”

“…While 3K0 cannot be studied by ESR, it is surprisingly amenable to study by NMR and shows an spectra were acquired with between 800 and 1024 t 1 increments. TOCSY spectra were acquired with t m Å 50 ms. unanticipated degree of signal dispersion of the amide resonances ( 16 ) . Measurement and analysis of the short-range Solvent saturation was applied for 1.5 s before the first 90Њ pulse and during the mixing time for NOESY spectra.…”

Local Protein Structures

“…A dynamic relationship would exist between the different kinds of helices as shown for instance between α-and π-helices [65]. 3 10 -helices, and to a lesser extent π-helices, have been proposed to be intermediates in the folding/unfolding of α-helices [66][67][68].…”

The effect of mutations on peptide models of the DNA binding helix of p53: Evidence for a correlation between structure and tumorigenesis

“…The spectra were processed using the MNMR package (Carlsberg Laboratory, Department of Chemistry, Denmark), and analyzed using XEASY. 33 3 J HN␣ coupling constants were determined using the method of Szyperski et al 34,35 CD spectra were recorded at 1°C on an Aviv 60DS spectropolarimeter in a rectangular 1 mm path length cuvette for concentrations up to 200 M; for concentrations higher than this a round cell with a 0.1 mm path length was used. All CD samples were prepared by addition of the solvent to a known quantity of lyophilized peptide; concentrations were 90 -120 M. The CD spectra of the peptides in 20 mM KCl and in 20 mM KCl/50% v/v TFE were smoothed with windows of 4 and 3, respectively.…”