Conformational preferences of a short Aib/Ala‐based water‐soluble peptide as a function of temperature

Abstract

The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To characterize helical and unfolded states adopted by water-soluble Aib-containing peptides, the conformational preference of Ac-Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Tyr-NH(2) was determined by CD, NMR and MD simulations as a function of temperature. Temperature-dependent CD data indicated the contribution of two major components, each an admixture of helical and extended/polyproline II structures. Both right- and left-handed helical conformations were detected from deconvolution of CD data and (13)C NMR experiments. The presence of a helical backbone, more pronounced at the N-terminal, and a temperature-induced shift in alpha-helix/3(10)-helix equilibrium, more pronounced at the C-terminal, emerged from NMR data. Starting from polyproline II, the N-terminal of the peptide folded into a helical backbone in MD simulations within 5 ns at 60 degrees C. Longer simulations showed a mixed-helical backbone to be stable over the entire peptide at 5 degrees C while at 60 degrees C the mixed-helix was either stable at the N-terminus or occurred in short stretches through out the peptide, along with a significant population of polyproline II. Our results point towards conformational heterogeneity of water-soluble Aib-based peptide helices and the associated subtleties. The problem of analyzing CD and NMR data of both left- and right-handed helices are discussed, especially the validity of the ellipticity ratio [theta](222)/[theta](207), as a reporter of alpha-/3(10)- population ratio, in right- and left-handed helical mixtures.

Sulfate ion interaction with ‘anion recognition’ short peptide motif at the N-terminus of an isolated helix: A conformational landscape

“…S2 Supplementary material), which might corroborate the role of the four residue segment 'L-G-K-Q' present at the N-terminus of CPS224Ac in recognition of sulfate ion. In aqueous solution, short peptides usually exist as conformational ensembles (Banerjee et al, 2009;Schweitzer-Stenner et al, 2007), however, for sulfate added species of CPS224Ac the observed increase in n-p* ($222 nm) band as well as the 'R-value' ([h] n-p* /[h] p-p* ) with decrease in temperature indicated the increment of helical population, with a preference towards predominantly a-helical form (Manning and Woody, 1991).…”

“…This might be either due to stabilization of helical conformation with change in helix-coil equilibrium towards helix or participation of non-helical residues in helix formation along with the stabilization of the existing helix. CD spectra of the model anchor helix (peptide ABGY in Banerjee and Basu (2002) and Banerjee et al (2009)) present at the C-terminus of the chimeric polypeptide CPS224Ac were also obtained in absence as well as in presence of sulfate ion separately. However, no appreciable change in CD spectra of ABGY were observed upon addition of sulfate ion ( Fig.…”

“…The sequence Leu-Gly-Lys-Gln, a C a NN structural motif appeared in protein DNA-glycosylase, was attached at the N-terminus of a model anchor helix: Ala-Aib-Ala-Lys-Ala-Aib-Lys-AlaLys-Ala-Aib-Gly-Gly-Tyr-NH 2 (ABGY) (Banerjee and Basu, 2002;Banerjee et al, 2009) using solid phase fmoc protocol. The overall sequence of the chimeric peptide: Ac-Leu-Gly-Lys-Gln-Ala-AibAla-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Gly-Gly-Tyr-NH 2 (CPS224Ac, MW 1757) would be an ideal candidate for exhibiting 'anion recognition' in isolated condition pertaining a conformational switching from the non-helical to helix conformation at the anion binding site, as observed in crystal structure (Denessiouk et al, 2005).…”

“…The underlined segment in the sequence was found to be attached with sulfate (SO 2À 4 ) ion in the reported crystal structure (Barrett et al, 1998). The segment was appended at the N-terminus of a designed model helix (Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-AibGly-Gly-Tyr-NH 2 ) (Banerjee and Basu, 2002;Banerjee et al, 2009) whose backbone conformation was attained without any tertiary interaction. Complementary spectroscopic techniques were used to characterize the conformational landscape of this short chimeric peptide (CPS224Ac) in a context free environment in absence as well as in presence of sulfate ion.…”

Highly Active Analogs of α-Factor and Their Activities Against Saccharomyces cerevisiae

“…4,30 Aib is sterically hindered by dialkylated side chains and thus its substitution generates a collapsed turn structure effectively. 34 Substituting Pro with Aib at position 8 and 11 causes 90% and 80% decreases in halo activity, respectively, as well as a 40% decrease in 5% shmoo assay compared to the native α-factor. Therefore, the dramatic reduction in activity strongly emphasizes critical role of the β-turn structures for pheromone activity.…”