Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. 3. Successive KL Repeats Induce Highly Stable β-Strands Capable of Forming Non-H-Bonded Aggregates

Abstract

Circular dichroism (CD) and Raman scattering were applied to the aqueous solution of minimalist LK peptides constructed with successive KL repeats leading to the following generic primary sequence: (KL)nK. Three peptides of this family, a 3-mer (n=1), a 9-mer (n=4), and a 15-mer (n=7), are analyzed in this report. Raman spectra of the 3-mer (KLK, a random chain) and its labile-hydrogen deuterated species yield a set of interesting information for analyzing longer peptides of this series. Although the CD spectrum of the 9-mer (KLKLKLKLK) reveals a signal traditionally assigned to a random structure, the corresponding Raman spectrum allows finding a mixture of conformations in solution, adopting predominantly beta-type structures. This fact proves the utility of Raman spectroscopy to eliminate eventual ambiguity concerning conformational assignments in peptides based only on the use of CD technique. Finally, the 15-mer (KLKLKLKLKLKLKLK) gives rise to CD and Raman spectra clearly assignable to a beta-type structure. On the basis of all the observed results on the 15-mer, we can confirm that this peptide may exist as isolated beta-strands at low concentration (sub-micromolar), flat-oriented at the air/water interface, whereas at high concentrations (millimolar), non-H-bonded immersible aggregates might be formed. A hypothetical model for these beta-strand aggregates could be proposed as stabilized by an interior hydrophobic core and a hydrophilic external face, formed by leucine and lysine side chains, respectively.

Low concentration structural dynamics of lanreotide and somatostatin‐14

“…Despite the presence of the strong band at 1634 cm −1 arising from D‐Nal residue, we could analyze the amide I (Figure a) and amide I' (observed in D 2 O, Figure b) regions. Upon backbone N‐deuteration, the amide I components manifest a 5‐ to‐ 12 cm −1 downshift, in agreement with previous observations in peptides and proteins . Considering our previously reported data on SST‐14 19 and octreotide, four components assigned to turn, β‐strand and random chain, were used for band decomposition (Table ).…”

“…In addition, the assignment of the observed bands to the amide vibrations needs the collection of Raman data in heavy water. For instance, D 2 O Raman spectra confirm the assignment of the amide III markers by their complete vanishing due to the NH→ND substitution in a peptide backbone . To check all these crucial points, we present in Figures a and b the Raman spectra obtained from (i) the solution containing lanreotide (red trace), (ii) the solvent contribution (blue trace), and finally (iii) the spectrum obtained from the subtraction of the latter two spectra (green trace).…”

“…On the basis of the above mentioned empirical relations, we could assign the components at ∼1303 and ∼1252 cm −1 to the i + 1 and i + 2 residues of a type‐II' β‐turn . On the other hand, classical Raman spectra have previously assigned the two components at ∼1265 and ∼1233 cm −1 to random chain and β‐strands, respectively . Finally, the fifth component of this region appearing at ∼1289 cm −1 has been recognized as a turn marker, since the earliest Raman studies .…”

“…The analysis of the amide (I and III) regions by band decomposition is obviously based on the choice of significant components. This goal has been achieved by means of our previously reported Raman spectra on other short peptides, forming β‐strands and turns in aqueous solution (see below for more details). More precisely, the characteristic components assigned to β‐strands, β‐turns and disordered chains (with a half‐width not exceeding ∼20 cm −1 ), were introduced as initial guess in the first stage of band decomposition.…”

Evidence of conformational changes in adsorbed lysozyme molecule on silver colloids

“…The contributions of the three secondary structures -turn, ␣-helix, ␤-family, and random coil -are expected to occur over the spectral windows 1635-1640 , 1650-1655, and 1665-1670 cm −1 and above 1680 cm −1 , respectively [29,30]. To study the correlation between these secondary structural components of the adsorbed protein molecule, the broad envelope of the amide I band of each spectrum needs to be deconvoluted into the contributions from each of them (Supplementary material in Fig.…”