Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution

Abstract

We have combined Fourier transform IR, polarized Raman spectroscopy, and vibrational CD measurements of the amide I′ band profile of alanyl-X-alanine tripeptides in 2 H 2 O to obtain the dihedral angles of their central amino acid residue. X represents glycine, valine, methionine, histidine, serine, proline, lysine, leucine, tryptophan, tyrosine, and phenylalanine. The experimental data were analyzed by means of a recently developed algorithm, which exploits the excitonic coupling between the amide modes of the two peptide groups. The results were checked by measuring the respective electronic CD spectra. The investigated peptides can be sorted into three classes. Valine, phenylalanine, tryptophan, histidine, and serine predominantly adopt an extended β-strand conformation. Cationic lysine and proline prefer a polyproline II-like structure. Alanine, methionine, glycine, and leucine populate these two conformations with comparable probability. Our results are in variance with the prediction of the random-coil model, but supportive of Flory's isolated-pair hypothesis. We combined the obtained structural propensities of the investigated residues and similar information about other residues in the literature (i.e., glutamate, aspartate, isoleucine, and glutamine) to predict possible conformations of the monomeric amyloid β peptide Aβ 1–42 in aqueous solution, which reproduces results from most recent spectroscopic studies. Thus, it is demonstrated that the unfolded state of peptides can be understood in terms of the intrinsic structural propensities of their amino acid residues.

The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations

“…Shi et al (24), for instance, used NMR and ECD measurements to study the structure of Ac-X 2 (A) 7 O 2 -NH 2 (XAO, X and O denote diaminobutyric acid and ornithine, respectively), and interpreted their results as indicating that the individual residues predominantly adopt a PPII conformation at room temperature. The results of Shi et al have been corroborated by numerous experimental and theoretical studies on short peptides, which all revealed a substantial PPII propensity for alanine (2,(4)(5)(6)(7)(8). This notion is also in perfect agreement with distributions that Serrano (25) and Avbelj and Baldwin (26) inferred from coil libraries, but at variance with a less restricted library investigated by Dobson and associates (27).…”

“…T he unfolded state of peptides and proteins has been the subject of an increasing number of experimental and theoretical studies (1)(2)(3)(4)(5)(6)(7)(8)(9), owing to the discovery of naturally disordered, although biologically functioning, proteins and peptides (9), and the general relevance for a thorough understanding of the protein folding process. In this context, the possible existence of local residue structure would certainly affect the initial phase of the folding process (10).…”

“…One might try to resolve the above-discussed conflicting results by proposing that the PPII propensity of alanine solely applies to very short peptides, i.e., tri-and tetra-peptides (6,36,37), whereas it becomes more disordered in longer ones. A clarification of this issue has a high bearing on the understanding of both the unfolded state of peptides and proteins, as well as the protein unfolding process, in view of the abundance of alanine in nature, and its high propensity for helix formation (38).…”

Correlation between Raman and X-ray crystallography data of (Pro-Pro-Gly)10

“…Raman microscopy is a valuable tool in assisting biocrystallographers [12,13], and it is now available on synchrotron beamlines [14]. Many Raman studies have been conducted to detect polyproline II conformation in oligo- [15,16], poly-peptides and proteins [17]. Raman optical activity [18] and UV-Raman resonance spectroscopy [19] are also valuable tools to extract secondary structural details.…”

α-N-Linked glycopeptides: conformational analysis and bioactivity as lectin ligands

“…A study published in 2004, for example, showed that AXA tripeptides (X being valine, tryptophan, histidine, and serine) predominantly adopt an extended β strand conformation, while AXA tripeptides, for which X is lysine and proline, prefer a polyproline II like (PPII) structure. 21 In contrast, the Ala Phe Ala sequence was found to fold as an inverse γ turn in water. 22 Therefore, it is not unambiguously clear whether the extended conformation observed for 1 and 2 is a direct consequence of peptide glycosylation.…”