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

Abstract

The solution structure of the hepta-alanine polypeptide Ac-X 2A7O2-NH2 (XAO) has been a matter of controversy in the current literature. On one side of the argument is a claim that the peptide adopts a mostly polyproline II ( We have used an excitonic coupling model to simulate the amide I band of the FTIR, vibrational circular dichroism, and isotropic and anisotropic Raman spectra of XAO, where, for each residue, the backbone dihedral angle was constrained by using the reported 3 JC␣HNH values and a modified Karplus relation. The best reproduction of the experimental data could only be achieved by assuming an ensemble of conformations, which contains various ␤-turn conformations (Ϸ26%), in addition to ␤-strand (Ϸ23%) and PPII (Ϸ50%) conformations. PPII is the dominant conformation in segments not involved in turn formations. Most of the residues were found to sample the bridge region connecting the PPII and right-handed helix troughs in the Ramachandran plot, which is part of the very heterogeneous ensemble of conformations generally termed type IV ␤-turn.alanine propensity ͉ amide I ͉ unfolded peptides ͉ vibrational spectroscopy T he unfolded state of peptides and proteins has been the subject of an increasing number of experimental and theoretical studies (1-9), 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). The existence of such locally ordered segments has first been proposed by Tiffany and Krimm (11) based on electronic circular dichroism (ECD) measurements on poly-L-proline, poly-L-lysine, and poly-L-glutamic acid. They concluded that charged polypeptides assume, at least locally, a rather ordered polyproline II (PPII) conformation, which is the structure adopted by trans-poly-L-proline. This notion was later confirmed by vibrational circular dichroism (VCD) studies on a variety of unfolded polypeptides and proteins (12,13).PPII is a rather regular structural motif in that it exhibits a perfect, left-handed threefold rotational symmetry (3 1 -helix) for its canonical conformation, with ( , ) ϭ (Ϫ78°, 146°) (14). Woody and coworkers (15-17) have published a series of papers proving that PPII gives rise to a far UV-ECD spectrum, which many in the scientific community still interpret as indicative of random coil (15). Recently, they reported a very convincing quantitative agreement between the PPII content of ␤II proteins, derived from crystallographic data, and ECD spectra (16). The PPII signal was also observed in the spectrum of the unfolded state of many proteins subjected to denaturing detergents (17). Thermal denaturation, however, often yields a conformation that is reflected by a weak, nearly symmetric, couplet with a positive maximum between 180 and 210 nm and a negative minimum between 210 and 230 nm (11,16,18). ECD ...

Amino Acids with Hydrogen‐Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

“…Vibrational and CD spectroscopy: The experimental setup for polarized Raman, IR, VCD, [26,40] and UVCD [40,45] experiments have been previously described in detail.…”

“…On another note, it is reasonable to assume that the non-natural amino acid ornithine (O), which carries a positive charge on its sidechain terminus and is shorter than that of K by one methylene group, can behave similarly to N and D. This would be completely in line with the recently discovered compact structure of the so called XAO peptide (X 2 A 7 O 2 ), X: aminobutyric acid, O: ornithine), which has been shown to be due to the sampling of various turn structures by its N-and/or C-terminal segments. [26,39] …”

“…In fact, very similar UVCD spectra have been observed for peptides for which turn and extended structures coexist in aqueous solution. [25,26] Figure 2 shows the amide I' band profiles of the IR, isotropic Raman, anisotropic Raman, and VCD spectra of the DNCTS peptides. The spectra of GAG are again shown for comparison.…”

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra

“…48,49 The structural propensities of the XAO peptide have been the matter of debate in scientific literature as reviewed by Adzhubei et al, but the model of a flexible structure not restricted by a regular pattern of hydrogen bonds and capable of fast conformational changes within the PPII region in φ/ψ space seems to be corroborated by all experiments. [50][51][52] While SAXS shows that the radius of gyration is much smaller than it would be for a fully extended structure 53 , spectroscopic methods indicate a high content of PPII conformation. 54,55 Although the ROA spectrum of a very similar peptide Ac-OO-A 7 -OO-NH 2 has been published before 11,55 , the ROA spectrum of the XAO peptide is, to the best knowledge of the authors, reported and assigned here for the first time.…”

Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model

“…Other recent studies also report a significant turn population in peptides (45-49) under various solvent conditions. Schweitzer-Stenner and Measey (49) report that the turn population is length-dependent, with only a small fraction in trimers and tetramers but a large fraction in seven-mers. Their focus is on ␤-turns, but the same conclusion would hold for inverse ␥-turns.…”