Conformation of model, alanine and proline containing tetrapeptides in water. Comparison of 13C-n.m.r. and CD results

The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy

The present article reports the conformation of cationic tetraalanine in aqueous solution. The determination of the dihedral angles of the two central amino acid residues was achieved by analyzing the amide I' band profile in the respective polarized visible Raman, Fourier transform-IR, and vibrational circular dichroism (VCD) spectra by means of a novel algorithm which utilizes the excitonic coupling between the amide I modes of nearest neighbor and second nearest peptide groups. It is an extension of a recently developed theory (Schweitzer-Stenner, R. Biophys. J., 2002, 83, 523-532). UV electronic circular dichroism (ECD) spectra of the peptides were used to validate the results of the structure analysis. The analyses yielded the dihedral angles (phi(12), psi(12)) = (-70 degrees, 155 degrees ) and (phi(23), psi(23)) = (-80 degrees, 145 degrees ). The obtained values are very close to the Ramachandran coordinates of the polyproline II helix (PPII). The data suggest that this is the conformation predominantly adopted by the peptide at room temperature. This notion was corroborated by the corresponding electronic circular dichroism spectrum. Tetraalanine exhibits a higher propensity for PPII than trialanine for which a 50:50 mixture of polyproline II and an extended beta-strand-like conformation was obtained from recent spectroscopic studies (Eker et al., J. Am. Chem. Soc. 2002, 124, 14330-14341). The temperature dependence of the CD spectra rule out that any cooperativity is involved in the strand if PPII transition. This led to the conclusion that solvent-peptide interactions give rise to the observed PPII stability. Our result can be utilized to understand why the denaturation of helix-forming peptides generally yields a PPII rather than a heterogeneous random conformation.

Solution conformation of tuftsin

Conformation of chemically synthesized tetrapeptide tuftsin, an important immunomodulator, with the sequence Thr-Lys-Pro-Arg-OH has been studied in aqueous solution as well as in a number of organic solvents viz. trifluoroethanol (TFE), methanol and dioxane by circular dichroism (CD) spectroscopy which reveals preferential occurrence of mixture of random coil and beta-turns, that has already been predicted as bioactive conformation of this peptide.

Conformation of a T-cell stimulating peptide of interleukin-1 beta protein: circular dichroism studies

A T-cell stimulating peptide Val-Gln-Gly-Glu-Glu-Ser-Asn-Asp-Lys-OH, the 163-171 fragment epitope of interleukin-1 beta (IL-1 beta), has been synthesized in solution phase and purified by reverse-phase high-performance liquid chromatography (RP-HPLC). The backbone conformation of the synthetic fragment, investigated in aqueous solution by circular dichroism (CD) spectroscopy, is qualitatively a mixture of beta-turns and random coil. Quantification of the CD spectra revealed the presence of a 9% beta-turn fraction in water at pH 7.0, suggesting the occurrence of the conformation for the epitope fragment in aqueous solution necessary for T-cell stimulation and antigenicity. Concomitant changes in CD spectra were observed with increases in the trifluoroethanol (TFE) concentration in water, and the beta-turn fraction in peptide increased to 28% at a concentration of 90% TFE. This helicogenic solvent, as well as other solvents such as methanol, acetonitrile and dioxane (all favouring an ordered structure in peptides), failed to induce any alpha-helical conformation in the IL-1 beta (163-171) fragment, and CD spectra were attributed to only beta-turn ordered structure. This beta-turn structure has also been found to be a theoretically preferred conformation using Chou-Fasman proclivity data and is in accordance with the presence of an all-beta-globular conformation for its parent molecule IL-1 beta. Thus, the beta-turn conformation is probably involved in retention of T-cell stimulation activity in this synthetic epitope.

Conformational preferences of sequential fragments of the hinge region of human IgA1 immunoglobulin molecule: II

The mean solution conformation of tetrapeptide fragments of the hinge region of human IgA1 molecule was investigated by CD and 13C-NMR methods. Distinct conformational differences for the partial sequences were found. Tetrapeptides with the Thr-Pro-Ser-Pro sequence were found to show a clear preference for the beta-turn conformation. Conformational equilibria of these peptides are only slightly affected by acetylation or pH changes. In the case of Pro-Thr-Pro-Ser tetrapeptides conformational equilibria are dominated by unordered forms.

Conformational preferences of the sequential fragments of the hinge region of the human IgA1 immunoglobulin molecule

The mean solution conformation of tetrapeptide fragments spanning the hinge region of human IgA1 was investigated by CD and 13C-NMR methods. Distinct conformational differences for the partial sequences of IgA1 were found. In a series of tetrapeptides having the Thr-Pro-Pro-Thr sequence, the Pro-Pro fragment was ordered to the structure of a type II polyproline helix, but with unordered forms prevailing in the equilibria. In the case of the Pro-Pro-Thr-Pro sequence, a distinct preference for the beta-turn conformation was found. Acetylation of this tetrapeptide shifts the equilibrium towards unordered forms containing some elements of the type II polyproline helix. The peptide Thr-Pro-Ser-Pro exists predominantly in the beta-turn conformation whereas Pro-Ser-Pro-Ser-NH2 has, for the most part an unordered conformation.

Comparison of conformational properties of proline and threonine residues

The conformational role of Thr was investigated by 13C-n.m.r. and CD methods using a following series of tetrapeptides: Thr-Ala-Ala-Ala, Ala-Thr-Ala-Ala, Ala-Ala-Thr-Ala and Ala-Ala-Ala-Thr. It was found that introduction of Thr in every position of the tetraalanine peptide chain distinctly influences conformational equilibria of the peptides. An increase of beta-turn forms in conformational equilibria is induced by ionization of the terminal carboxyl group, independent of threonine position in the peptide chain. Threonine in position 1 or 3 of the peptide chain seems to have some importance for beta-turn formation in acid solution.

A potentiometric and spectroscopic study of the proton and copper(II) complexes of methionine enkephalin and some related ligands

The results are reported of a potentiometric and spectrophotometric study of the proton and copper(II) complexes of methionine enkephalin and four related pentapeptides which all show greater biological activity than their parent enkephalin. Measurements were carried out at 25 degrees C and I = 0.10 mol dm-3 (KNO3). All the ligands studied form stable copper(II) complexes comparable to those formed by pentaglycine, with the peptide chain locked in a folded conformation by NNN or NNNN coordination to the metal ion. There is no indication of bonding through the tyrosine-phenolate oxygen atoms or the methionine sulfurs.

A conformational study of a glutamine- and proline-rich cereal seed protein, C hordein

A combination of c.d. spectroscopy and computer prediction is used to show that C hordein has an unusual secondary structure with an absence of alpha-helix and beta-sheet, but the presence of regularly repeated beta-turns. This is associated with a repetitive primary structure based mainly on blocks of eight residues. Similar spectral changes occurred when the protein was heated from 6 to 86 degrees C in aq. 70% (v/v) ethanol or dissolved in increasing concentrations (50-100%, v/v) of trifluoroethanol in water. The studies indicated that the conformation is stabilized by strong hydrophobic interactions and by extensive hydrogen-bonding.

Proline- and alanine-rich N-terminal extension of the basic bovine beta-crystallin B1 chains

The amino acid sequence of the N-terminal region of the two basic bovine beta-crystallin B1 chains has been analyzed. The results reveal that beta B1b is derived in vivo from the primary gene product beta B1a by removal of a short N-terminal sequence. It appears that the beta B1 chains have the same domain structure as observed in other beta- and gamma-crystallin chains. They have, however, a very long N-terminal extension in comparison with other beta-chains. This extension is mainly composed of a remarkable Pro- and Ala-rich sequence, which suggests an interaction of these structural proteins with the cytoskeleton and/or the plasma membranes of the lens cells.