Conformational Analysis of XA and AX Dipeptides in Water by Electronic Circular Dichroism and¹H NMR Spectroscopy

Abstract

We measured the temperature-dependent electronic circular dichroism (ECD) spectra of AX, XA, and XG dipeptides in D2O. The spectra of all XA and AX peptides indicate a substantial population of the polyproline II (PPII) conformation, while the ECD spectra of LG, KG, PG, and AG were found to be quantitatively different from the alanine-based dipeptides. Additional UV absorption data indicate that the ECD spectra of the XG peptides stem from electronic coupling between the peptide and the C-terminal group, and that spectral differences reflect different orientations of the latter. We also measured the 1H NMR spectra of the investigated dipeptides to determine the 3JHalphaNH coupling constants for the C-terminal residue. The observed temperature dependence of the ECD spectra and the respective room-temperature 3JHalphaNH coupling constants were analyzed by a two-state model encompassing PPII and a beta-like conformation. The PPII propensity of alanine in the XA series is only slightly modulated by the N-terminal side chain, and is larger than 50%. As compared to AA, XA peptides containing L, P, S, K V, E, T, and I all cause a relative stabilization of the extended beta-strand conformation. The PPII fractions of XA peptides varied between 0.64 for AA and 0.58 for DA, whereas the PPII fractions of AX peptides were much lower. From the investigated AX peptides, only AL and AQ showed the expected PPII propensity. We found that AT, AI, and AV clearly prefer an extended beta-strand conformation. A quantitative comparison of AA, AAA, and AAAA revealed a hierarchy AAAA > AAA approximately AA for the PPII population, in agreement with predictions from MD calculations and results from Raman optical activity studies (McColl et al. J. Am. Chem. Soc. 2004, 126, 5076).

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.…”

Circular dichroism eigenspectra of polyproline II and β‐strand conformers of trialanine in water: Singular value decomposition analysis

“…[4][5][6][7][8][9][10][11][12][13] Furthermore, the potential energy surfaces of those small oligopeptides are fairly shallow so that the population of b-strand conformer is not negligibly small or even dominant in some cases. 6,12,[14][15][16][17][18] If a given unfolded protein is viewed as a chain of locally ordered short segments of oligopeptides with either PPII or b-strand conformations and if there is no long-range correlation between different segments along the chain, the notion that unfolded and denatured proteins adopt fairly random local conformations might not be valid and should be properly modified. One of the immediate consequences of such changes of viewpoints on denatured protein structures is that the configuration space of denatured protein structures could be significantly narrower than that of completely random structures.…”

“…Quite a number of spectroscopic studies to ultimately determine solution structures of trialanine in water have been performed. 5,[15][16][17] They include vibrational spectroscopic studies with IR absorption and isotropic and anisotropic Raman scattering, 11,12,17,[24][25][26][27] vibrational and electronic circular dichroism (CD), 9,[41][42][43][44][45][46][47][48] resonance Raman scattering, two-dimensional IR spectroscopy, 19,20 NMR, 30,31,[41][42][43][44][45][46][47][48][49] and classical and semiquantum mechanical molecular dynamics (MD) simulations. 38,39,50,51 Despite these experimental and theoretical efforts, the conclusions drawn by a number of workers using different spectroscopic techniques have been found to be often inconsistent with each other.…”

The Structure of Unfolded Peptides and Proteins Explored by Vibrational Spectroscopy

“…This particularly concerns alanine, whose propensity in the unfolded state has led to a very controversial debate (68,69,94,99,119,125) . While spectroscopic data indicate that different amino acids such as alanine and valine show rather different propensities (PPII and β -strand) (25,26,37) , ECD and NMR data, as well as computational results, seem to suggest that nearly all amino acids except glycine have a rather high PPII propensity (98,117) .…”