Disorder and order in unfolded and disordered peptides and proteins: A view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β‐type like turn conformations

Abstract

In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side-chain conformations of these peptides, we determined the (3)J(H(α),H(β)) coupling constants and derived the population of three rotamers with χ1 -angles of -60°, 180° and 60°, which were correlated with residue propensities by DFT-calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx-turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx-turns to a significant extent. The temperature dependence of the UVCD spectra and (3)J(H(N)H(α)) constants suggest that the turn populations of GDG and GNG are practically temperature-independent, indicating enthalpic and entropic stabilization. The temperature-independent J-coupling and UVCD spectra of GNG require a three-state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides.

Probing conformational propensities of histidine in different protonation states of the unblocked glycyl‐histidyl‐glycine peptide by vibrational and NMR spectroscopy

“…Unblocked peptides have the advantage of providing a better spectral resolution in the structure‐sensitive amide I′ region than blocked peptides. In agreement with Grdadolnik et al and Shi et al , their data reveal a dominant sampling of the pPII/β‐strand region of the Ramachandran plot, but they also showed that residues with charged and polar amino acid residues can sample a variety of turn like conformations . Their pPII fractions varied between 0.72 for A and approximately 0.2 for aspartic acid (D p ).…”

“…The values for Δ G ( T R ) were calculated from the pPII/β mole fraction ratio obtained from the conformational analysis . Eqn is based on the experimentally backed assumption that even in the presence of multiple conformers, the temperature dependence of the Gibbs energy landscape can practically be accounted for by a two‐state model, which assumes that the population of minor turn fractions does not change with temperature …”

“…Generally, the influence of the protonation state of the terminal groups on the conformational distribution of x in GxG has been shown to be negligible, but residues with charged side chains might be an exception. A comparison of GDG and the related aspartate dipeptide did not reveal any influence of the terminal charges on ionized D GD i G, but the protonation of D i itself shifts the pPII⇔β‐strand equilibrium toward the β‐strand and produces sampling of so called asx‐turn structures . However, there is no guarantee that H in GHG is as well isolated from the protonation state of the terminal groups as aspartic acid in GDG.…”

Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

“…On the contrary, residues with hydrophobic and bulky side chains like valine or isoleucine prefer a more extended β‐strand‐like conformation over pPII 4c,g,i,j,o. 5 Interestingly, the polar protonated aspartic acid residue exhibits the largest β‐strand‐to‐pPII ratio, which might reflect stabilization by side chain–backbone hydrogen bonding 4k,n. Generally, all residues show a much larger preference for the pPII/β‐strand region (70–80 %) and a lesser tendency to populate right‐handed helical regions (4–15 %) 4n,o.…”

pH-Independence of Trialanine and the Effects of Termini Blocking in Short Peptides: A Combined Vibrational, NMR, UVCD, and Molecular Dynamics Study

“…This observation indicates that the population of turn conformations might not be very temperature dependent, in agreement with recent theoretical predictions and experimental results. 83, 91 For the C-terminal residue, we obtained pPII fractions of 0.67, 0.60, for cationic and zwitterionic AAA, respectively.…”