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

Abstract

Local structure in unfolded proteins, especially turn segments, has been suggested to initiate the hierarchical protein-folding process. To determine the intrinsic propensity to form such turn structures, amide I' band profiles of the Raman, IR, and vibrational circular dichroism (VCD) spectra, and several structure-sensitive NMR J-coupling constants, have been measured for a series of GxG (x=D, N, T, C) peptides, in which the central x residues are abundant in various turn motifs in folded proteins. In addition, we revisited earlier measured GSG experimental data. To check whether this relatively high propensity for these residues to sample turns reflects an intrinsic propensity, the experimental data were analyzed in terms of conformational distributions that can be described as a superposition of two-dimensional Gaussian distributions associated with different so-called mesostates. The analysis reveals that the investigated residues sample dihedral angles similar to those found in the corner residues of various turns, namely, type I/I', II/II', and IV β-turns. Aspartic acid (D) was found to predominantly sample regions attributed to turns, including distributions at the upper border of the upper-right quadrant of the Ramachandran plot, which bear some resemblance to asx-turns observed in proteins. This conformation enables hydrogen bonding between the side-chain carboxylate and the C-terminal amide group. Altogether, the study shows that the high propensity for T, S, C, N, and D to be located in turn motifs reflects, to a substantial degree, an intrinsic property and supports the role of these residues as initiation sites for hierarchical folding processes that can lead to compact structures in the unfolded state of peptides and proteins.

Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities

“…Derived ΔG values for PII to β transitions show a good correlation to those derived for dipeptides23. We have detected significant turn structures in AcGNPNH 2 , AcGTPNH 2 and AcGDPNH 2 (pH = 2 and 6)44. Results from this study have broad implications on the early-stage events of protein folding.…”

“…The smaller 3 J αN values for AcGXGNH 2 are consistent to X samples all three major backbone conformations in AcGXGNH 2 , while X samples only PII and β conformations in AcGXPNH 2 (Thr, Asn and Asp are excluded). For AcGXPNH 2 (X = Thr, Asn and Asp), X is expected to form turn structures44; it explains smaller observed 3 J αN values for these residues in AcGXPNH 2 compared to those in AcGXGNH 2 . For all other amino acids, contents of α conformations in AcGXGNH 2 can be calculated from equation (1), in which 3 J αN (α) is assigned to be 4.11 Hz, corresponding to a ϕ value of −60° (Table 1).…”

Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors

“…19 For further details of the (u,w) 2 -motifs see Hollingsworth et al 19 (B) The natural distributions of residues occurring in select (u,w) 2 -motif contexts (colored dots) are displayed with that full dataset as a background (gray) and the relevant basins from A outlined for reference. The colored distributions correspond to residues from some of the most prominent (u,w) 2 While much work has been done on the relationships between amino acid sequence and conformation, [13][14][15][16] less has been done to explore the details of how the conformation of a residue depends on the conformation of its neighboring residues, irrespective of amino acid type. 13,17,18 Recently, we published a study of local protein conformations that focused on what we called (u,w) 2 -motifs; each such motif corresponds to a particular path of four sequential Caatoms-named residues i to i 1 3 -that is defined by the conformations of the two central residues: 19 In that study, we developed a list of the 101 most common (u,w) 2 -motifs that occur in proteins.…”

“…The populations of each group are as follows: aXa-59,596; aXb-7,951; aXd-6,160; aXP II -7,073; bXa-3,601; bXb-34,525; bXd-8,480; bXP II -12,846; dXa-11,253; dXb-6,203; dXd-3,933; dXP II -4,552; P II Xa-3,897; P II Xb-11,877; P II Xd-6,659; P II XP 198. Low contour levels in the observed distributions are colored blue (0-10), light brown (11)(12)(13)(14)(15)(16)(17)(18)(19)(20), green (21)(22)(23)(24)(25)(26)(27)(28)(29)(30), and white (31-40). Higher contours then use a repeated pattern of teal, orange, blue, red, green, and purple for every additional 10 observations.…”

Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

“…Thus, the fact that the 3 J HNa coupling constants of the dipeptides are distributed in the range from 5.5 to 9.6 Hz indicates that the backbone conformations of dipeptides are mixtures of PP II and b-strand structures consistent with the experimental finding by Avbelj et al (2006) who showed that the fractional populations of PP II and b-strand conformations are dominant in 19 blocked amino-acids (N-acetyl-X-N 0 -methylamide) except for Gly. In our previous work, we also showed that the CD spectra of the blocked dipeptides can be described as a linear combination of the CD eigenspectra of the PP II and bstrand conformations (Oh et al 2010(Oh et al , 2012 and further examined the validity of a two-state approximation by comparing our results with previous works done by other groups (Hagarman et al , 2011. However, it should also be emphasized that the fitting analysis method using reference values of two representative conformations such as PP II and b-strand is intrinsically approximate in nature.…”