Local order in the unfolded state: conformational biases and nearest neighbor interactions

Abstract

The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.

Figure 1

The funneled energy landscape representing the process of going from unfolded state to native state. (Taken from ref. [9] and modified).

Figure 2

(A) The chemical structure of the alanine dipeptide with backbone φ,ψ angles noted; (B) The Ramachandran plot depicted the local random coil distribution of the alanine residue of the alanine dipeptide; (C) The experimentally obtained Ramachandran plot of the alanine residue of the alanine dipeptide in water as reported by Toal et al. [15]. (Taken from ref. [15] and modified.

Figure 3

(left panel): Ultraviolet circular dichroism (UVCD) spectra of poly-L-proline II, (middle panel): poly-L-glutamic acid, and (right panel): poly-L-lysine measured as a function of temperature which show a characteristic pPII signals. (Taken and modified form from [87]).

Figure 4

Isotropic Raman, anisotropic Raman, infrared (IR), and vibrational circular dirchroism (VCD) amide I profiles of tripeptides simulated for different conformational ensembles, i.e., 100% pPII (solid line), 100% β-strand (dashed line), 50:50 mixture of pPII and β-strand (dashed gray), and 100% right-handed helical (dashed-dot-dot). (Taken from ref. [101] with permission).

Figure 5

(A) The change in ³J(H^NH^α) with temperature for Ala 2–7 residues of the X₂A₇O₂-NH₂ peptide; (B) The UV-CD spectra of XAO at □ (blue) 1 °C; ○ (green) 35 °C; □ (red) 45 °C; and □ (black) 55 °C. (Taken from ref. [50] and modified).

Figure 6

Ramachandran map superimposing the backbone distributions of all residues and all conformational families of the XAO peptide calculated by MD SA with NMR derived time-averaged restraints. The green boxes indicate the two dominant conformational clusters centered at ϕ = −160°, (mainly extended β-strand-like structures) and ϕ = −70° (pPII and β-turn-like conformations). (Taken from ref. [69] and modified).

Figure 7

Graphical representation of six Karplus relationships [111,112] of six J-coupling constants which depend differently on the dihedral angles ϕ (upper and middle panels) and ψ (bottom panels).

Figure 8

Three-dimensional distribution function in (φ,ψ) space obtained by simulating amide I profiles and NMR coupling constants for trialanine. (Taken from ref. [101] with permission).

Figure 9

Unblocked AAA (upper), AdP (middle), and unlocked GAG peptide (lower panel).

Figure 10

Amide I’ region of the infrared and vibrational circular dichroism spectra of A₅W in D₂O. The red lines result from a simulation using a conformational distribution reflecting the Ramachandran plot obtained from MD simulations with a ff03* force field. The black lines reflect the results of a fit with an adjustable conformational model describable as superposition of two-dimensional Gaussian distributions associated with pPII, β-strand, right-handed helical, and inverse γ-turn-like conformations. The blue line was computed with a refined model, which additionally considered a further modified distribution as mentioned in the results. (Taken from ref. [153] with permission).

Figure 11

Ramachandran plots for cationic AAA (upper panel) and zwitterionic AAA (middle panel) and AdP (lower panel) obtained by MD simulations using the OPLS force field and SPC/E water model. (Taken from ref. [15] with permission).

Figure 12

Comparison of (a) pPII; and (b) β-strand populations for guest residues as obtained by Rucker et al. for PxP (blue) [163], Shi et al. for GGxGG (red) [51], Hagarman et al. for GxG (green) [52,77,138], and Grdadolnik et al. [76] for XdP (purple).

Figure 13

UV-CD spectra around the maximum dichroism value for PPP, PAP, PGP, PLP, PMP, PIP, PVP, PNP, PQP. (Taken from ref. [163] with permission).

Figure 14

Conformational distributions of the central residue in GAG, GVG, GLG, and GEG obtained from analysis of amide I’ band profiles and J coupling constants, illustrating the 2D distribution approach used by Hagarman et al. (Taken from ref. [52] with permission).

Figure 15

Conformation distribution of the central residue in unblocked GDG illustrating the high turn propensities of aspartic acid. Taken from [78] and modified.

Figure 16

Experimental (black line) and fitted (red line) ATR-absorbance (Upper) and Raman (Lower) spectra (amide III region) for four dipeptides: (A), glycine; (B), arginine; (C), methionine; and (D), isoleucine. The three colored components are gray (band A) PII; blue (band B) αR; red (band C) β. Taken from ref. [76] with permission.

Figure 17

Distribution obtained in the upper left quadrant of the Ramachandran plot for Alanine using (A) all secondary structure conformations in the protein database (i.e., an unrestricted library) or (B) only those alanine residues in a coil conformations (i.e., helices, sheets, turns omitted). The number of cases was normalized values to 1000. Each axis marker represents an 18° interval. Taken from ref. [75] with permission.

Figure 18

Basin preferences in different coil libraries. Probability distribution in the Ramachandran plane of all residues (except Gly and Pro) for the (A) entire PDB, (B) library without helices and sheets (C) library without helices, sheets, and turns, and (D) library without helices, sheets, turns, and terminal, pre-proline, and most exposed residues. Basin fractions for the 20 amino acids are shown in adjacent panels for the corresponding libraries described in panels A–D. (Taken from ref. [81] and modified).

Figure 19

Representation of the change of the electrostatic solvation free energy induced by substituting the fifth alanine residue of a hepta-alanine peptide by valine. Changes are plotted for pPII and β-strand conformations, as indicated. (Taken from ref. [85] with permission).

Figure 20

Representation of the change of the electrostatic solvation free energy induced by substituting the fifth alanine residue of a hepta-alanine peptide by valine. Changes are plotted for pPII and β-strand conformations, as indicated. Taken form ref. [81] and modified.

Figure 21

Representation of the molar fractions of amino acid residues indicated on the abscissa in GXG and XXX peptides. The code for the bars is defined in the inset of the figure. The data were taken from [138] for GAG, GVG, GDG and GKG and from [118,140] for AAA, VVV, protonated DDD and protonated KKK.