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. 2018 Jan 4;19(1):37-42.
doi: 10.1002/cbic.201700548. Epub 2017 Nov 16.

Propensity for cis-Proline Formation in Unfolded Proteins

Affiliations

Propensity for cis-Proline Formation in Unfolded Proteins

T Reid Alderson et al. Chembiochem. .

Abstract

In unfolded proteins, peptide bonds involving Pro residues exist in equilibrium between the minor cis and major trans conformations. Folded proteins predominantly contain trans-Pro bonds, and slow cis-trans Pro isomerization in the unfolded state is often found to be a rate-limiting step in protein folding. Moreover, kinases and phosphatases that act upon Ser/Thr-Pro motifs exhibit preferential recognition of either the cis- or trans-Pro conformer. Here, NMR spectra obtained at both atmospheric and high pressures indicate that the population of cis-Pro falls well below previous estimates, an effect attributed to the use of short peptides with charged termini in most prior model studies. For the intrinsically disordered protein α-synuclein, cis-Pro populations at all of its five X-Pro bonds are less than 5 %, with only modest ionic strength dependence and no detectable effect of the previously demonstrated interaction between the N- and C-terminal halves of the protein. Comparison to small peptides with the same amino-acid sequence indicates that peptides, particularly those with unblocked, oppositely charged amino and carboxyl end groups, strongly overestimate the amount of cis-Pro.

Keywords: NMR spectroscopy; alpha-synuclein; cis-proline; high pressure; isomerization; protein folding.

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Figures

Figure 1
Figure 1
Identification of cis-Pro bonds in αS. (A) 2D 1H-15N HSQC of 0.9 mM 13C,15N-αS at pH 6, 288 K. Resonances impacted by the cis/trans state of nearby Pro residues are colored (P108, red; P117, P120, orange; P128, green; P138, blue). (BE) Zoomed-in regions corresponding to the boxed areas from (A) are shown at a lower contour level. The major trans- and minor cis-Pro peaks are indicated with their assignments. See Figure S1 for the full, low-contour spectrum
Figure 2
Figure 2
Fractions of cis-Pro bonds in αS and comparison to oligo-peptides. All samples were at pH 6, 288 K. The fraction of cis-Pro is shown for each Pro residue in αS (red), with error bars representing one standard deviation from the mean. Upon the addition of 1160 mM NaCl, the fraction of cis-Pro increases (grey), indicative of decreased electrostatic repulsion in the acidic C-terminal region of αS. Blocked, tetra-peptides (blue) in general contain elevated levels of cis-Pro, whereas hexa- (teal) and octa-peptides (cyan) approach the values seen in full length αS.
Figure 3
Figure 3
The isolated C-terminal region of αS retains its native cis-Pro fractions. (A) Depiction of αS and its three regions: the amphipathic N-terminal region (NTR), the hydrophobic NAC region, and the acidic C-terminal region (CTR). The isolated CTR (bottom) contains an S87C mutation. (B) 2D 1H-15N HSQC spectra of full-length αS (red) and the isolated CTR (black). Buffer conditions were as in Figure 1, except that 5 mM BME was added to the isolated CTR to prevent disulfide formation. The peak indicated with an asterisk arises from an impurity. (C) Quantification of the cis-Pro fractions in both full-length αS and its isolated CTR. (D) Zoomed-in region from panel (B) showing resonances affected by cis-Pro. (E) Combined and weighted HN and 15N chemical shift perturbations (CSPs) between full-length αS and its isolated CTR.
Figure 4
Figure 4
Quantification of cis-Pro bonds in two pressure-denatured proteins. (A) 1.6 mM 13C,15N-labeled α-crystallin domain of HSP27 (cHSP27) at 2.5 kbar in 30 mM sodium phosphate, pH 7, 2 mM EDTA, 2 mM benzamidine, 288 K. (B) 0.75 mM 2H,13C,15N-labeled ubiquitin-(V17A/V26A) at 2.5 kbar in 20 mM potassium phosphate buffer, pH 6.4, 2 mM benzamidine, 288 K. In both (A) and (B), colored resonances have distinguishable assignments for the trans and cis conformations. (C) Boxed region of (A) at a lower contour level; c and t denote cis and trans, respectively. (D,E) Average cis-Pro fraction at each Pro residue for the samples in (A) and (B).

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