End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

Abstract

Characterization of the unfolded state is essential for the understanding of the protein folding reaction. We performed time-resolved FRET measurements to gain information on the dimensions and the internal dynamics of unfolded polypeptide chains. Using an approach based on global analysis of data obtained from two different donor–acceptor pairs allowed for the determination of distance distribution functions and diffusion constants between the chromophores. Results on a polypeptide chain consisting of 16 Gly-Ser repeats between the FRET chromophores reveal an increase in the average end-to-end distance from 18.9 to 39.2 Å between 0 and 8 M GdmCl. The increase in chain dimensions is accompanied by an increase in the end-to-end diffusion constant from (3.6 ± 1.0) × 10 −7 cm 2 s −1 in water to (14.8 ± 2.5) × 10 −7 cm 2 s −1 in 8 M GdmCl. This finding suggests that intrachain interactions in water exist even in very flexible chains lacking hydrophobic groups, which indicates intramolecular hydrogen bond formation. The interactions are broken upon denaturant binding, which leads to increased chain flexibility and longer average end-to-end distances. This finding implies that rapid collapse of polypeptide chains during refolding of denaturant-unfolded proteins is an intrinsic property of polypeptide chains and can, at least in part, be ascribed to nonspecific intramolecular hydrogen bonding. Despite decreased intrachain diffusion constants, the conformational search is accelerated in the collapsed state because of shorter diffusion distances. The measured distance distribution functions and diffusion constants in combination with Szabo–Schulten–Schulten theory were able to reproduce experimentally determined rate constants for end-to-end loop formation.

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

“…* This choice ensures that the results from the Gillespie- separated by a sufficiently long stretch of the chain (>ca.10 residues) at room temperature. [85][86][87][88][89][90][91] This corresponds to the characteristic motional time scale…”

“…Although the results vary, the consensus estimate appears to be D tr $ 10 À6 cm 2 s À1 for a pair of sites separated by a sufficiently long stretch of the chain (>ca.10 residues) at room temperature. [85][86][87][88][89][90][91] This corresponds to the characteristic motional time scale s tr ¼ d 2 0 /D tr $ 2 ns. The results of the computations employing the above set of parameters, d 0 , L, and s tr , are presented in Figure 5 (red bars).…”

Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH

“…These forces determine the dimensions of unfolded and disordered proteins and have been suggested to impact processes such as the coupled binding and folding of IDPs, 5 or the rate of protein folding reactions. [6][7][8] However, the dimensions of unfolded proteins and IDPs also depend critically on solution conditions such as ionic strength, 4,9 temperature, 10 osmolytes, 11 or denaturants, 2,[12][13][14] implying that the complex interplay between chain-chain and chainsolvent interactions has to be unraveled before quantitative predictions of the size of unstructured polypeptide chains and their effect on folding or binding will be possible.…”

Reconfiguration dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant

“…Like the Rouse model the end to end distribution of the polymer chain remains Gaussian in SDCRIF as well. Experiments also showed that Gaussian Distributions of end to end distances of proteins are not too bad approximations [11,62]. Any deviations from the Gaussian behavior is negligibly small [63].…”