Dataset Information

Stochastic emergence of multiple intermediates detected by single-molecule quasi-static mechanical unfolding of protein.

ABSTRACT: Experimental probing of a protein-folding energy landscape can be challenging, and energy landscapes comprising multiple intermediates have not yet been defined. Here, we quasi-statically unfolded single molecules of staphylococcal nuclease by constant-rate mechanical stretching with a feedback positioning system. Multiple discrete transition states were detected as force peaks, and only some of the multiple transition states emerged stochastically in each trial. This finding was confirmed by molecular dynamics simulations, and agreed with another result of the simulations which showed that individual trajectories took highly heterogeneous pathways. The presence of Ca2+ did not change the location of the transition states, but changed the frequency of the emergence. Transition states emerged more frequently in stabilized domains. The simulations also confirmed this feature, and showed that the stabilized domains had rugged energy surfaces. The mean energy required per residue to disrupt secondary structures was a few times the thermal energy (1-3 kBT), which agreed with the stochastic feature. Thus, single-molecule quasi-static measurement has achieved notable success in detecting stochastic features of a huge number of possible conformations of a protein.

SUBMITTER: Fukagawa A

PROVIDER: S-EPMC5036639 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Stochastic emergence of multiple intermediates detected by single-molecule quasi-static mechanical unfolding of protein.

Fukagawa Akihiro A Hiroshima Michio M Sakane Isao I Tokunaga Makio M

Biophysics (Nagoya-shi, Japan) 20090904

Experimental probing of a protein-folding energy landscape can be challenging, and energy landscapes comprising multiple intermediates have not yet been defined. Here, we quasi-statically unfolded single molecules of staphylococcal nuclease by constant-rate mechanical stretching with a feedback positioning system. Multiple discrete transition states were detected as force peaks, and only some of the multiple transition states emerged stochastically in each trial. This finding was confirmed by mo ...[more]

PMID: 27857576

Similar Datasets

Project description:Precise quantification of the energetics and interactions that stabilize membrane proteins in a lipid bilayer is a long-sought goal. Toward this end, atomic force microscopy has been used to unfold individual membrane proteins embedded in their native lipid bilayer, typically by retracting the cantilever at a constant velocity. Recently, unfolding intermediates separated by as few as two amino acids were detected using focused-ion-beam-modified ultrashort cantilevers. However, unambiguously discriminating between such closely spaced states remains challenging, in part because any individual unfolding trajectory only occupies a subset of the total number of intermediates. Moreover, structural assignment of these intermediates via worm-like-chain analysis is hindered by brief dwell times compounded with thermal and instrumental noise. To overcome these issues, we moved the cantilever in a sawtooth pattern of 6-12 nm, offset by 0.25-1 nm per cycle, generating a "zigzag" force ramp of alternating positive and negative loading rates. We applied this protocol to the model membrane protein bacteriorhodopsin (bR). In contrast to conventional studies that extract bR's photoactive retinal along with the first transmembrane helix, we unfolded bR in the presence of its retinal. To do so, we introduced a previously developed enzymatic-cleavage site between helices E and F and pulled from the top of the E helix using a site-specific, covalent attachment. The resulting zigzag unfolding trajectories occupied 40% more states per trajectory and occupied those states for longer times than traditional constant-velocity records. In total, we identified 31 intermediates during the unfolding of five helices of EF-cleaved bR. These included a previously reported, mechanically robust intermediate located between helices C and B that, with our enhanced resolution, is now shown to be two distinct states separated by three amino acids. Interestingly, another intermediate directly interacted with the retinal, an interaction confirmed by removing the retinal.

Project description:Magnesium and its alloys have the intrinsic capability of degrading over time in vivo without leaving toxic degradation products. They are therefore suitable for use as biodegradable scaffolds that are replaced by the regenerated tissues. One of the main concerns for such applications, particularly in load-bearing areas, is the sufficient mechanical integrity of the scaffold before sufficient volumes of de novo tissue is generated. In the majority of the previous studies on the effects of biodegradation on the mechanical properties of porous biomaterials, the change in the elastic modulus has been studied. In this study, variations in the static and fatigue mechanical behavior of porous structures made of two different Mg alloys (AZ63 and M2) over different dissolution times ( 6, 12, and 24 h) have been investigated. The results showed an increase in the mechanical properties obtained from stress-strain curve (elastic modulus, yield stress, plateau stress, and energy absorption) after 6-12 h and a sharp decrease after 24 h. The initial increase in the mechanical properties may be attributed to the accumulation of corrosion products in the pores of the porous structure before degradation has considerably proceeded. The effects of mineral deposition was more pronounced for the elastic modulus as compared to other mechanical properties. That may be due to insufficient integration of the deposited particles in the structure of the magnesium alloys. While the bonding of the parts being combined in a composite-like material is of great importance in determining its yield stress, the effects of bonding strength of both parts is much lower in determining the elastic modulus. The results of the current study also showed that the dissolution rates of the studied Mg alloys were too high for direct use in human body. © 2018 Authors Journal of Biomedical Materials Research Part A Published by Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 1798-1811, 2018.

Project description:Alkaline phosphatase is an enzyme with a typical alpha/beta hydrolase fold. The conformational stability of the human placental alkaline phosphatase was examined with the chemical denaturant urea. The red shifts of fluorescence spectra show a complex unfolding process involving multiple equilibrium intermediates indicating differential stability of the subdomains of the enzyme. None of these unfolding intermediates were observed in the presence of 83 mM NaCl, indicating the importance of ionic interactions in the stabilization of the unfolding intermediates. Guanidinium chloride, on the other hand, could stabilize one of the unfolding intermediates, which is not a salt effect. Some of the unfolding intermediates were also observed in circular dichroism spectroscopy, which clearly indicates steady loss of helical structure during unfolding, but very little change was observed for the beta strand content until the late stage of the unfolding process. The enzyme does not lose its phosphate-binding ability after substantial tertiary structure changes, suggesting that the substrate-binding region is more resistant to chemical denaturant than the other structural domains. Global analysis of the fluorescence spectral change demonstrated the following folding-unfolding process of the enzyme: N <--> I(1) <--> I(2) <--> I(3) <--> I(4) <--> I(5) <--> D. These discrete intermediates are stable at urea concentrations of 2.6, 4.1, 4.7, 5.5, 6.6, and 7.7 M, respectively. These intermediates are further characterized by acrylamide and/or potassium iodide quenching of the intrinsic fluorescence of the enzyme and by the hydrophobic probes, 1-anilinonaphthalene-8-sulfonic acid and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid. The stepwise unfolding process was interpreted by the folding energy landscape in terms of the unique structure of the enzyme. The rigid central beta-strand domain is surrounded by the peripheral alpha-helical and coil structures, which are marginally stable toward a chemical denaturant.

Dataset Information

Stochastic emergence of multiple intermediates detected by single-molecule quasi-static mechanical unfolding of protein.

Publications

Stochastic emergence of multiple intermediates detected by single-molecule quasi-static mechanical unfolding of protein.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets