RETRACTED: Probing osmolyte participation in the unfolding transition state of a protein

Dougan, Lorna; Genchev, Georgi Z.; Lü, Hui; Fernández, Julio M.

doi:10.1073/pnas.1101934108

Cited by 15 publications

(8 citation statements)

References 49 publications

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“…Such a discrepancy can stem from the different reaction coordinate probed in the force spectroscopy experiments, where the end-to-end length of the protein is recorded over time, and also from the different molecular mechanisms underlying the mechanical unfolding process. The accumulated evidence through both experiments and molecular dynamics simulations demonstrates that water insertion within the structural mechanical clamp is a key and necessary step to trigger mechanical unfolding (30,37,41,64,65). Indeed, recent experiments have shown that the value of ⌬x measured for protein unfolding under force is determined by the bridging length of solvent molecules at the transition state structure of the reaction (30).…”

Section: Discussionmentioning

confidence: 99%

Direct Quantification of the Attempt Frequency Determining the Mechanical Unfolding of Ubiquitin Protein

Popa

Fernández

Garcia-Manyes

2011

Journal of Biological Chemistry

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Understanding protein dynamics requires a comprehensive knowledge of the underlying potential energy surface that governs the motion of each individual protein molecule. Single molecule mechanical studies have provided the unprecedented opportunity to study the individual unfolding pathways along a well defined coordinate, the end-to-end length of the protein. In these experiments, unfolding requires surmounting an energy barrier that separates the native from the extended state. A deep understanding of protein dynamics relies on the accurate determination of the free energy surface that governs the (un)folding reaction. In the case of small proteins, the (un)folding process is generally described by a two-state scenario, whereby the native and unfolded states are separated by a prominent energy barrier (1). The conversion between these two states has been traditionally given the treatment of a firstorder chemical reaction, where the concentration of the reactant species, the native state of the protein, decreases exponentially with time (2). Such a simplified kinetic analysis provides the framework to study the (un)folding reaction in terms of the Eyring transition state theory (TST), 3 which allows quantification of the rate constant for a given chemical reaction as a function of temperature (3, 4)where ‡ is the prefactor, k B is the Boltzmann constant, T is the absolute temperature, and ⌬G ‡ is the activation energy. In this simplified equation,where C°is the standard state concentration, h is the Planck's constant, and n is the order of the reaction. The factor (k B T/h) is a frequency factor, equal to 6 ps Ϫ1 at 300 K, for the crossing of the transition state. The generalized transmission coefficient, ␥(T), relates the actual rate of the reaction to that obtained from the simple transition state theory, in which ␥(T) ϭ 1. Over the last two decades, a great number of studies have reported the effect of temperature on the (un)folding kinetics of a plethora of distinct proteins using different biochemistry bulk techniques. With a few exceptions (5), the apparent consensus (6) is that although protein unfolding usually follows simple Arrhenius kinetics, the folding kinetics exhibit more complex dependences with temperature, resulting in curvature in the ln k f versus 1/T plots (7-12). The origin of such non-Arrhenius behavior during the folding reaction can be generically explained either in terms of the rate of escape from different minima along a rough energy landscape, thus yielding super-Arrhenius kinetics, or most likely, based on the hydrophobic effect, involving a large change in heat capacity during the folding process (13-15), with the heat capacity of the transition state placed somewhere in between the folded and unfolded states (16).Single molecule force spectroscopy has provided a new vista on the molecular mechanisms underlying protein (un)folding at the subnanometer scale (17). In stark contrast with protein unfolding experiments conducted using traditional bulk experiments, where the radius of g...

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Section: Discussionmentioning

confidence: 99%

Direct Quantification of the Attempt Frequency Determining the Mechanical Unfolding of Ubiquitin Protein

Popa

Fernández

Garcia-Manyes

2011

Journal of Biological Chemistry

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“…In particular, because osmolyte molecules are larger than water molecules, the small osmolytes were reported to increase the unfolding distance of proteins by amounts that correlate with their molecular size. It should be noted, however, that larger osmolytes such as sorbitol and sucrose were instead found to leave the unfolding distance of I27 unchanged, indicating their inability to partake in solvent bridging (6).…”

Section: Introductionmentioning

confidence: 96%

“…A previous SMFS study of mechanical unfolding of protein ubiquitin reported that the presence of glycerol as a cosolvent in aqueous solution leads to an increase of the protein's unfolding distance (4). Other SMFS studies reported that glycerol (5), ethylene glycol, and propylene glycol (6) increase the unfolding distance of the I27 titin module of the human muscle. Based on the Ansatz that the unfolding distance of proteins may be determined by the bridging length of solvent molecules at the unfolding transition state (7,8), the mentioned SMFS studies concluded that small osmolyte molecules bridge the critical b-strands of proteins under mechanical tension, leaving their distinct signature on their unfolding distance.…”

Section: Introductionmentioning

confidence: 99%

Worm-Like Ising Model for Protein Mechanical Unfolding under the Effect of Osmolytes

Aioanei

Brucale

Tessari

et al. 2012

Biophysical Journal

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We show via single-molecule mechanical unfolding experiments that the osmolyte glycerol stabilizes the native state of the human cardiac I27 titin module against unfolding without shifting its unfolding transition state on the mechanical reaction coordinate. Taken together with similar findings on the immunoglobulin-binding domain of streptococcal protein G (GB1), these experimental results suggest that osmolytes act on proteins through a common mechanism that does not entail a shift of their unfolding transition state. We investigate the above common mechanism via an Ising-like model for protein mechanical unfolding that adds worm-like-chain behavior to a recent generalization of the Wako-Saitô-Muñoz-Eaton model with support for group-transfer free energies. The thermodynamics of the model are exactly solvable, while protein kinetics under mechanical tension can be simulated via Monte Carlo algorithms. Notably, our force-clamp and velocity-clamp simulations exhibit no shift in the position of the unfolding transition state of GB1 and I27 under the effect of various osmolytes. The excellent agreement between experiment and simulation strongly suggests that osmolytes do not assume a structural role at the mechanical unfolding transition state of proteins, acting instead by adjusting the solvent quality for the protein chain analyte.

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“…All the pKa values were obtained by pH measurement of a solution of 4 wt% of the desired compound with 40 mL volume using a pHmeter. Numbers in parentheses are collected from PubChem [27][28][29]; molecular size is obtained from [30]; * estimated value.…”

Section: Understanding the Adsorption Mechanismmentioning

confidence: 99%

An Insight into the Separation of 1,2-Propanediol, Ethylene Glycol, Acetol and Glycerol from an Aqueous Solution by Adsorption on Activated Carbon

et al. 2021

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Glycerol conversion processes such as aqueous phase reforming and hydrogenolysis generate value-added compounds highly diluted in water. Because distillation is a high energy demand separation step, adsorption could be an attractive alternative to recover these chemicals. Adsorption isotherms of 1,2-propanediol, acetol, ethylene glycol and glycerol onto activated carbon were determined by batch adsorption experiments. These isotherms were fitted slightly better to the Freundlich equation than to the Langmuir equation. Acetol is the compound with the highest adsorption at concentrations smaller than 1 M. Properties of the adsorbate such as the −OH group number, chain length, molecular size and dipole moment, besides characteristics of the adsorbent such as the surface area, oxygen and ash content, are considered to explain the observed results. Moreover, adsorption experiments were performed with mixtures of compounds and it was determined that the molar amount adsorbed is less than predicted from the adsorption isotherms of the individual compounds treated separately. In addition, the influence of the activated carbon thermal pre-treatment temperature on the adsorption capacity has been studied, the optimum being 800 °C. An analysis of the influence of the activated carbon characteristics showed that the most important parameters are the total pore volume and the ash content.

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RETRACTED: Probing osmolyte participation in the unfolding transition state of a protein

Cited by 15 publications

References 49 publications

Direct Quantification of the Attempt Frequency Determining the Mechanical Unfolding of Ubiquitin Protein

Direct Quantification of the Attempt Frequency Determining the Mechanical Unfolding of Ubiquitin Protein

Worm-Like Ising Model for Protein Mechanical Unfolding under the Effect of Osmolytes

An Insight into the Separation of 1,2-Propanediol, Ethylene Glycol, Acetol and Glycerol from an Aqueous Solution by Adsorption on Activated Carbon

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