Pressure-jump studies of the folding/unfolding of trp repressor

Desai, Gayatri; Panick, Gunda; Zein, M.; Winter, Roland; Royer, Catherine A.

doi:10.1006/jmbi.1999.2692

Cited by 85 publications

(70 citation statements)

References 55 publications

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“…[11][12][13][14][15] The solvent-exposed -helix give peak frequencies to be lower than the characteristic frequencies for the buried -helix (the peak at around 1650 cm À1 ). [15][16][17] Zhu et al 18 reported that the peak around 1630 cm À1 of threebundle helix protein ( 3 D) is assigned to the solvated -helix. Therefore, we assigned the peaks at 1632 and 1652 cm À1 of (-l-) 2 to the solvated and buried -helices, respectively.…”

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confidence: 99%

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Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)₂ studied by FTIR spectroscopy

Takekiyo

Takeda

Isogai³

et al. 2006

Biopolymers

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The pressure‐induced structural changes of a de novo designed four‐helix bundle protein, (α‐l‐α)2, in aqueous solution have been investigated by FTIR spectroscopy. Changes in the amide I' band intensity show that pressure induces disruption of tertiary interactions and stabilizes the solvated α‐helical form. This may suggest that the exposure of the hydrophobic core to the solvent by pressure is not a sufficient condition for pressure‐induced unfolding of the α‐helices of proteins. © 2006 Wiley Periodicals, Inc. Biopolymers 85:185–188, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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confidence: 99%

“…Bands of the solvated and buried -helix structures remain distinct at 1380 MPa. Recently, FTIR study by Desai et al 17 reported that the -helices of trp-repressor, which has high -helix content, are stabilized under high pressure. The present result is similar to that of trp-repressor, and the -helices of (-l-) 2 are not unfolded even at 1380 MPa.…”

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confidence: 99%

Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)₂ studied by FTIR spectroscopy

Takekiyo

Takeda

Isogai³

et al. 2006

Biopolymers

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“…To firmly establish the connection between this theoretical framework and reality, a generation of experiments have been devised to probe the details of the early folding events and to explore the topography of the folding landscape. A powerful technique that has received recent attention is the pressure dependence of protein-folding kinetics (1)(2)(3)(4)(5)(6). Developing the theoretical tools to interpret these pressure experiments on light of landscape theory is the focus of this paper.…”

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Pressure-induced protein-folding/unfolding kinetics

Hillson

Onuchic

Garcı́a

1999

Proc. Natl. Acad. Sci. U.S.A.

111

103

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We use an off-lattice minimalist model to describe the effects of pressure in slowing down the folding͞unfolding kinetics of proteins when subjected to increasingly larger pressures. The potential energy function used to describe the interactions between beads in the model includes the effects of pressure on the pairwise interaction of hydrophobic groups in water. We show that pressure affects the participation of contacts in the transition state. More significantly, pressure exponentially decreases the chain reconfigurational diffusion coefficient. These results are consistent with experimental results on the kinetics of pressure-denaturation of staphylococcal nuclease.pressure denaturation ͉ hydrophobic effect ͉ activation volumes ͉ water penetration ͉ energy landscape P roteins are responsible for most of the functions that occur in living organisms. Their activity, however, depends on their three-dimensional structure and dynamics, and for this reason protein folding has been a central problem in molecular biology. Energy landscapes and the funnel concept have provided the theoretical framework for a quantitative understanding of the folding problem. To firmly establish the connection between this theoretical framework and reality, a generation of experiments have been devised to probe the details of the early folding events and to explore the topography of the folding landscape. A powerful technique that has received recent attention is the pressure dependence of protein-folding kinetics (1-6). Developing the theoretical tools to interpret these pressure experiments on light of landscape theory is the focus of this paper.Proteins undergo reversible folding͞unfolding transitions when subjected to hydrostatic pressures of 2-10 kilobars (kbar) (1). Despite the fact that folded proteins are highly incompressible (7,8), pressure induces conformational changes that reduce the overall volume of the system. This decrease in volume results from the exposure of hydrophobic groups in the interior of the protein to solvent. The effects of pressure on the dynamic structure of water interacting with proteins and polymers are complex but well studied (4, 9-11). Water will balance the tendency of forming an open structure resulting from directional hydrogen bond interactions, with the tendency to pack as Lennard-Jones particles to reduce its volume. This balance is shifted with the application of pressure. The dynamic fluctuations of a protein in aqueous solvent will, as a consequence, be affected by pressure. Equilibrium solvation properties are also affected by pressure.Kauzmann (12) pointed out that the pressure dependence of protein unfolding is in disagreement with the hydrophobic core model. His objections were based on the observation that change in volume (⌬V) upon unfolding is positive at low P, but negative for P ϭ 1-2 kbar. The transfer of hydrocarbons into water shows exactly the opposite behavior. A solution to this puzzle was recently suggested by Hummer et al. (4) by focusing on the pressure-dependent trans...

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“…Likewise, SH3 protein has been shown to contain a highly polarized TSE in which water molecules are removed after the ratelimiting step for folding [86], whereas pressure jump relaxation studies of Staphylococcal Nuclease (SNase) show that most of the water molecules are expelled from the hydrophobic core before the TSE is reached [71]. Cold shock protein B (CspB) also appears to have a dehydrated TSE [87], although many other proteins, such as tryptophan repressor [88] and CI2 for example [89], exhibit a hydrated TSE. In short, the role of water molecules in guiding folding through the TSE, particularly how hydration may affect folding rates and mechanisms, is a subject of intense study [71,90,91], but no general principles have been elucidated at present.…”

Section: Wet or Dry Transition State Ensemble?mentioning

confidence: 99%

Minimizing frustration by folding in an aqueous environment

Mattos

Clark

2008

Archives of Biochemistry and Biophysics

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Although life as we know it evolved in an aqueous medium, the properties of water are not completely understood. In this review, we focus on the role of water in guiding protein folding and stability. Specifically, we discuss the mechanisms of protein folding in an aqueous environment, the effects of water on the folding energy landscape as well as the transition state ensemble, and interactions of water with the folded state. We show that water cannot be viewed as a passive solvent, but rather, plays a very active role in the life of a protein.

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Pressure-jump studies of the folding/unfolding of trp repressor

Cited by 85 publications

References 55 publications

Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)₂ studied by FTIR spectroscopy

Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)₂ studied by FTIR spectroscopy

Pressure-induced protein-folding/unfolding kinetics

Minimizing frustration by folding in an aqueous environment

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Pressure-jump studies of the folding/unfolding of trp repressor

Cited by 85 publications

References 55 publications

Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)2 studied by FTIR spectroscopy

Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)2 studied by FTIR spectroscopy

Pressure-induced protein-folding/unfolding kinetics

Minimizing frustration by folding in an aqueous environment

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Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)₂ studied by FTIR spectroscopy

Pressure stability of the α‐helix structure in a de novo designed protein (α‐l‐α)₂ studied by FTIR spectroscopy