Thermodynamics and Kinetics of the Pressure Unfolding of Phosphoglycerate Kinase

Osváth, Szabolcs; Quynh, Luu Manh; Smeller, László

doi:10.1021/bi900922f

Cited by 10 publications

(2 citation statements)

References 38 publications

(57 reference statements)

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“…2.1) (Dill and Chan 1977;Bryngelson et al 1995). The protein folding is a complex phenomenon (Osvath et al 2003(Osvath et al , 2009Gruebele 2009). Although some proteins fold co-translationally or quickly after being synthesized, there are some which face the danger of misfolding, if they are not assisted by chaperone.…”

Section: The Thermodynamic Picturementioning

confidence: 99%

Protein Denaturation on p-T Axes – Thermodynamics and Analysis

Smeller

2015

Subcellular Biochemistry

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Proteins are essential players in the vast majority of molecular level life processes. Since their structure is in most cases substantial for their correct function, study of their structural changes attracted great interest in the past decades. The three dimensional structure of proteins is influenced by several factors including temperature, pH, presence of chaotropic and cosmotropic agents, or presence of denaturants. Although pressure is an equally important thermodynamic parameter as temperature, pressure studies are considerably less frequent in the literature, probably due to the technical difficulties associated to the pressure studies. Although the first steps in the high-pressure protein study have been done 100 years ago with Bridgman's ground breaking work, the field was silent until the modern spectroscopic techniques allowed the characterization of the protein structural changes, while the protein was under pressure. Recently a number of proteins were studied under pressure, and complete pressure-temperature phase diagrams were determined for several of them. This review summarizes the thermodynamic background of the typical elliptic p-T phase diagram, its limitations and the possible reasons for deviations of the experimental diagrams from the theoretical one. Finally we show some examples of experimentally determined pressure-temperature phase diagrams.

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Section: The Thermodynamic Picturementioning

confidence: 99%

Protein Denaturation on p-T Axes – Thermodynamics and Analysis

Smeller

2015

Subcellular Biochemistry

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“…Because of the different pressure-dependencies of these two potentials, they produce different folding-phase behaviors of proteins on the P – T plane. Here, we investigate these two different pressure-dependent desolvation potentials and compare it to the known behavior of a well-studied protein under high hydrostatic pressure, phosphoglycerate kinase (PGK), based on experimental evidence. − Before presenting the results, we give an overview of pressure denaturation relevant to the current investigation.…”

Section: Introductionmentioning

confidence: 99%

A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure

Gasic

Cheung

2020

J. Phys. Chem. B

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Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure-dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse-grained molecular simulations of protein folding and unfolding under hydrostatic pressure. Although both PMF includes a desolvation barrier separating the well of a direct contact and the well of a solvent-mediated contact, how these features vary with hydrostatic pressure is still debated. There is a need of a systematic comparison of these two PMFs on a protein. We investigated the two different pressure-dependencies on the desolvation potential in a structure-based protein model using coarse-grained molecular 2 simulations. We compared them to the known behavior a real protein based on experimental evidence. We showed that the protein's folding transition curve on the pressure-temperature phase diagram depends on the relationship between the potential well minima and pressure. For protein that reduces the total volume under pressure, it is essential for the PMF to carry the feature that the direct contact well is essential less stable than the water-mediated contact well at high pressure.We also comment on the practicality and importance of structure-based minimalist models for understanding the phenomenological behavior of a protein under a wide range of phase space.

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High-Pressure Fluorescence Applications

Dellarole

Royer

2013

Methods in Molecular Biology

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Fluorescence is the most widely used technique to study the effect of pressure on biochemical systems. The use of pressure as a physical variable sheds light into volumetric characteristics of reactions. Here we focus on the effect of pressure on protein solutions using a simple unfolding example in order to illustrate the applications of the methodology. Topics covered in this review include the relationships between practical aspects and technical limitations; the effect of pressure and the study of protein cavities; the interpretation of thermodynamic and relaxation kinetics; and the study of relaxation amplitudes. Finally, we discuss the insights available from the combination of fluorescence and other methods adapted to high pressure, such as SAXS or NMR. Because of the simplicity and accessibility of high-pressure fluorescence, the technique is a starting point that complements appropriately multi-methodological approaches related to understanding protein function, disfunction, and folding from the volumetric point of view.

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Thermodynamics and Kinetics of the Pressure Unfolding of Phosphoglycerate Kinase

Cited by 10 publications

References 38 publications

Protein Denaturation on p-T Axes – Thermodynamics and Analysis

Protein Denaturation on p-T Axes – Thermodynamics and Analysis

A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure

High-Pressure Fluorescence Applications

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