Determination of the Volumetric Properties of Proteins and Other Solutes Using Pressure Perturbation Calorimetry

Lin, Lung‐Nan; Brandts, John F.; Brandts, J.Michael; Plotnikov, Valerian

doi:10.1006/abio.2001.5524

Cited by 175 publications

(352 citation statements)

References 38 publications

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“…Results supporting the existence of hydration shells around aliphatic hydrocarbons were found by Lin et al (29), who used pressure perturbation calorimetry to measure the structuremaking or structure-breaking behavior in water of the various amino acid side chains in proteins. They found that aliphatic amino acids (and also proline) change from being structuremaking in water near 0°C to being structure-breaking as the temperature increases above 25°C (see their figure 3).…”

Section: The Dynamic Hydration Shell Explains Why Hydrophobic Free Ensupporting

confidence: 58%

Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding

Baldwin

2014

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

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Kauzmann's explanation of how the hydrophobic factor drives protein folding is reexamined. His explanation said that hydrocarbon hydration shells are formed, possibly of clathrate water, and they explain why hydrocarbons have uniquely low solubilities in water. His explanation was not universally accepted because of skepticism about the clathrate hydration shell. A revised version is given here in which a dynamic hydration shell is formed by van der Waals (vdw) attraction, as proposed in 1985 by Jorgensen et al. [Jorgensen WL, Gao J, Ravimohan C (1985) J Phys Chem 89:3470-3473]. The vdw hydration shell is implicit in theories of hydrophobicity that contain the vdw interaction between hydrocarbon C and water O atoms. To test the vdw shell model against the known hydration energetics of alkanes, the energetics should be based on the Ben-Naim standard state (solute transfer between fixed positions in the gas and liquid phases). Then the energetics are proportional to n, the number of water molecules correlated with an alkane by vdw attraction, given by the simulations of Jorgensen et al. The energetics show that the decrease in entropy upon hydration is the root cause of hydrophobicity; it probably results from extensive ordering of water molecules in the vdw shell. The puzzle of how hydrophobic free energy can be proportional to nonpolar surface area when the free energy is unfavorable and the only known interaction (the vdw attraction) is favorable, is resolved by finding that the unfavorable free energy is produced by the vdw shell.hydrophobic hydration | cavity work | protein stability W hen Kauzmann reviewed in 1959 (1) the possible sources of the free energy needed to drive protein folding, he found that that the known factors are not sufficient. He asked what the missing factor could be, and he ruled out peptide Hbonds because they do not provide enough free energy, based on Schellman's (2) analysis of the problem in 1955. Then he discovered the previously unknown hydrophobic factor after observing that known DG values for transfer of hydrocarbons out of water into other solvents could supply the missing free energy. Then he needed to assume that the interior of a folded protein is water-free and the nonpolar side chains are buried inside the protein as folding occurs. In 1960 the 2-Å structure of myoglobin by Kendrew et al. (3) confirmed these predictions.Kauzmann's Explanation (1959, 1987) of How the Hydrophobic Factor Works in Protein Folding Kauzmann was confident of his prediction that the hydrophobic factor should be the missing factor and he gave an explanation of how it should work. He accepted the 1945 proposal by Frank and Evans (4) that a hydrocarbon probably forms a hydration shell when it dissolves in water. Forming a hydration shell would explain why there is a large decrease in entropy (ΔS h ) and an unfavorable change in free energy (ΔG h ) when a hydrocarbon dissolves in water (see Kauzmann's Evidence for a Hydration Shell). Moreover, the hydration shell would also explain why there is a la...

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Section: The Dynamic Hydration Shell Explains Why Hydrophobic Free Ensupporting

confidence: 58%

Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding

Baldwin

2014

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

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“…We use Fourier transform infrared (FT-IR) spectroscopy (30 -33) and pressure perturbation calorimetry (32,34) to probe the secondary structure and hydration of the protein, respectively. We find that, whereas ␣-helical rPrP undergoes aggregation at high temperature into a ␤-sheet-rich structure, it is markedly resistant to pressure, displaying almost no change in secondary structure up to 4 kilobars (kb).…”

Section: The Prion Protein (Prp)mentioning

confidence: 99%

“…In contrast to pressure, thermal denaturation of rPrP is an irreversible process. The overall hydration of ␣-rPrP and ␤-rPrP was evaluated by pressure perturbation calorimetry (PPC), which provides information on the hydration of the proteins during thermal denaturation through measurement of the heat induced by small periodic changes of gas pressure (32,34). Overall, our results show denaturation of recombinant full-length prion protein by high pressure without the use of temperature or denaturants; newly formed aggregates are less hydrated and have more cavities than native prion protein and late aggregates.…”

Section: The Prion Protein (Prp)mentioning

confidence: 99%

Hydration and Packing Effects on Prion Folding and β-Sheet Conversion

Cordeiro

Kraineva

Ravindra

et al. 2004

Journal of Biological Chemistry

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The main hypothesis for prion diseases proposes that the cellular protein (PrP C ) can be altered into a misfolded, ␤-sheet-rich isoform (PrP Sc ), which undergoes aggregation and triggers the onset of transmissible spongiform encephalopathies. Here, we compare the stability against pressure and the thermomechanical properties of the ␣-helical and ␤-sheet conformations of recombinant murine prion protein, designated as ␣-rPrP and ␤-rPrP, respectively. High temperature induces aggregates and a large gain in intermolecular antiparallel ␤-sheet (␤-rPrP), a conformation that shares structural similarity with PrP Sc . ␣-rPrP is highly stable, and only pressures above 5 kilobars (1 kilobar ‫؍‬ 100 MegaPascals) cause reversible denaturation, a process that leads to a random and turnrich conformation with concomitant loss of ␣-helix, as measured by Fourier transform infrared spectroscopy. In contrast, aggregates of ␤-rPrP are very sensitive to pressure, undergoing transition into a dissociated species that differs from the denatured form derived from ␣-rPrP. The higher susceptibility to pressure of ␤-rPrP can be explained by its less hydrated structure. Pressure perturbation calorimetry supports the view that the accessible surface area of ␣-rPrP is much higher than that of ␤-rPrP, which explains the lower degree of hydration of ␤-rPrP. Our findings shed new light on the mechanism of prion conversion and show how water plays a prominent role. Our results allow us to propose a volume and free energy diagram of the different species involved in the conversion and aggregation. The existence of different folded conformations as well as different denatured states of PrP may explain the elusive character of its conversion into a pathogenic form.

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“…Despite the laborious nature of pressure techniques, numerous studies were devoted to determine the thermodynamic properties of pressure-induced protein unfolding [1][2][3][4][5][6][7][8][9][10][11][12][13]. Relatively high pressures are required to determine the volumetric properties of proteins, and that is probably the most serious obstacle for the pressure to become a standard descriptor of the thermodynamic state of a protein.…”

Section: Introductionmentioning

confidence: 99%

High pressure spectrofluorimetry – a tool to determine protein-ligand binding volume

Skvarnavičius

Toleikis

Grigaliunas

et al. 2017

J. Phys.: Conf. Ser.

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Determination of the Volumetric Properties of Proteins and Other Solutes Using Pressure Perturbation Calorimetry

Cited by 175 publications

References 38 publications

Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding

Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding

Hydration and Packing Effects on Prion Folding and β-Sheet Conversion

High pressure spectrofluorimetry – a tool to determine protein-ligand binding volume

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