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Somkuti J, Smeller L. High pressure effects on allergen food proteins. Biophys Chem 2013; 183:19-29. [DOI: 10.1016/j.bpc.2013.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
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2
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Chatterjee S, Basumallick I. Transfer Thermodynamics of Protein in Denaturing and Stabilizing Media. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200800005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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3
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Size dependence of cavity volume: A molecular dynamics study. Biophys Chem 2012; 161:46-9. [DOI: 10.1016/j.bpc.2011.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/14/2011] [Accepted: 10/16/2011] [Indexed: 11/18/2022]
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4
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Sirotkin VA, Winter R. Volume Changes Associated with Guanidine Hydrochloride, Temperature, and Ethanol Induced Unfolding of Lysozyme. J Phys Chem B 2010; 114:16881-6. [DOI: 10.1021/jp105627w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir A. Sirotkin
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, 420008, Kazan, Russia, and Faculty of Chemistry, Physical Chemistry I, Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- A. M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, 420008, Kazan, Russia, and Faculty of Chemistry, Physical Chemistry I, Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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5
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Gee MB, Smith PE. Kirkwood-Buff theory of molecular and protein association, aggregation, and cellular crowding. J Chem Phys 2009; 131:165101. [PMID: 19894976 PMCID: PMC2780464 DOI: 10.1063/1.3253299] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 10/01/2009] [Indexed: 11/15/2022] Open
Abstract
An analysis of the effect of a cosolvent on the association of a solute in solution using the Kirkwood-Buff theory of solutions is presented. The approach builds on the previous results of Ben-Naim by extending the range of applicability to include any number of components at finite concentrations in both closed and semiopen systems. The derived expressions, which are exact, provide a foundation for the analysis and rationalization of cosolvent effects on molecular and biomolecular equilibria including protein association, aggregation, and cellular crowding. A slightly different view of cellular crowding is subsequently obtained. In particular, it is observed that the addition of large cosolvents still favors the associated form even when traditional excluded volume effects are absent.
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Affiliation(s)
- Moon Bae Gee
- Department of Chemistry, 213 CBC Building, Kansas State University, Manhattan, Kansas 66506-0401, USA
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6
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Structural transition of a homopolymer in solvents mixture. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2008. [DOI: 10.1016/j.msec.2007.10.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Auton M, Bolen DW, Rösgen J. Structural thermodynamics of protein preferential solvation: Osmolyte solvation of proteins, aminoacids, and peptides. Proteins 2008; 73:802-13. [DOI: 10.1002/prot.22103] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Pierce V, Kang M, Aburi M, Weerasinghe S, Smith PE. Recent applications of Kirkwood-Buff theory to biological systems. Cell Biochem Biophys 2007; 50:1-22. [PMID: 18043873 PMCID: PMC2566781 DOI: 10.1007/s12013-007-9005-0] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 11/02/2007] [Indexed: 12/01/2022]
Abstract
The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.
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Affiliation(s)
- Veronica Pierce
- Department of Chemistry, 111 Willard Hall, Kansas State University, Manhattan, KS 66506-3701, USA
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Smith PE. Equilibrium dialysis data and the relationships between preferential interaction parameters for biological systems in terms of Kirkwood-Buff integrals. J Phys Chem B 2007; 110:2862-8. [PMID: 16471896 DOI: 10.1021/jp056100e] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Equilibrium dialysis data has provided valuable information concerning the preferential interaction of a cosolvent with a biomolecule in aqueous solutions. Here, we formulate the experimental data in terms of Kirkwood-Buff (KB) theory, resulting in equations that provide a simple physical picture of the dialysis experiment and thereby the interaction of a cosolvent with a biomolecule. These results are then used to establish exact relationships between preferential interaction coefficients, defined in different ensembles and/or using different concentration scales, in terms of KB integrals. It is then argued that the molality based equilibrium dialysis data represent the situation most relevant to computer simulations performed in either open or closed systems.
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Affiliation(s)
- Paul E Smith
- Department of Chemistry, 111 Willard Hall, Kansas State University, Manhattan, Kansas 66506-3701, USA.
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11
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Yamazaki T, Imai T, Hirata F, Kovalenko A. Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation. J Phys Chem B 2007; 111:1206-12. [PMID: 17266276 DOI: 10.1021/jp064615f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We explain the molecular mechanism of the effect of urea and glycerol cosolvents on the partial molar volume (PMV) change associated with the pressure denaturation of staphylococcal nuclease (SNase) protein recently observed in experiments. Native and denatured conformations of SNase are produced by using molecular dynamics simulations in water, and the PMV is obtained from the integral equation theory of molecular liquids called 3D-RISM, which is based on statistical mechanics. The PMV of the native SNase in water predicted by 3D-RISM theory is in good agreement with experiment. The PMV changes associated with pressure denaturation in water and in water-urea and water-glycerol mixtures are qualitatively reproduced. By analyzing the results obtained, we found two interesting cosolvent effects on the PMV: (1) both urea and glycerol cosolvents increase the PMVs of both native and denatured SNase compared to those in water and (2) both urea and glycerol cosolvents increase the PMV of denatured SNase more than that of native SNase. We also showed that these two observations can be explained in terms of the thermal volume, which is related to the packing effect of solvent molecules.
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Affiliation(s)
- Takeshi Yamazaki
- Department of Mechanical Engineering, University of Alberta, and National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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12
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Moghaddam MS, Chan HS. Pressure and temperature dependence of hydrophobic hydration: Volumetric, compressibility, and thermodynamic signatures. J Chem Phys 2007; 126:114507. [PMID: 17381220 DOI: 10.1063/1.2539179] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The combined effect of pressure and temperature on hydrophobic hydration of a nonpolar methanelike solute is investigated by extensive simulations in the TIP4P model of water. Using test-particle insertion techniques, free energies of hydration under a range of pressures from 1 to 3000 atm are computed at eight temperatures ranging from 278.15 to 368.15 K. Corresponding enthalpy, entropy, and heat capacity accompanying the hydration process are estimated from the temperature dependence of the free energies. Partial molar and excess volumes calculated using pressure derivatives of the simulated free energies are consistent with those determined by direct volume simulations; but direct volume determination offers more reliable estimates for compressibility. At 298.15 K, partial molar and excess isothermal compressibilities of methane are negative at 1 atm. Partial molar and excess adiabatic (isentropic) compressibilities are estimated to be also negative under the same conditions. But partial molar and excess isothermal compressibilities are positive at high pressures, with a crossover from negative to positive compressibility at approximately 100-1000 atm. This trend is consistent with experiments on aliphatic amino acids and pressure-unfolded states of proteins. For the range of pressures simulated, hydration heat capacity exhibits little pressure dependence, also in apparent agreement with experiment. When pressure is raised at constant room temperature, hydration free energy increases while its entropic component remains essentially constant. Thus, the increasing unfavorability of hydration under raised pressure is seen as largely an enthalpic effect. Ramifications of the findings of the authors for biopolymer conformational transitions are discussed.
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Affiliation(s)
- Maria Sabaye Moghaddam
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Dzwolak W. Tuning amyloidogenic conformations through cosolvents and hydrostatic pressure: when the soft matter becomes even softer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:470-80. [PMID: 16480937 DOI: 10.1016/j.bbapap.2005.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2005] [Revised: 11/29/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022]
Abstract
Compact packing, burial of hydrophobic side-chains, and low free energy levels of folded conformations contribute to stability of native proteins. Essentially, the same factors are implicated in an even higher stability of mature amyloid fibrils. Although both native insulin and insulin amyloid are resistant to high pressure and influence of cosolvents, intermediate aggregation-prone conformations are susceptible to either condition. Consequently, insulin fibrillation may be tuned under hydrostatic pressure or-- through cosolvents and cosolutes-- by preferential exclusion or binding. Paradoxically, under high pressure, which generally disfavors aggregation of insulin, an alternative "low-volume" aggregation pathway, which leads to unique circular amyloid is permitted. Likewise, cosolvents are capable of preventing, or altering amyloidogenesis of insulin. As a result of cosolvent-induced perturbation, distinct conformational variants of fibrils are formed. Such variants, when used as templates for seeding daughter generations, reproduce initial folding patterns regardless of environmental biases. By the close analogy, this suggests that the "prion strains" phenomenon may mirror a generic, common feature in amyloids. The susceptibility of amyloidogenic conformations to pressure and cosolvents is likely to arise from their "frustration", as unfolding results in less-densely packed side-chains, void volumes, and exposure of hydrophobic groups. The effects of cosolvents and pressure are discussed in the context of studies on other amyloidogenic protein models, amyloid polymorphism, and "strains".
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Affiliation(s)
- Wojciech Dzwolak
- Institute of High Pressure Physics, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw, Poland.
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Mitra L, Smolin N, Ravindra R, Royer C, Winter R. Pressure perturbation calorimetric studies of the solvation properties and the thermal unfolding of proteins in solution—experiments and theoretical interpretation. Phys Chem Chem Phys 2006; 8:1249-65. [PMID: 16633605 DOI: 10.1039/b516608j] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used pressure perturbation calorimetry (PPC), a relatively new and efficient technique, to study the solvation and volumetric properties of amino acids and peptides as well as of proteins in their native and unfolded state. In PPC, the coefficient of thermal expansion of the partial volume of the protein is deduced from the heat consumed or produced after small isothermal pressure jumps, which strongly depends on the interaction of the protein with the solvent or cosolvent at the protein-solvent interface. Furthermore, the effects of various chaotropic and kosmotropic cosolvents on the volume and expansivity changes of proteins were measured over a wide concentration range with high precision. Depending on the type of cosolvent and its concentration, specific differences were found for the solvation properties and unfolding behaviour of the proteins, and the volume change upon unfolding may even change sign. To yield a molecular interpretation of the different terms contributing to the partial protein volume and its temperature dependence, and hence a better understanding of the PPC data, molecular dynamics computer simulations on SNase were also carried out and compared with the experimental data. The PPC studies introduced aim to obtain more insight into the basic thermodynamic properties of protein solvation and volume effects accompanying structural transformations of proteins in various cosolvents on one hand, as these form the basis for understanding their physiological functions and their use in drug designing and formulations, but also to initiate further valuable applications in studies of other biomolecular and chemical systems.
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Affiliation(s)
- Lally Mitra
- University of Dortmund, Department of Chemistry, Physical Chemistry I--Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
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Masson P, Balny C. Linear and non-linear pressure dependence of enzyme catalytic parameters. Biochim Biophys Acta Gen Subj 2005; 1724:440-50. [PMID: 15951113 DOI: 10.1016/j.bbagen.2005.05.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 05/03/2005] [Accepted: 05/04/2005] [Indexed: 11/21/2022]
Abstract
The pressure dependence of enzyme catalytic parameters allows volume changes associated with substrate binding and activation volumes for the chemical steps to be determined. Because catalytic constants are composite parameters, elementary volume change contributions can be calculated from the pressure differentiation of kinetic constants. Linear and non-linear pressure-dependence of single-step enzyme reactions and steady-state catalytic parameters can be observed. Non-linearity can be interpreted either in terms of interdependence between the pressure and other environmental parameters (i.e., temperature, solvent composition, pH), pressure-induced enzyme unfolding, compressibility changes and pressure-induced rate limiting changes. These different situations are illustrated with several examples.
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Affiliation(s)
- Patrick Masson
- Centre de Recherches du Service de Santé des Armées, Département de Toxicologie, Unité d'Enzymologie, BP. 87, 38702 La Tronche cédex, France.
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