1
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Puglisi R, Cioni P, Gabellieri E, Presciuttini G, Pastore A, Temussi PA. Heat and cold denaturation of yeast frataxin: The effect of pressure. Biophys J 2022; 121:1502-1511. [PMID: 35278425 PMCID: PMC9072581 DOI: 10.1016/j.bpj.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/14/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022] Open
Abstract
Yfh1 is a yeast protein with the peculiar characteristic to undergo, in the absence of salt, cold denaturation at temperatures above the water freezing point. This feature makes the protein particularly interesting for studies aiming at understanding the rules that determine protein fold stability. Here, we present the phase diagram of Yfh1 unfolding as a function of pressure (0.1-500 MPa) and temperature 278-313 K (5-40°C) both in the absence and in the presence of stabilizers using Trp fluorescence as a monitor. The protein showed a remarkable sensitivity to pressure: at 293 K, pressures around 10 MPa are sufficient to cause 50% of unfolding. Higher pressures were required for the unfolding of the protein in the presence of stabilizers. The phase diagram on the pressure-temperature plane together with a critical comparison between our results and those found in the literature allowed us to draw conclusions on the mechanism of the unfolding process under different environmental conditions.
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Affiliation(s)
- Rita Puglisi
- UK-DRI at King's College London, The Wohl Institute, London, (UK)
| | | | | | | | - Annalisa Pastore
- UK-DRI at King's College London, The Wohl Institute, London, (UK); European Synchrotron Radiation Facility, Grenoble, (France).
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2
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Fernández Del Río B, Rey A. Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures. J Phys Chem B 2021; 125:6179-6191. [PMID: 34100621 PMCID: PMC8478274 DOI: 10.1021/acs.jpcb.1c03313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based models are coarse-grained representations of the interactions responsible for the protein folding process. In their simplest form, they use only the native contact map of a given protein to predict the main features of its folding process by computer simulation. Given their limitations, these models are frequently complemented with sequence-dependent contributions or additional information. Specifically, to analyze the effect of pressure on the folding/unfolding transition, special forms of these interaction potentials are employed, which may a priori determine the outcome of the simulations. In this work, we have tried to keep the original simplicity of structure-based models. Therefore, we have used folded structures that have been experimentally determined at different pressures to define native contact maps and thus interactions dependent on pressure. Despite the apparently tiny structural differences induced by pressure, our simulation results provide different thermodynamic and kinetic behaviors, which roughly correspond to experimental observations (when there is a possible comparison) of two proteins used as benchmarks, hen egg-white lysozyme and dihydrofolate reductase. Therefore, this work shows the feasibility of using experimental native structures at different pressures to analyze the global effects of this physical property on the protein folding process.
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Affiliation(s)
- Beatriz Fernández Del Río
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Antonio Rey
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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3
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Hopkins JR, Crean RM, Catici DAM, Sewell AK, Arcus VL, Van der Kamp MW, Cole DK, Pudney CR. Peptide cargo tunes a network of correlated motions in human leucocyte antigens. FEBS J 2020; 287:3777-3793. [PMID: 32134551 PMCID: PMC8651013 DOI: 10.1111/febs.15278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
Most biomolecular interactions are typically thought to increase the (local) rigidity of a complex, for example, in drug‐target binding. However, detailed analysis of specific biomolecular complexes can reveal a more subtle interplay between binding and rigidity. Here, we focussed on the human leucocyte antigen (HLA), which plays a crucial role in the adaptive immune system by presenting peptides for recognition by the αβ T‐cell receptor (TCR). The role that the peptide plays in tuning HLA flexibility during TCR recognition is potentially crucial in determining the functional outcome of an immune response, with obvious relevance to the growing list of immunotherapies that target the T‐cell compartment. We have applied high‐pressure/temperature perturbation experiments, combined with molecular dynamics simulations, to explore the drivers that affect molecular flexibility for a series of different peptide–HLA complexes. We find that different peptide sequences affect peptide–HLA flexibility in different ways, with the peptide cargo tuning a network of correlated motions throughout the pHLA complex, including in areas remote from the peptide‐binding interface, in a manner that could influence T‐cell antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Rory M Crean
- Department of Biology and Biochemistry, University of Bath, UK.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | | | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Christopher R Pudney
- Department of Biology and Biochemistry, University of Bath, UK.,Centre for Therapeutic Innovation, University of Bath, UK
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4
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Vondracek H, Alfarano S, Hoberg C, Kolling I, Novelli F, Sebastiani F, Brubach JB, Roy P, Schwaab G, Havenith M. Urea's match in the hydrogen-bond network? A high pressure THz study. Biophys Chem 2019; 254:106240. [PMID: 31442764 DOI: 10.1016/j.bpc.2019.106240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/14/2019] [Accepted: 07/27/2019] [Indexed: 11/28/2022]
Abstract
We present results of the measurement of the low frequency spectrum of solvated urea. The study revealed a blue shift of the intramolecular mode of urea centered at 150 cm-1 of Δν= 17 cm-1 upon increasing the pressure up to 10 kbar. The blue shift scaled linearly with the increase in density and was attributed to a stiffening of the water-urea intermolecular potential. We deduced an increase in the number of affected water molecules from 1 to 2 up to 5-7, which corresponds to the sterical coordination number of urea. The increase in hydration number can be explained by an suppression of the NH2 inversion and the hydrogen bond switching around the NH2 group. Pressure induced sterical constraints are proposed to hinder the rapid switching of hydrogen bond partners and make the water around urea less bulk-like than under ambient conditions.
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Affiliation(s)
- Hendrik Vondracek
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Serena Alfarano
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Claudius Hoberg
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Inga Kolling
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Fabio Novelli
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Federico Sebastiani
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Jean-Blaise Brubach
- Ligne AILES - Synchrotron SOLEIL, L'Orme des Merisiers, F-91192 Gif-sur-Yvette, France
| | - Pascale Roy
- Ligne AILES - Synchrotron SOLEIL, L'Orme des Merisiers, F-91192 Gif-sur-Yvette, France
| | - Gerhard Schwaab
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany
| | - Martina Havenith
- Ruhr-Universität Bochum, LS Physikalische Chemie II, Universitätsstraße 150, 44801 Bochum, Germany.
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5
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Evaluation and correlation of solubility and solvation energetics of DL-phenylalanine and DL-serine in water and aqueous ethylene glycol solutions. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.11.084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Chen CR, Makhatadze GI. Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding. J Phys Chem B 2017; 121:8300-8310. [PMID: 28795561 DOI: 10.1021/acs.jpcb.7b05831] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pressure is a well-known environmental stressor that can either stabilize or destabilize proteins. The volumetric change upon protein unfolding determines the effect of pressure on protein stability, where negative volume changes destabilized proteins at high pressures. High temperature often accompanies high pressure, for example, in the ocean depths near hydrothermal vents or near faults, so it is important to study the effect of temperature on the volumetric change upon unfolding. We previously detailed the magnitude and sign of the molecular determinants of volumetric change, allowing us to quantitatively predict the volumetric change upon protein unfolding. Here, we present a comprehensive analysis of the temperature dependence of the volumetric components of proteins, showing that hydration volume is the primary component that defines expansivities of the native and unfolded states and void volume only contributes slightly to the folded state expansivity.
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Affiliation(s)
- Calvin R Chen
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 8th Street, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , 110 8th Street, Troy, New York 12180, United States
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7
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Halalipour A, Duff MR, Howell EE, Reyes-De-Corcuera JI. Glucose oxidase stabilization against thermal inactivation using high hydrostatic pressure and hydrophobic modification. Biotechnol Bioeng 2016; 114:516-525. [DOI: 10.1002/bit.26185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/14/2016] [Accepted: 09/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Ali Halalipour
- Department of Food Science and Technology; University of Georgia; Food Science Building, 100 Cedar St. Athens, Georgia 30602
| | - Michael R. Duff
- Department of Biochemistry, Cellular and Molecular Biology; University of Tennessee; Knoxville Tennessee
| | - Elizabeth E. Howell
- Department of Biochemistry, Cellular and Molecular Biology; University of Tennessee; Knoxville Tennessee
| | - José I. Reyes-De-Corcuera
- Department of Food Science and Technology; University of Georgia; Food Science Building, 100 Cedar St. Athens, Georgia 30602
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8
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Picart-Palmade L, Chevalier-Lucia D, Lange R, Facchiano A, Pennacchio A, Staiano M, D’Auria S. The fluorescent monomeric protein Kusabira Orange. Pressure effect on its structure and stability. Biochem Biophys Rep 2016; 7:138-143. [PMID: 28955900 PMCID: PMC5613304 DOI: 10.1016/j.bbrep.2016.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/11/2016] [Accepted: 06/01/2016] [Indexed: 11/26/2022] Open
Abstract
The structure and stability of the fluorescent protein monomeric Kusabira Orange (mKO), a GFP-like protein, was studied under different pressure levels and in different chemical environments. At different pH values (between pH 7.4 and pH 4.0) and under a pressure up to 600 MPa (at 25 °C), mKO did not show significant fluorescence spectral changes, indicating a structural stability of the protein. In more extreme chemical conditions (at pH 4.0 in the presence of 0.8 M guanidine hydrochloride), a marked reduction of mKO fluorescence intensity emission was observed at pressures above 300 MPa. This fluorescence emission quenching may be due to the loss of the intermolecular bonds and, consequently, to the destructuration of the mKO chromophore structure. Since the electrostatic and hydrophobic interactions as well as the salt bridges present in proteins are usually perturbed under high pressure, the reduction of mKO fluorescence intensity emission is associated to the perturbation of the protein salt bridges network.
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Affiliation(s)
- L. Picart-Palmade
- Université de Montpellier, UMR IATE, cc023, 2 Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - D. Chevalier-Lucia
- Université de Montpellier, UMR IATE, cc023, 2 Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - R. Lange
- Université de Montpellier, UMR IATE, cc023, 2 Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - A. Facchiano
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma, 64, I-83100 Avellino, Italy
| | - A. Pennacchio
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma, 64, I-83100 Avellino, Italy
| | - M. Staiano
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma, 64, I-83100 Avellino, Italy
| | - S. D’Auria
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma, 64, I-83100 Avellino, Italy
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9
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Use of low-field nuclear magnetic resonance to characterize water properties in frozen chicken breasts thawed under high pressure. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2189-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Temperature and pressure effects on C112S azurin: Volume, expansivity, and flexibility changes. Proteins 2014; 82:1787-98. [DOI: 10.1002/prot.24532] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/10/2014] [Accepted: 01/28/2014] [Indexed: 11/07/2022]
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11
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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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12
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Chemical Transfer Energies of Some Homologous Amino Acids and the –CH2– Group in Aqueous DMF: Solvent Effect on Hydrophobic Hydration and Three Dimensional Solvent Structure. J SOLUTION CHEM 2013. [DOI: 10.1007/s10953-013-0103-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Pozzi EA, Schwall LR, Jimenez R, Weber JM. Pressure-induced changes in the fluorescence behavior of red fluorescent proteins. J Phys Chem B 2012; 116:10311-6. [PMID: 22861177 PMCID: PMC4022145 DOI: 10.1021/jp306093h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We present an experimental study on the fluorescence behavior of the red fluorescent proteins TagRFP-S, TagRFP-T, mCherry, mOrange2, mStrawberry, and mKO as a function of pressure up to several GPa. TagRFP-S, TagRFP-T, mOrange2, and mStrawberry show an initial increase in fluorescence intensity upon application of pressure above ambient conditions. At higher pressures, the fluorescence intensity decreases dramatically for all proteins under study, probably due to denaturing of the proteins. Small blue shifts in the fluorescence spectra with increasing pressure were seen in all proteins under study, hinting at increased rigidity of the chromophore environment. In addition, mOrange2 and mStrawberry exhibit strong and abrupt changes in their fluorescence spectra at certain pressures. These changes are likely due to structural modifications of the hydrogen bonding environment of the chromophore. The strong differences in behavior between proteins with identical or very similar chromophores highlight how the chromophore environment contributes to pressure-induced behavior of the fluorescence performance.
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Affiliation(s)
- Eric A. Pozzi
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
| | - Linda R. Schwall
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
| | - Ralph Jimenez
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
| | - J. Mathias Weber
- JILA, NIST and Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0440, USA
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14
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Puthenpurackal Narayanan S, Maeno A, Matsuo H, Oda M, Morii H, Akasaka K. Extensively hydrated but folded: a novel state of globular proteins stabilized at high pressure and low temperature. Biophys J 2012; 102:L8-10. [PMID: 22339877 DOI: 10.1016/j.bpj.2011.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/09/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022] Open
Abstract
We studied conformational fluctuations of the transcription factor c-Myb R2 subdomain (52 residues with three Trp) at high pressure and low temperature (5°C) using two different spectroscopic methods, Trp fluorescence and (1)H NMR, on its chemically stable mutant C130I (pseudo-wild-type (WT(S))), which has a large internal cavity. As pressure was increased from 3 to 300 MPa, the Trp fluorescence λ(max) of WT(S) shifted from 342 to ∼355 nm, clearly showing that the three Trp rings become fully exposed to the polar environment, which usually is taken to indicate that the protein underwent unfolding. In contrast, as pressure was increased from 3 to 300 MPa, the high-field-shifted (1)H NMR signals characteristic of the folded state showed a still higher-field shift, but no significant changes in their intensity. The last result unequivocally shows that the protein remains largely folded at 300 MPa. The apparent discrepancy between the two predictions would only be solved if one were to postulate the existence of an extensively hydrated but folded state in WT(S). Intriguingly, such a state was not found in a cavity-filling mutant of WT(S), C130I/V103L, suggesting that this state is mediated by cavity hydration. The generality and significance of this state in proteins are discussed.
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15
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Girard E, Marchal S, Perez J, Finet S, Kahn R, Fourme R, Marassio G, Dhaussy AC, Prangé T, Giffard M, Dulin F, Bonneté F, Lange R, Abraini JH, Mezouar M, Colloc'h N. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure. Biophys J 2010; 98:2365-73. [PMID: 20483346 DOI: 10.1016/j.bpj.2010.01.058] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022] Open
Abstract
Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms.
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Affiliation(s)
- Eric Girard
- Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA CNRS UJF, Grenoble, France
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16
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Rivalain N, Roquain J, Demazeau G. Development of high hydrostatic pressure in biosciences: pressure effect on biological structures and potential applications in biotechnologies. Biotechnol Adv 2010; 28:659-72. [PMID: 20398747 DOI: 10.1016/j.biotechadv.2010.04.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 04/01/2010] [Accepted: 04/04/2010] [Indexed: 11/16/2022]
Abstract
Compared to temperature, the development of pressure as a tool in the research field has emerged only recently (at the end of the XIXth century). Following several developments in Physics and Chemistry during the first half of the XXth century (in particular the synthesis of diamond in 1953-1954), high pressures were applied in Food Science, especially in Japan. The main objective was then to achieve the decontamination of foods while preserving their organoleptic properties. Now, a new step is engaged: the biological applications of high pressures, from food to pharmaceuticals and biomedical applications. This paper will focus on three main points: (i) a brief presentation of the pressure parameter and its characteristics, (ii) a description of the pressure effects on biological constituents from simple to more complex structures and (iii) a review of the different domains for which the application of high pressures is able to initiate potential developments in Biotechnologies.
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Affiliation(s)
- Nolwennig Rivalain
- ICMCB-CNRS - Université de Bordeaux - 87, avenue du Dr. Albert Schweitzer, PESSAC Cedex, France
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17
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High pressure stabilization of collagen structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1151-8. [DOI: 10.1016/j.bbapap.2009.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 03/31/2009] [Accepted: 04/06/2009] [Indexed: 11/20/2022]
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18
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Crisman RL, Randolph TW. Refolding of proteins from inclusion bodies is favored by a diminished hydrophobic effect at elevated pressures. Biotechnol Bioeng 2009; 102:483-92. [DOI: 10.1002/bit.22082] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Wilton DJ, Tunnicliffe RB, Kamatari YO, Akasaka K, Williamson MP. Pressure-induced changes in the solution structure of the GB1 domain of protein G. Proteins 2008; 71:1432-40. [PMID: 18076052 DOI: 10.1002/prot.21832] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The solution structure of the GB1 domain of protein G at a pressure of 2 kbar is presented. The structure was calculated as a change from an energy-minimised low-pressure structure using (1)H chemical shifts. Two separate changes can be characterised: a compression/distortion, which is linear with pressure; and a stabilisation of an alternative folded state. On application of pressure, linear chemical shift changes reveal that the backbone structure changes by about 0.2 A root mean square, and is compressed by about 1% overall. The alpha-helix compresses, particularly at the C-terminal end, and moves toward the beta-sheet, while the beta-sheet is twisted, with the corners closest to the alpha-helix curling up towards it. The largest changes in structure are along the second beta-strand, which becomes more twisted. This strand is where the protein binds to IgG. Curved chemical shift changes with pressure indicate that high pressure also populates an alternative structure with a distortion towards the C-terminal end of the helix, which is likely to be caused by insertion of a water molecule.
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Affiliation(s)
- David J Wilton
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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20
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Starikov EB, Nordén B. Enthalpy−Entropy Compensation: A Phantom or Something Useful? J Phys Chem B 2007; 111:14431-5. [DOI: 10.1021/jp075784i] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Evgeni B. Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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21
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Baden N, Hirota S, Takabe T, Funasaki N, Terazima M. Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time domain. J Chem Phys 2007; 127:175103. [PMID: 17994853 DOI: 10.1063/1.2780860] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- N Baden
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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22
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Vázquez-Pérez AR, Fernández-Velasco DA. Pressure and Denaturants in the Unfolding of Triosephosphate Isomerase: The Monomeric Intermediates of the Enzymes from Saccharomyces cerevisiae and Entamoeba histolytica. Biochemistry 2007; 46:8624-33. [PMID: 17595057 DOI: 10.1021/bi061879j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triosephosphate isomerase (TIM) is a dimeric enzyme formed by two identical (beta/alpha)8 barrels. In this work, we compare the unfolding and refolding of the TIMs from Entamoeba histolytica (EhTIM) and baker's yeast (yTIM). A monomeric intermediate was detected in the GdnHCl-induced unfolding of EhTIM. The thermodynamic, spectroscopic, catalytic, and hydrodynamic properties of this intermediate were found to be very similar to those previously described for a monomeric intermediate of yTIM observed in GdnHCl. Monomer unfolding was reversible for both TIMs; however, the dissociation step was reversible in yTIM and irreversible in EhTIM. Monomer unfolding induced by high pressure in the presence of GdnHCl was a reversible process. DeltaGUnf, DeltaVUnf, and P1/2 were obtained for the 0.7-1.2 M GdnHCl range. The linear extrapolation of these thermodynamic parameters to the absence of denaturant showed the same values for both intermediates. The DeltaVUnfH2O values calculated for EhTIM and yTIM monomeric intermediates are the same within experimental error (-57 +/- 10 and -76 +/- 14 mL/mol, respectively). These DeltaVUnf H2O values are smaller than those reported for the unfolding of monomeric proteins of similar size, suggesting that TIM intermediates are only partially hydrated. |DeltaVUnf| increased with denaturant concentration; this behavior is probably related to structural changes in the unfolded state induced by GdnHCl and pressure. From the thermodynamic parameters that were obtained, it is predicted that in the absence of denaturants, pressure would induce monomer unfolding (P1/2 approximately 140 MPa) prior to dimer dissociation (P1/2 approximately 580 MPa). Therefore, dimerization prevents the pressure unfolding of the monomer.
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Affiliation(s)
- Adrián R Vázquez-Pérez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, México D.F., 04510 Mexico
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Nicolai E, Di Venere A, Rosato N, Rossi A, Finazzi Agro' A, Mei G. Physico-chemical properties of molten dimer ascorbate oxidase. FEBS J 2006; 273:5194-204. [PMID: 17059465 DOI: 10.1111/j.1742-4658.2006.05515.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The possible presence of dimeric unfolding intermediates might offer a clue to understanding the relationship between tertiary and quaternary structure formation in dimers. Ascorbate oxidase is a large dimeric enzyme that displays such an intermediate along its unfolding pathway. In this study the combined effect of high pressure and denaturing agents gave new insight on this intermediate and on the mechanism of its formation. The transition from native dimer to the dimeric intermediate is characterized by the release of copper ions forming the tri-nuclear copper center located at the interface between domain 2 and 3 of each subunit. This transition, which is pH-dependent, is accompanied by a decrease in volume, probably associated to electrostriction due to the loosening of intra-subunit electrostatic interactions. The dimeric species is present even at 3 x 10(8) Pa, providing evidence that mechanically or chemically induced unfolding lead to a similar intermediate state. Instead, dissociation occurs with an extremely large and negative volume change (DeltaV approximately -200 mL.mol(-1)) by pressurization in the presence of moderate amounts of denaturant. This volume change can be ascribed to the elimination of voids at the subunit interface. Furthermore, the combination of guanidine and high pressure uncovers the presence of a marginally stable (DeltaG approximately 2 kcal.mol(-1)) monomeric species (which was not observed in previous equilibrium unfolding measurements) that might be populated in the early folding steps of ascorbate oxidase. These findings provide new aspects of the protein folding pathway, further supporting the important role of quaternary interactions in the folding strategy of large dimeric enzymes.
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Cheung JK, Shah P, Truskett TM. Heteropolymer collapse theory for protein folding in the pressure-temperature plane. Biophys J 2006; 91:2427-35. [PMID: 16844760 PMCID: PMC1562399 DOI: 10.1529/biophysj.106.081802] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We revisit a heteropolymer collapse theory originally introduced to explore how the balance between hydrophobic interactions and configurational entropy determines the thermal stability of globular proteins at ambient pressure. We generalize the theory by introducing a basic statistical mechanical treatment for how pressure impacts the solvent-mediated interactions between hydrophobic amino-acid residues. In particular, we estimate the strength of the hydrophobic interactions using a molecular thermodynamic model for the interfacial free energy between liquid water and a curved hydrophobic solute. The model, which also reproduces many of the distinctive thermodynamic properties of aqueous solutions in bulk and interfacial environments, predicts that the water-solute interfacial free energy is significantly reduced by the application of high hydrostatic pressures. This allows water to penetrate into folded heteropolymers at high pressure and break apart their hydrophobic cores, a scenario suggested earlier by information theory calculations. As a result, folded heteropolymers are predicted to display the kind of closed region of stability in the pressure-temperature plane exhibited by native proteins. We compare predictions of the collapse theory with experimental data for several proteins.
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Affiliation(s)
- Jason K Cheung
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
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Giel-Pietraszuk M, Barciszewski J. A nature of conformational changes of yeast tRNAPhe. Int J Biol Macromol 2005; 37:109-14. [PMID: 16236354 DOI: 10.1016/j.ijbiomac.2005.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 09/08/2005] [Accepted: 09/08/2005] [Indexed: 10/25/2022]
Abstract
We analysed conformational changes of yeast tRNA(Phe) induced by high hydrostatic pressure (HHP) measured by Fourier-transform infrared (FTIR) and fluorescence spectroscopies. High pressure influences RNA conformation without other cofactors, such as metal ions and salts. FTIR spectra of yeast tRNA(Phe) recorded at high hydrostatic pressure up to 13 kbar with and without magnesium ions showed a shift of the bands towards higher frequencies. That blue shift is due to an increase a higher energy of bonds as a result of shortening of hydrogen bonds followed by dehydration of tRNA. The fluorescence spectra of Y-base tRNA(Phe) at high pressure up to 3 kbar showed a decrease of the intensity band at 430 nm as a consequence of conformational rearrangement of the anticodon loop leading to exposure of Y-base side chain to the solution. We suggest that structural transition of nucleic acids is driven by the changes of water structure from tetrahedral to a cubic-like geometry induced by high pressure and, in consequence, due to economy of hydration.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland.
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Mignaco JA, Lima LMTR, Rosenthal A, Foguel D, Silva JL. Highlights of the 3rd International Conference on High Pressure Bioscience and Biotechnology. Braz J Med Biol Res 2005; 38:1147-55. [PMID: 16082454 DOI: 10.1590/s0100-879x2005000800001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The 3rd International Conference on High Pressure Bioscience and Biotechnology was held in the city of Rio de Janeiro from September 27 to September 30, 2004. The meeting, promoted by the International Association of High Pressure Bioscience and Biotechnology (IAHPBB), congregated top scientists and researchers from all over the world. In common, they shared the use of hydrostatic pressure for research, technical development, or industrial applications. The meeting consisted of invited lectures, contributed papers and a well-attended poster session. Very exciting discussions were held inside and outside the sessions, and the goals of discussing state-of-the-art data and establishing working collaborations and co-operations were fully attained.
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Affiliation(s)
- J A Mignaco
- Instituto de Bioquímica Médica, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Brasil
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