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Avagyan S, Makhatadze GI. Volumetric Properties of the Transition State Ensemble for Protein Folding. J Phys Chem B 2022; 126:7615-7620. [PMID: 36150186 DOI: 10.1021/acs.jpcb.2c05437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding how high hydrostatic pressure affects biomacromolecular interaction is important for deciphering the molecular mechanisms by which organisms adapt to live at the bottom of the ocean. The relative effect of hydrostatic pressure on the rates of folding/unfolding reactions is defined by the volumetric properties of the transition state ensemble relative to the folded and unfolded states. All-atom structure-based molecular dynamics simulations combined with quantitative computational protocol to compute volumes from three-dimensional coordinates allow volumetric mapping of protein folding landscape. This, is turn, provides qualitative understanding of the effects of hydrostatic pressure on energy landscape of proteins. The computational results for six different proteins are directly benchmark against experimental data and show an excellent agreement. Both experiments and computation show that the transition-state ensemble volume appears to be in-between the folded and unfolded state volumes, and thus the hydrostatic pressure accelerates protein unfolding.
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Affiliation(s)
- Samvel Avagyan
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department on Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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2
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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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Bollati M, Diomede L, Giorgino T, Natale C, Fagnani E, Boniardi I, Barbiroli A, Alemani R, Beeg M, Gobbi M, Fakin A, Mastrangelo E, Milani M, Presciuttini G, Gabellieri E, Cioni P, de Rosa M. A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation. Comput Struct Biotechnol J 2021; 19:6355-6365. [PMID: 34938411 PMCID: PMC8649582 DOI: 10.1016/j.csbj.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 01/02/2023] Open
Abstract
Gelsolin comprises six homologous domains, named G1 to G6. Single point substitutions in this protein are responsible for AGel amyloidosis, a hereditary disease causing progressive corneal lattice dystrophy, cutis laxa, and polyneuropathy. Although several different amyloidogenic variants of gelsolin have been identified, only the most common mutants present in the G2 domain have been thoroughly characterized, leading to clarification of the functional mechanism. The molecular events underlying the pathological aggregation of 3 recently identified mutations, namely A551P, E553K and M517R, all localized at the interface between G4 and G5, are here explored for the first time. Structural studies point to destabilization of the interface between G4 and G5 due to three structural determinants: β-strand breaking, steric hindrance and/or charge repulsion, all implying impairment of interdomain contacts. Such rearrangements decrease the temperature and pressure stability of gelsolin but do not alter its susceptibility to furin cleavage, the first event in the canonical aggregation pathway. These variants also have a greater tendency to aggregate in the unproteolysed forms and exhibit higher proteotoxicity in a C. elegans-based assay. Our data suggest that aggregation of G4G5 variants follows an alternative, likely proteolysis-independent, pathway.
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Affiliation(s)
- Michela Bollati
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Toni Giorgino
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Carmina Natale
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Elisa Fagnani
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Irene Boniardi
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, Milano, Italy
| | - Rebecca Alemani
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Marten Beeg
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Marco Gobbi
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Eloise Mastrangelo
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Mario Milani
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | | | - Edi Gabellieri
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Patrizia Cioni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Matteo de Rosa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
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Dreydoppel M, Becker P, Raum HN, Gröger S, Balbach J, Weininger U. Equilibrium and Kinetic Unfolding of GB1: Stabilization of the Native State by Pressure. J Phys Chem B 2018; 122:8846-8852. [PMID: 30185038 DOI: 10.1021/acs.jpcb.8b06888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
NMR spectroscopy allows an all-atom view on pressure-induced protein folding, separate detection of different folding states, determination of their population, and the measurement of the folding kinetics at equilibrium. Here, we studied the folding of protein GB1 at pH 2 in a temperature and pressure dependent way. We find that the midpoints of temperature-induced unfolding increase with higher pressure. NMR relaxation dispersion experiments disclosed that the unfolding kinetics slow down at elevated pressure while the folding kinetics stay virtually the same. Therefore, pressure is stabilizing the native state of GB1. These findings extend the knowledge of the influence of pressure on protein folding kinetics, where so far typically a destabilization by increased activation volumes of folding was observed. Our findings thus point toward an exceptional section in the pressure-temperature phase diagram of protein unfolding. The stabilization of the native state could potentially be caused by a shift of p Ka values of glutamates and aspartates in favor of the negatively charged state as judged from pH sensitive chemical shifts.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Paul Becker
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Heiner N Raum
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Stefan Gröger
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
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Ingr M, Kutálková E, Hrnčiřík J, Lange R. Equilibria of oligomeric proteins under high pressure - A theoretical description. J Theor Biol 2016; 411:16-26. [PMID: 27717844 DOI: 10.1016/j.jtbi.2016.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/14/2016] [Accepted: 10/03/2016] [Indexed: 01/18/2023]
Abstract
High pressure methods have become a useful tool for studying protein structure and stability. Using them, various physico-chemical processes including protein unfolding, aggregation, oligomer dissociation or enzyme-activity decrease were studied on many different proteins. Oligomeric protein dissociation is a process that can perfectly utilize the potential of high-pressure techniques, as the high pressure shifts the equilibria to higher concentrations making them better observable by spectroscopic methods. This can be especially useful when the oligomeric form is highly stable at atmospheric pressure. These applications may be, however, hindered by less intensive experimental response as well as interference of the oligomerization equilibria with unfolding or aggregation of the subunits, but also by more complex theoretical description. In this study we develop mathematical models describing different kinds of oligomerization equilibria, both closed (equilibrium of monomer and the highest possible oligomer without any intermediates) and consecutive. Closed homooligomer equilibria are discussed for any oligomerization degree, while the more complex heterooligomer equilibria and the consecutive equilibria in both homo- and heterooligomers are taken into account only for dimers and trimers. In all the cases, fractions of all the relevant forms are evaluated as functions of pressure and concentration. Significant points (inflection points and extremes) of the resulting transition curves, that can be determined experimentally, are evaluated as functions of pressure and/or concentration. These functions can be further used in order to evaluate the thermodynamic parameters of the system, i.e. atmospheric-pressure equilibrium constants and volume changes of the individual steps of the oligomer-dissociation processes.
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Affiliation(s)
- Marek Ingr
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, nám. T. G. Masaryka 5555, 76001 Zlín, Czechia; Charles University in Prague, Faculty of Science, Department of Biochemistry, Hlavova 2030, 12843 Prague 2, Czechia.
| | - Eva Kutálková
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, nám. T. G. Masaryka 5555, 76001 Zlín, Czechia
| | - Josef Hrnčiřík
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, nám. T. G. Masaryka 5555, 76001 Zlín, Czechia
| | - Reinhard Lange
- Université Montpellier, INRA UMR IATE, Biochimie et Technologie Alimentaires, cc023, Place Eugene Bataillon, 34095 Montpellier Cedex 05, France
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On the effect of hydrostatic pressure on the conformational stability of globular proteins. Biopolymers 2015; 103:711-8. [DOI: 10.1002/bip.22736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/20/2015] [Accepted: 08/17/2015] [Indexed: 11/07/2022]
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Meadows CW, Balakrishnan G, Kier BL, Spiro TG, Klinman JP. Temperature-Jump Fluorescence Provides Evidence for Fully Reversible Microsecond Dynamics in a Thermophilic Alcohol Dehydrogenase. J Am Chem Soc 2015. [PMID: 26223665 PMCID: PMC4970856 DOI: 10.1021/jacs.5b04413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Protein
dynamics on the microsecond (μs) time scale were
investigated by temperature-jump fluorescence spectroscopy as a function
of temperature in two variants of a thermophilic alcohol dehydrogenase:
W87F and W87F:H43A. Both mutants exhibit a fast, temperature-independent
μs decrease in fluorescence followed by a slower full recovery
of the initial fluorescence. The results, which rule out an ionizing
histidine as the origin of the fluorescence quenching, are discussed
in the context of a Trp49-containing dimer interface that acts as
a conduit for thermally activated structural change within the protein
interior.
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Affiliation(s)
| | - Gurusamy Balakrishnan
- ∥Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Brandon L Kier
- ∥Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Thomas G Spiro
- ∥Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Inhibitor and substrate binding induced stability of HIV-1 protease against sequential dissociation and unfolding revealed by high pressure spectroscopy and kinetics. PLoS One 2015; 10:e0119099. [PMID: 25781460 PMCID: PMC4362767 DOI: 10.1371/journal.pone.0119099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 01/28/2015] [Indexed: 01/10/2023] Open
Abstract
High-pressure methods have become an interesting tool of investigation of structural stability of proteins. They are used to study protein unfolding, but dissociation of oligomeric proteins can be addressed this way, too. HIV-1 protease, although an interesting object of biophysical experiments, has not been studied at high pressure yet. In this study HIV-1 protease is investigated by high pressure (up to 600 MPa) fluorescence spectroscopy of either the inherent tryptophan residues or external 8-anilino-1-naphtalenesulfonic acid at 25°C. A fast concentration-dependent structural transition is detected that corresponds to the dimer-monomer equilibrium. This transition is followed by a slow concentration independent transition that can be assigned to the monomer unfolding. In the presence of a tight-binding inhibitor none of these transitions are observed, which confirms the stabilizing effect of inhibitor. High-pressure enzyme kinetics (up to 350 MPa) also reveals the stabilizing effect of substrate. Unfolding of the protease can thus proceed only from the monomeric state after dimer dissociation and is unfavourable at atmospheric pressure. Dimer-destabilizing effect of high pressure is caused by negative volume change of dimer dissociation of -32.5 mL/mol. It helps us to determine the atmospheric pressure dimerization constant of 0.92 μM. High-pressure methods thus enable the investigation of structural phenomena that are difficult or impossible to measure at atmospheric pressure.
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