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Grosskopf JD, Sidabras JW, Altenbach C, Anderson JR, Mett RR, Strangeway RA, Hyde JS, Hubbell WL, Lerch MT. A pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593074. [PMID: 38766191 PMCID: PMC11100676 DOI: 10.1101/2024.05.07.593074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary and tertiary structure and for monitoring conformational changes in proteins of any degree of complexity, including membrane proteins, with high sensitivity. SDSL-EPR also provides information on protein dynamics in the time scale of ps-µs using continuous wave lineshape analysis and spin lattice relaxation time methods. However, the functionally important time domain of µs-ms, corresponding to large-scale protein motions, is inaccessible to those methods. To extend SDSL-EPR to the longer time domain, the perturbation method of pressure-jump relaxation is implemented. Here, we describe a complete high-pressure EPR system at Q-band for both static pressure and millisecond-timescale pressure-jump measurements on spin-labeled proteins. The instrument enables pressure jumps both up and down from any holding pressure, ranging from atmospheric pressure to the maximum pressure capacity of the system components (~3500 bar). To demonstrate the utility of the system, we characterize a local folding-unfolding equilibrium of T4 lysozyme. The results illustrate the ability of the system to measure thermodynamic and kinetic parameters of protein conformational exchange on the millisecond timescale.
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Affiliation(s)
- Julian D Grosskopf
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christian Altenbach
- Department of Chemistry and Biochemistry and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Jim R Anderson
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Richard R Mett
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Robert A Strangeway
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - James S Hyde
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Michael T Lerch
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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2
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Pastore A, Temussi PA. Unfolding under Pressure: An NMR Perspective. Chembiochem 2023; 24:e202300164. [PMID: 37154795 DOI: 10.1002/cbic.202300164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
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Affiliation(s)
- Annalisa Pastore
- European Synchrotron Radiation Facilities, 71 Ave des Martyrs, 38000, Grenoble, France
- The Wohl Institute, King's College London, 5 Cutcombe Rd, SE59RT, London, UK
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3
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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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4
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Dubois C, Planelles-Herrero VJ, Tillatte-Tripodi C, Delbecq S, Mammri L, Sirkia EM, Ropars V, Roumestand C, Barthe P. Pressure and Chemical Unfolding of an α-Helical Bundle Protein: The GH2 Domain of the Protein Adaptor GIPC1. Int J Mol Sci 2021; 22:ijms22073597. [PMID: 33808390 PMCID: PMC8037465 DOI: 10.3390/ijms22073597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
When combined with NMR spectroscopy, high hydrostatic pressure is an alternative perturbation method used to destabilize globular proteins that has proven to be particularly well suited for exploring the unfolding energy landscape of small single-domain proteins. To date, investigations of the unfolding landscape of all-β or mixed-α/β protein scaffolds are well documented, whereas such data are lacking for all-α protein domains. Here we report the NMR study of the unfolding pathways of GIPC1-GH2, a small α-helical bundle domain made of four antiparallel α-helices. High-pressure perturbation was combined with NMR spectroscopy to unravel the unfolding landscape at three different temperatures. The results were compared to those obtained from classical chemical denaturation. Whatever the perturbation used, the loss of secondary and tertiary contacts within the protein scaffold is almost simultaneous. The unfolding transition appeared very cooperative when using high pressure at high temperature, as was the case for chemical denaturation, whereas it was found more progressive at low temperature, suggesting the existence of a complex folding pathway.
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Affiliation(s)
- Cécile Dubois
- Centre de Biologie Structurale INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (C.T.-T.); (S.D.); (L.M.); (P.B.)
| | - Vicente J. Planelles-Herrero
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248 Paris, France; (V.J.P.-H.); (E.M.S.); (V.R.)
| | - Camille Tillatte-Tripodi
- Centre de Biologie Structurale INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (C.T.-T.); (S.D.); (L.M.); (P.B.)
| | - Stéphane Delbecq
- Centre de Biologie Structurale INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (C.T.-T.); (S.D.); (L.M.); (P.B.)
| | - Léa Mammri
- Centre de Biologie Structurale INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (C.T.-T.); (S.D.); (L.M.); (P.B.)
| | - Elena M. Sirkia
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248 Paris, France; (V.J.P.-H.); (E.M.S.); (V.R.)
| | - Virginie Ropars
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, Sorbonne Université, CNRS UMR144, 75248 Paris, France; (V.J.P.-H.); (E.M.S.); (V.R.)
| | - Christian Roumestand
- Centre de Biologie Structurale INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (C.T.-T.); (S.D.); (L.M.); (P.B.)
- Correspondence:
| | - Philippe Barthe
- Centre de Biologie Structurale INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (C.T.-T.); (S.D.); (L.M.); (P.B.)
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5
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Dubois C, Herrada I, Barthe P, Roumestand C. Combining High-Pressure Perturbation with NMR Spectroscopy for a Structural and Dynamical Characterization of Protein Folding Pathways. Molecules 2020; 25:E5551. [PMID: 33256081 PMCID: PMC7731413 DOI: 10.3390/molecules25235551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
High-hydrostatic pressure is an alternative perturbation method that can be used to destabilize globular proteins. Generally perfectly reversible, pressure exerts local effects on regions or domains of a protein containing internal voids, contrary to heat or chemical denaturant that destabilize protein structures uniformly. When combined with NMR spectroscopy, high pressure (HP) allows one to monitor at a residue-level resolution the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. The use of HP-NMR has long been hampered by technical difficulties. Owing to the recent development of commercially available high-pressure sample cells, HP-NMR experiments can now be routinely performed. This review summarizes recent advances of HP-NMR techniques for the characterization at a quasi-atomic resolution of the protein folding energy landscape.
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Affiliation(s)
| | | | | | - Christian Roumestand
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (I.H.); (P.B.)
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6
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The effects of cosolutes and crowding on the kinetics of protein condensate formation based on liquid-liquid phase separation: a pressure-jump relaxation study. Sci Rep 2020; 10:17245. [PMID: 33057154 PMCID: PMC7566631 DOI: 10.1038/s41598-020-74271-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
Biomolecular assembly processes based on liquid-liquid phase separation (LLPS) are ubiquitous in the biological cell. To fully understand the role of LLPS in biological self-assembly, it is necessary to characterize also their kinetics of formation and dissolution. Here, we introduce the pressure-jump relaxation technique in concert with UV/Vis and FTIR spectroscopy as well as light microscopy to characterize the evolution of LLPS formation and dissolution in a time-dependent manner. As a model system undergoing LLPS we used the globular eye-lens protein γD-crystallin. As cosolutes and macromolecular crowding are known to affect the stability and dynamics of biomolecular condensates in cellulo, we extended our kinetic study by addressing also the impact of urea, the deep-sea osmolyte trimethylamine-N-oxide (TMAO) and a crowding agent on the transformation kinetics of the LLPS system. As a prerequisite for the kinetic studies, the phase diagram of γD-crystallin at the different solution conditions also had to be determined. The formation of the droplet phase was found to be a very rapid process and can be switched on and off on the 1-4 s timescale. Theoretical treatment using the Johnson-Mehl-Avrami-Kolmogorov model indicates that the LLPS proceeds via a diffusion-limited nucleation and growth mechanism at subcritical protein concentrations, a scenario which is also expected to prevail within biologically relevant crowded systems. Compared to the marked effect the cosolutes take on the stability of the LLPS region, their effect at biologically relevant concentrations on the phase transformation kinetics is very small, which might be a particular advantage in the cellular context, as a fast switching capability of the transition should not be compromised by the presence of cellular cosolutes.
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7
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Roche J, Royer CA. Lessons from pressure denaturation of proteins. J R Soc Interface 2018; 15:rsif.2018.0244. [PMID: 30282759 DOI: 10.1098/rsif.2018.0244] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022] Open
Abstract
Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.
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Affiliation(s)
- Julien Roche
- Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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8
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Caro JA, Wand AJ. Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology. Methods 2018; 148:67-80. [PMID: 29964175 PMCID: PMC6133745 DOI: 10.1016/j.ymeth.2018.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 01/15/2023] Open
Abstract
Pressure and temperature are the two fundamental variables of thermodynamics. Temperature and chemical perturbation are central experimental tools for the exploration of macromolecular structure and dynamics. Though it has long been recognized that hydrostatic pressure offers a complementary and often unique view of macromolecular structure, stability and dynamics, it has not been employed nearly as much. For solution NMR applications the limited use of high-pressure is undoubtedly traced to difficulties of employing pressure in the context of modern multinuclear and multidimensional NMR. Limitations in pressure tolerant NMR sample cells have been overcome and enable detailed studies of macromolecular energy landscapes, hydration, dynamics and function. Here we review the practical considerations for studies of biological macromolecules at elevated pressure, with a particular emphasis on applications in protein biophysics and structural biology.
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Affiliation(s)
- José A Caro
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States.
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9
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Abstract
This year, 2014, marks the 100th anniversary of the first publication reporting the denaturation of proteins by high hydrostatic pressure (Bridgman 1914). Since that time a large and recently increasing number of studies of pressure effects on protein stability have been published, yet the mechanism for the action of pressure on proteins remains subject to considerable debate. This review will present an overview from this author's perspective of where this debate stands today.
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Affiliation(s)
- Catherine A Royer
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,
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10
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Dias CL, Chan HS. Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J Phys Chem B 2014; 118:7488-7509. [DOI: 10.1021/jp501935f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cristiano L. Dias
- Department
of Physics, New Jersey Institute of Technology, University Heights, Tiernan Hall, Room 463, Newark, New Jersey 07102, United States
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| | - Hue Sun Chan
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
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11
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Abstract
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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12
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Akasaka K, Kitahara R, Kamatari YO. Exploring the folding energy landscape with pressure. Arch Biochem Biophys 2013; 531:110-5. [DOI: 10.1016/j.abb.2012.11.016] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 11/29/2022]
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13
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Fourme R, Girard E, Akasaka K. High-pressure macromolecular crystallography and NMR: status, achievements and prospects. Curr Opin Struct Biol 2012; 22:636-42. [PMID: 22959123 DOI: 10.1016/j.sbi.2012.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/08/2012] [Accepted: 07/09/2012] [Indexed: 10/27/2022]
Abstract
Biomacromolecules are thermodynamic entities that exist in general as an equilibrium mixture of the basic folded state and various higher-energy substates including all functionally relevant ones. Under physiological conditions, however, the higher-energy substates are usually undetectable on spectroscopy, as their equilibrium populations are extremely low. Hydrostatic pressure gives a general solution to this problem. As proteins generally have smaller partial molar volumes in higher-energy states than in the basic folded state, pressure can shift the equilibrium toward the former substantially, and allows their direct detection and analysis with X-ray crystallography or NMR spectroscopy at elevated pressures. These techniques are now mature, and their status and selected applications are presented with future prospects.
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Affiliation(s)
- Roger Fourme
- Synchrotron Soleil, BP48 Saint Aubin, 91192 Gif sur Yvette, France.
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14
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Kremer W, Arnold M, Munte CE, Hartl R, Erlach MB, Koehler J, Meier A, Kalbitzer HR. Pulsed pressure perturbations, an extra dimension in NMR spectroscopy of proteins. J Am Chem Soc 2011; 133:13646-51. [PMID: 21774550 DOI: 10.1021/ja2050698] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The introduction of multidimensional NMR spectroscopy was a breakthrough in biological NMR methodology because it allowed the unequivocal correlation of different spin states of the system. The introduction of large pressure perturbations in the corresponding radio frequency (RF) pulse sequences adds an extra structural dimension into these experiments. We have developed a microprocessor-controlled pressure jump unit that is able to introduce fast, strong pressure changes at any point in the pulse sequences. Repetitive pressure changes of 80 MPa in the sample tube are thus feasible in less than 30 ms. Two general forms of these experiments are proposed here, the pressure perturbation transient state spectroscopy (PPTSS) and the pressure perturbation state correlation spectroscopy (PPSCS). PPTSS can be used to measure the rate constants and the activation energies and activation volumes for the transition between different conformational states including the folded and unfolded state of proteins, for polymerization-depolymerization processes, and for ligand binding at atomic resolution. PPSCS spectroscopy correlates the NMR parameters of different pressure-induced states of the system, thus allowing the measurement of properties of a given pressure induced state such as a folding intermediate in a different state, for example, the folded state. Selected examples for PPTSS and PPSCS spectroscopy are presented in this Article.
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Affiliation(s)
- Werner Kremer
- Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstrasse 31, D-93047 Regensburg, Germany
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15
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Rouget JB, Aksel T, Roche J, Saldana JL, Garcia AE, Barrick D, Royer CA. Size and sequence and the volume change of protein folding. J Am Chem Soc 2011; 133:6020-7. [PMID: 21446709 PMCID: PMC3151578 DOI: 10.1021/ja200228w] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The application of hydrostatic pressure generally leads to protein unfolding, implying, in accordance with Le Chatelier's principle, that the unfolded state has a smaller molar volume than the folded state. However, the origin of the volume change upon unfolding, ΔV(u), has yet to be determined. We have examined systematically the effects of protein size and sequence on the value of ΔV(u) using as a model system a series of deletion variants of the ankyrin repeat domain of the Notch receptor. The results provide strong evidence in support of the notion that the major contributing factor to pressure effects on proteins is their imperfect internal packing in the folded state. These packing defects appear to be specifically localized in the 3D structure, in contrast to the uniformly distributed effects of temperature and denaturants that depend upon hydration of exposed surface area upon unfolding. Given its local nature, the extent to which pressure globally affects protein structure can inform on the degree of cooperativity and long-range coupling intrinsic to the folded state. We also show that the energetics of the protein's conformations can significantly modulate their volumetric properties, providing further insight into protein stability.
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Affiliation(s)
- Jean-Baptiste Rouget
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR5048, Université Montpellier 1&2, Montpellier France
| | - Tural Aksel
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD USA
| | - Julien Roche
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR5048, Université Montpellier 1&2, Montpellier France
- Department of Physics and Applied Physics and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY USA
| | - Jean-Louis Saldana
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR5048, Université Montpellier 1&2, Montpellier France
| | - Angel E. Garcia
- Department of Physics and Applied Physics and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY USA
| | - Doug Barrick
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore MD USA
| | - Catherine A. Royer
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR5048, Université Montpellier 1&2, Montpellier France
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Heuert U, Krumova M, Hempel G, Schiewek M, Blume A. NMR probe for pressure-jump experiments up to 250 bars and 3 ms jump time. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:105102. [PMID: 21034114 DOI: 10.1063/1.3481164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We describe the design and performance of a pressure-jump instrument for time-resolved NMR experiments. Initial pressure of up to 250 bars can be produced by means of a HPLC pump and distilled water as a pressure-transmitting liquid. Fast pressure release at a time resolution of 3 ms is achieved using a fast acting valve driven by a piezostack close to the sample chamber. The pressure-jump cell is placed together with two valves in an especially designed NMR probe, which can be used in standard spectrometers with wide-bore magnets. All functions of the instrument are personal computer controlled. The equipment is designed for investigations on systems of biological interest, especially lipid-water dispersions. A theoretical consideration implies that probably the limited speed of valve opening determines the lower boundary of the jump time. The performance is illustrated by time-resolved NMR spectra across the phase transition of a phospholipid-water dispersion after a pressure jump from 100 bars to atmospheric pressure.
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Affiliation(s)
- U Heuert
- Insitut für Physik, Martin-Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle/Saale, Germany
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17
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Rouget JB, Schroer MA, Jeworrek C, Pühse M, Saldana JL, Bessin Y, Tolan M, Barrick D, Winter R, Royer CA. Unique features of the folding landscape of a repeat protein revealed by pressure perturbation. Biophys J 2010; 98:2712-21. [PMID: 20513416 DOI: 10.1016/j.bpj.2010.02.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/14/2010] [Accepted: 02/26/2010] [Indexed: 11/29/2022] Open
Abstract
The volumetric properties of proteins yield information about the changes in packing and hydration between various states along the folding reaction coordinate and are also intimately linked to the energetics and dynamics of these conformations. These volumetric characteristics can be accessed via pressure perturbation methods. In this work, we report high-pressure unfolding studies of the ankyrin domain of the Notch receptor (Nank1-7) using fluorescence, small-angle x-ray scattering, and Fourier transform infrared spectroscopy. Both equilibrium and pressure-jump kinetic fluorescence experiments were consistent with a simple two-state folding/unfolding transition under pressure, with a rather small volume change for unfolding compared to proteins of similar molecular weight. High-pressure fluorescence, Fourier transform infrared spectroscopy, and small-angle x-ray scattering measurements revealed that increasing urea over a very small range leads to a more expanded pressure unfolded state with a significant decrease in helical content. These observations underscore the conformational diversity of the unfolded-state basin. The temperature dependence of pressure-jump fluorescence relaxation measurements demonstrated that at low temperatures, the folding transition state ensemble (TSE) lies close in volume to the folded state, consistent with significant dehydration at the barrier. In contrast, the thermal expansivity of the TSE was found to be equivalent to that of the unfolded state, indicating that the interactions that constrain the folded-state thermal expansivity have not been established at the folding barrier. This behavior reveals a high degree of plasticity of the TSE of Nank1-7.
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Affiliation(s)
- Jean-Baptiste Rouget
- Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
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18
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Erlach MB, Munte CE, Kremer W, Hartl R, Rochelt D, Niesner D, Kalbitzer HR. Ceramic cells for high pressure NMR spectroscopy of proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 204:196-199. [PMID: 20359919 DOI: 10.1016/j.jmr.2010.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/09/2010] [Accepted: 02/15/2010] [Indexed: 05/29/2023]
Abstract
Application of high pressure to biological macromolecules can be used to find new structural states with a smaller specific volume of the system. High pressure NMR spectroscopy is a most promising analytical tool for the study of these states at atomic resolution. High pressure quartz cells are difficult to handle, high quality sapphire high pressure cells are difficult to obtain commercially. In this work, we describe the use of high pressure ceramic cells produced from yttrium stabilized ZrO(2) that are capable of resisting pressures up to 200 MPa. Since the new cells should also be usable in the easily damageable cryoprobes a completely new autoclave for these cells has been constructed, including an improved method for pressure transmission, an integrated safety jacket, a displacement body, and a fast self-closing emergency valve.
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Affiliation(s)
- Markus Beck Erlach
- Department of Biophysics, University of Regensburg, Universitätsstrasse 31, D-93040 Regensburg, Germany
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19
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Bridges MD, Hideg K, Hubbell WL. Resolving Conformational and Rotameric Exchange in Spin-Labeled Proteins Using Saturation Recovery EPR. APPLIED MAGNETIC RESONANCE 2010; 37:363. [PMID: 20157634 PMCID: PMC2821067 DOI: 10.1007/s00723-009-0079-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The function of many proteins involves equilibria between conformational substates, and to elucidate mechanisms of function it is essential to have experimental tools to detect the presence of conformational substates and to determine the time scale of exchange between them. Site-directed spin labeling (SDSL) has the potential to serve this purpose. In proteins containing a nitroxide side chain (R1), multicomponent electron paramagnetic resonance (EPR) spectra can arise either from equilibria involving different conformational substates or rotamers of R1. To employ SDSL to uniquely identify conformational equilibria, it is thus essential to distinguish between these origins of multicomponent spectra. Here we show that this is possible based on the time scale for exchange of the nitroxide between distinct environments that give rise to multicomponent EPR spectra; rotamer exchange for R1 lies in the ≈0.1-1 μs range, while conformational exchange is at least an order of magnitude slower. The time scales of exchange events are determined by saturation recovery EPR, and in favorable cases, the exchange rate constants between substates with lifetimes of approximately 1-70 μs can be estimated by the approach.
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Affiliation(s)
- Michael D. Bridges
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-7008, USA
| | - Kálmán Hideg
- Institute of Organic and Medical Chemistry, University of Pécs, Szigeti str. 12, 7624 Pecs, Hungary
| | - Wayne L. Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-7008, USA
- Jules Stein Eye Institute, UCLA School of Medicine, Los Angeles, CA 90095-7008, USA
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20
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Abstract
Troponin is the singular Ca(2+)-sensitive protein in the contraction of vertebrate striated muscles. Troponin C (TnC), the Ca(2+)-binding subunit of the troponin complex, has two distinct domains, C and N, which have different properties despite their extensive structural homology. In this work, we analyzed the thermodynamic stability of the isolated N-domain of TnC using a fluorescent mutant with Phe 29 replaced by Trp (F29W/N-domain, residues 1-90). The complete unfolding of the N-domain of TnC in the absence or presence of Ca(2+) was achieved by combining high hydrostatic pressure and urea, a maneuver that allowed us to calculate the thermodynamic parameters (DeltaV and DeltaG(atm)). In this study, we propose that part of the affinity for Ca(2+) is contributed by the free-energy change of folding of the N- and C-domains that takes place when Ca(2+) binds. The importance of the free-energy change for the structural and regulatory functions of the TnC isolated domains was evaluated. Our results shed light on how the coupling between folding and ion binding contributes to the fine adjustment of the affinity for Ca(2+) in EF-hand proteins, which is crucial to function.
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21
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Rocha CB, Suarez MC, Yu A, Ballard L, Sorenson MM, Foguel D, Silva JL. Volume and free energy of folding for troponin C C-domain: linkage to ion binding and N-domain interaction. Biochemistry 2008; 47:5047-58. [PMID: 18393534 DOI: 10.1021/bi702058t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Troponin C (TnC) is an 18-kDa acidic protein of the EF-hand family that serves as the trigger for muscle contraction. In this study, we investigated the thermodynamic stability of the C-domain of TnC in all its occupancy states (apo, Mg (2+)-, and Ca (2+)-bound states) using a fluorescent mutant with Phe 105 replaced by Trp (F105W/C-domain, residues 88-162) and (1)H NMR spectroscopy. High hydrostatic pressure was employed as a perturbing agent, in combination with urea or without it. On the basis of changes in Trp emission, the C-domain apo state was denatured by pressure (in the range of 1-1000 bar) in the absence of urea. The fluorescence data were corroborated by following the changes in the (1)H NMR signal of Histidine 128. Addition of Ca (2+) or Mg (2+) increased the C-domain stability so that complete denaturation was attained only by the combined use of high hydrostatic pressure and either 7-8 M or 1.5-2 M urea, respectively. The (1)H NMR spectra in the presence of Ca (2+) was typical of a highly structured protein and allowed us to follow the changes in the local environment of several amino-acid residues as a function of pressure at 4 M Urea. Different residues presented different volume changes, but those that are in the hydrophobic core portrayed values very similar to that obtained for tryptophan 105 as measured by fluorescence, indicating that it is indeed a good probe for the overall tertiary structure. From these experiments, we calculated the thermodynamic parameters (Delta G degrees atm and Delta V) that govern the folding of the C-domain in all its possible physiological states and constructed a thermodynamic cycle. Furthermore, a comparison of the volume and free-energy changes of folding of isolated C-domain with those of intact TnC (F105W) revealed that the N-domain has little effect on the structure of the C-domain, even in the presence of Ca (2+). The volume and free-energy diagrams reveal a landscape of different conformations from the less structured, denatured apo form to the highly structured, Ca (2+)-bound form. The large change in folding free energy of the C-domain that takes place when Ca (2+) binds may explain the much higher Ca (2+) affinity of sites III and IV, 2 orders of magnitude higher than the affinity of sites I and II.
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Affiliation(s)
- Cristiane Barbosa Rocha
- Instituto de Bioquímica Médica, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro 21941-590, Rio de Janeiro, RJ, Brazil
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22
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Mitra L, Hata K, Kono R, Maeno A, Isom D, Rouget JB, Winter R, Akasaka K, García-Moreno B, Royer CA. Vi -Value Analysis: A Pressure-Based Method for Mapping the Folding Transition State Ensemble of Proteins. J Am Chem Soc 2007; 129:14108-9. [DOI: 10.1021/ja073576y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lally Mitra
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Kazumi Hata
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Ryohei Kono
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Akihiro Maeno
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Daniel Isom
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Jean-Baptiste Rouget
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Roland Winter
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Kazuyuki Akasaka
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Bertrand García-Moreno
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
| | - Catherine A. Royer
- Department of Chemistry, Physical Chemistry I, Otto-Hahn Str. 6, University of Dortmund, D-44227 Dortmund, Germany, Department of Biotechnological Science, School of Biology-Oriented Science & Technology, Kinki University, Kinokawa, Wakayama, 649-6493 Japan, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, CNRS, UMR5048, Centre de Biochimie Structurale, Montpellier F-34090, France, and INSERM, U554, Montpellier F-34090, France
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23
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Royer CA. The nature of the transition state ensemble and the mechanisms of protein folding: a review. Arch Biochem Biophys 2007; 469:34-45. [PMID: 17923105 DOI: 10.1016/j.abb.2007.08.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/28/2007] [Accepted: 08/01/2007] [Indexed: 11/30/2022]
Affiliation(s)
- Catherine A Royer
- Institut National de la Santé et de la Recherche Médicale, Unité 554, Montpellier, France.
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24
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Ravel P, Kister G, Malliavin TE, Delsuc MA. A general algorithm for peak-tracking in multi-dimensional NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2007; 37:265-75. [PMID: 17294057 DOI: 10.1007/s10858-006-9136-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 12/07/2006] [Accepted: 12/12/2006] [Indexed: 05/13/2023]
Abstract
We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).
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Affiliation(s)
- P Ravel
- CNRS UMR5048, Centre de Biochimie Structurale, 34090, Montpellier, France.
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25
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Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM. Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. J Mol Biol 2007; 367:752-63. [PMID: 17292912 PMCID: PMC1853337 DOI: 10.1016/j.jmb.2006.12.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 12/07/2006] [Accepted: 12/10/2006] [Indexed: 01/07/2023]
Abstract
Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded states. To gain a more complete picture requires that we perturb these structures in a continuous manner, something mutagenesis cannot achieve. With high pressure crystallographic methods it is now possible to explore the detailed properties of proteins while continuously varying thermodynamic parameters. Here, we detail the structural response of the cavity-containing mutant L99A of T4 lysozyme, as well as its pseudo wild-type (WT*) counterpart, to hydrostatic pressure. Surprisingly, the cavity has almost no effect on the pressure response: virtually the same changes are observed in WT* as in L99A under pressure. The cavity is most rigid, while other regions deform substantially. This implies that while some residues may increase the thermodynamic stability of a protein, they may also be structurally irrelevant. As recently shown, the cavity fills with water at pressures above 100 MPa while retaining its overall size. The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone.
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Affiliation(s)
- Marcus D Collins
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
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26
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Noguchi M, Ropars V, Roumestand C, Suizu F. Proto‐oncogene TCL1: more than just a coactivator for Akt. FASEB J 2007; 21:2273-84. [PMID: 17360849 DOI: 10.1096/fj.06-7684com] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serine threonine kinase Akt, also called PKB (protein kinase B), plays a central role in regulating intracellular survival. Deregulation of this Akt signaling pathway underlies various human neoplastic diseases. Recently, the proto-oncogene TCL1 (T cell leukemia 1), with a previously unknown physiological function, was shown to interact with the Akt pleckstrin homology domain, enhancing Akt kinase activity; hence, it functions as an Akt kinase coactivator. In contrast to pathological conditions in which the TCL1 gene is highly activated in various human neoplasmic diseases, the physiological expression of TCL1 is tightly limited to early developmental cells as well as various developmental stages of immune cells. The NBRE (nerve growth factor-responsive element) of the proximal TCL1 promoter sequences can regulate the restricted physiological expression of TCL1 in a negative feedback mechanism. Further, based on the NMR structural studies of Akt-TCL1 protein complexes, an inhibitory peptide, "Akt-in," consisting of the betaA strand of TCL1, has been identified and has therapeutic potential. This review article summarizes and discusses recent advances in the understanding of TCL1-Akt functional interaction in order to clarify the biological action of the proto-oncogene TCL1 family and the development avenues for a suppressive drug specific for Akt, a core intracellular survival regulator.
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Affiliation(s)
- Masayuki Noguchi
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
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27
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Ropars V, Bouguet-Bonnet S, Auguin D, Barthe P, Canet D, Roumestand C. Unraveling protein dynamics through fast spectral density mapping. JOURNAL OF BIOMOLECULAR NMR 2007; 37:159-77. [PMID: 17237978 DOI: 10.1007/s10858-006-9091-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 09/22/2006] [Indexed: 05/13/2023]
Abstract
Spectral density mapping at multiple NMR field strengths is probably the best method to describe the dynamical behavior of a protein in solution through the analysis of 15N heteronuclear relaxation parameters. Nevertheless, such analyses are scarcely reported in the literature, probably because this method is excessively demanding in spectrometer measuring time. Indeed, when using n different magnetic fields and assuming the validity of the high frequency approximation, the discrete sampling of the spectral density function with 2n + 1 points needs the measurement of 3n 15N heteronuclear relaxation measurements (n R1, n R2, and n15N{1H}NOEs). Based on further approximations, we proposed a new strategy that allows us to describe the spectral density with n + 2 points, with the measurement of a total of n + 2 heteronuclear relaxation parameters. Applied to the dynamics analysis of the protein p13( MTCP1) at three different NMR fields, this approach allowed us to divide by nearly a factor of two the total measuring time, without altering further results obtained by the "model free" analysis of the resulting spectral densities. Furthermore, simulations have shown that this strategy remains applicable to any low isotropically tumbling protein (tauc>3 ns), and is valid for the types of motion generally envisaged for proteins.
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Affiliation(s)
- Virginie Ropars
- Centre de Biochimie Structurale, UMR UM1/5048 CNRS/554 INSERM, 29 rue de Navacelles, 34090, Montpellier Cedex, France
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28
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Brun L, Isom DG, Velu P, García-Moreno B, Royer CA. Hydration of the folding transition state ensemble of a protein. Biochemistry 2006; 45:3473-80. [PMID: 16533028 PMCID: PMC4442614 DOI: 10.1021/bi052638z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complete description of the mechanisms of protein folding requires knowledge of the structural and physical character of the folding transition state ensembles (TSEs). A key question concerning the role of hydration of the hydrophobic core in determining folding mechanisms remains. To address this, we probed the state of hydration of the TSE of staphylococcal nuclease (SNase) by examining the fluorescence-detected pressure-jump relaxation behavior of six SNase variants in which a residue in the hydrophobic core, Val-66, was replaced with polar or ionizable residues (Lys, Arg, His, Asp, Glu, and Asn). Because of a large positive activation volume for folding, the major effect of pressure on the wild-type protein is to decrease the folding rate. By the time wild-type SNase reaches the folding transition state, most water has already been expelled from its hydrophobic core. In contrast, the major effect of pressure on the variant proteins is an increase in the unfolding rate due to a large negative activation volume for unfolding. This results from a significant increase in the level of hydration of the TSE when an internal ionizable group is present. These data confirm that the role of water in the folding reaction can differ from protein to protein and that even a single substitution in a critical position can modulate significantly the properties of the TSE.
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29
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Affiliation(s)
- Kazuyuki Akasaka
- School of biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa-shi, Wakayama 649-6493, Japan.
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30
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Balny C. What lies in the future of high-pressure bioscience? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:632-9. [PMID: 16275135 DOI: 10.1016/j.bbapap.2005.10.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Revised: 09/22/2005] [Accepted: 10/06/2005] [Indexed: 11/28/2022]
Abstract
Without being comprehensive in this mini-review, I will address perspectives, some speculative, for the development and use of high pressure to explore biochemical phenomena. This will be illustrated with several examples.
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Affiliation(s)
- Claude Balny
- INSERM U710, IFR 122, Université Montpellier 2, Place Eugène Bataillon, CC105, 34095 Montpellier, Cédex 5, France.
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31
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Li H, Akasaka K. Conformational fluctuations of proteins revealed by variable pressure NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:331-45. [PMID: 16448868 DOI: 10.1016/j.bbapap.2005.12.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 12/12/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022]
Abstract
With the high-resolution variable-pressure NMR spectroscopy, one can study conformational fluctuations of proteins in a much wider conformational space than hitherto explored by NMR and other spectroscopic techniques. This is because a protein in solution generally exists as a dynamic mixture of conformers mutually differing in partial molar volume, and pressure can select the population of a conformer according to its relative volume. In this review, we describe how variable-pressure NMR can be used to probe conformational fluctuations of proteins in a wide conformational space from the folded to the fully unfolded structures, with actual examples. Furthermore, the newly emerging technique "NMR snapshots" expresses amply fluctuating protein structures as changes in atomic coordinates. Finally, the concept of conformational fluctuation is extended to include intermolecular association leading to amyloidosis.
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Affiliation(s)
- Hua Li
- RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan
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32
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Torrent J, Font J, Herberhold H, Marchal S, Ribó M, Ruan K, Winter R, Vilanova M, Lange R. The use of pressure-jump relaxation kinetics to study protein folding landscapes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:489-96. [PMID: 16481228 DOI: 10.1016/j.bbapap.2006.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 12/07/2005] [Accepted: 01/03/2006] [Indexed: 10/25/2022]
Abstract
Pressure-jump induced relaxation kinetics can be used to study both protein unfolding and refolding. These processes can be initiated by upward and downward pressure-jumps of amplitudes of a few 10 to 100 MPa, with a dead-time on the order of milliseconds. In many cases, the relaxation times can be easily determined when the pressure cell is connected to a spectroscopic detection device, such as a spectrofluorimeter. Adiabatic heating or cooling can be limited by small pressure-jump amplitudes and a special design of the sample cell. Here, we discuss the application of this method to four proteins: 33-kDa and 23-kDa proteins from photo-system II, a variant of the green fluorescent protein, and a fluorescent variant of ribonuclease A. The thermodynamically predicted equivalency of upward and downward pressure-jump induced protein relaxation kinetics for typical two-state folders was observed for the 33-kDa protein, only. In contrast, the three other proteins showed significantly different kinetics for pressure-jumps in opposite directions. These results cannot be explained by sequential reaction schemes. Instead, they are in line with a more complex free energy landscape involving multiple pathways.
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Affiliation(s)
- Joan Torrent
- INSERM U710, Université Montpellier 2, CC105, Place Eugène Bataillon, 34095 Montpellier Cédex 5, France
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33
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Royer CA. Insights into the role of hydration in protein structure and stability obtained through hydrostatic pressure studies. Braz J Med Biol Res 2005; 38:1167-73. [PMID: 16082456 DOI: 10.1590/s0100-879x2005000800003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A thorough understanding of protein structure and stability requires that we elucidate the molecular basis for the effects of both temperature and pressure on protein conformational transitions. While temperature effects are relatively well understood and the change in heat capacity upon unfolding has been reasonably well parameterized, the state of understanding of pressure effects is much less advanced. Ultimately, a quantitative parameterization of the volume changes (at the basis of pressure effects) accompanying protein conformational transitions will be required. The present report introduces a qualitative hypothesis based on available model compound data for the molecular basis of volume change upon protein unfolding and its dependence on temperature.
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Affiliation(s)
- C A Royer
- Centre de Biochimie Structurale, Montpellier Cedex, France.
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34
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Tan CY, Xu CH, Wong J, Shen JR, Sakuma S, Yamamoto Y, Lange R, Balny C, Ruan KC. Pressure equilibrium and jump study on unfolding of 23-kDa protein from spinach photosystem II. Biophys J 2004; 88:1264-75. [PMID: 15531632 PMCID: PMC1305128 DOI: 10.1529/biophysj.104.050435] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pressure-induced unfolding of 23-kDa protein from spinach photosystem II has been systematically investigated at various experimental conditions. Thermodynamic equilibrium studies indicate that the protein is very sensitive to pressure. At 20 degrees C and pH 5.5, 23-kDa protein shows a reversible two-state unfolding transition under pressure with a midpoint near 160 MPa, which is much lower than most natural proteins studied to date. The free energy (DeltaG(u)) and volume change (DeltaV(u)) for the unfolding are 5.9 kcal/mol and -160 ml/mol, respectively. It was found that NaCl and sucrose significantly stabilize the protein from unfolding and the stabilization is associated not only with an increase in DeltaG(u) but also with a decrease in DeltaV(u). The pressure-jump studies of 23-kDa protein reveal a negative activation volume for unfolding (-66.2 ml/mol) and a positive activation volume for refolding (84.1 ml/mol), indicating that, in terms of system volume, the protein transition state lies between the folded and unfolded states. Examination of the temperature effect on the unfolding kinetics indicates that the thermal expansibility of the transition state and the unfolded state of 23-kDa protein are closer to each other and they are larger than that of the native state. The diverse pressure-refolding pathways of 23-kDa protein in some conditions were revealed in pressure-jump kinetics.
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Affiliation(s)
- Cui-Yan Tan
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, China
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35
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Kitahara R, Akasaka K. Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding. Proc Natl Acad Sci U S A 2003; 100:3167-72. [PMID: 12629216 PMCID: PMC152264 DOI: 10.1073/pnas.0630309100] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic detailed structural study of a transiently existing folding intermediate is severely limited because of its short life. In ubiquitin, we found that a pressure-stabilized equilibrium conformer shares a common structural feature with the proline-trapped kinetic intermediate found in a pulse-labeling (1)H(2)H exchange NMR study [Briggs, M. S. & Roder, H. (1992) Proc. Natl. Acad. Sci. USA 89, 2017-2021]. The conformer is locally unfolded in the entire segment from residues 33 to 42 and in C-terminal residues 70-76. The close structural identity of an equilibrium intermediate stabilized under pressure with a transiently observed folding intermediate is likely to be general in terms of a folding funnel common to both experiments.
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Affiliation(s)
- Ryo Kitahara
- Department of Molecular Science, Graduate School of Science and Technology, Kobe University, Rokkodai-cho, Kobe 657-8501, Japan
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Kitahara R, Kato M, Taniguchi Y. High-pressure 1H NMR study of pressure-induced structural changes in the heme environments of metcyanomyoglobins. Protein Sci 2003; 12:207-17. [PMID: 12538884 PMCID: PMC2312426 DOI: 10.1110/ps.4620103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2001] [Revised: 08/27/2002] [Accepted: 07/29/2002] [Indexed: 10/27/2022]
Abstract
The effect of pressure on the heme environment structure of sperm whale and horse heart metcyanomyoglobins was investigated up to 300 MPa by high-pressure (1)H NMR spectroscopy. Pressure-induced changes in the distances between the observed protons and the heme iron atom were estimated from changes in the dipolar shift due to the paramagnetic effect on the protons. The changes showed that the heme peripheral structure as a whole was compressed by pressure; the movements of the protons in the heme peripheral residues were in the range of +0.16 to -0.54 A/300 MPa. One-dimensional compressibilities for the protons, excluding the protons of the distal His residue, were in the range of 1.0 x 10(-4) to 6.1 x 10(-4)/MPa. The movements of the protons induced by pressure correlated well with the distance between the protons and cavities in the protein. The distal His residue (His 64) moved toward the outside of the heme pocket, but remained in the pocket even at 300 MPa. This movement was driven dominantly by a change in the dihedral angle around the C(alpha)-C(beta) rotational bond of the residue. Comparative work on horse heart metcyanomyoglobin implied that the conformational change of the His 64 imidazole ring was larger in the horse heart metcyanomyoglobin than in the sperm whale metcyanomyoglobin.
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Affiliation(s)
- Ryo Kitahara
- Department of Applied Chemistry, College of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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