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Yamasaki K, Yamasaki T, Takahashi M, Suematsu H. A mixing microfluidic chip for real-time NMR monitoring of macromolecular reaction. J Biochem 2021; 170:363-368. [PMID: 33831188 DOI: 10.1093/jb/mvab048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/02/2021] [Indexed: 11/12/2022] Open
Abstract
NMR spectroscopy permits real-time monitoring of reactions that involve changes in the spectra of reactants. MICCS (MIcro Channeled Cell for Synthesis monitoring) is a microfluidic chip for such purposes, which is used to rapidly activate reactions by mixing the reactant solutions in the chip inserted into the typical NMR tube. Although it allows monitoring of chemical reactions of small compounds, its simple mixing system dependent on diffusion in the microchannel was not suitable for macromolecules such as proteins with low diffusion rates. Here we developed a new microfluidic chip based on MICCS by incorporating a mixer of split-and-recombination type within the microchannel. We applied it to monitoring of the protein-folding reaction in a stopped-flow mode. A solution of denaturant-unfolded RNase A was injected from a syringe pump into the microchip set inside the NMR magnet and mixed with a buffer for dilution to reach the folding condition. Immediately after dilution, the reaction was initiated and detected by a series of NMR measurements that were synchronized with activation and inactivation of the pump. The process was repeated for accumulation of the data. By analyzing the change of the spectra by factor analysis, a kinetic constant of 0.57 min-1 was obtained.
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Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 3058566, Japan
| | - Tomoko Yamasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 3058566, Japan
| | - Masaharu Takahashi
- Planning Headquarters, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 3058560, Japan
| | - Hiroto Suematsu
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo, 1968558, Japan
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2
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Construction of Highly Stable Cytotoxic Nuclear-Directed Ribonucleases. Molecules 2018; 23:molecules23123273. [PMID: 30544927 PMCID: PMC6321540 DOI: 10.3390/molecules23123273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 02/01/2023] Open
Abstract
Ribonucleases are proteins whose use is promising in anticancer therapy. We have previously constructed different human pancreatic ribonuclease variants that are selectively cytotoxic for tumor cells by introducing a nuclear localization signal into their sequence. However, these modifications produced an important decrease in their stability compromising their behavior in vivo. Here, we show that we can significantly increase the thermal stability of these cytotoxic proteins by introducing additional disulfide bonds by site-directed mutagenesis. One of these variants increases its thermal stability by around 17 °C, without affecting its catalytic activity while maintaining the cytotoxic activity against tumor cells. We also show that the most stable variant is significantly more resistant to proteolysis when incubated with proteinase K or with human sera, suggesting that its half-live could be increased in vivo once administered.
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3
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Wood K, Mata JP, Garvey CJ, Wu CM, Hamilton WA, Abbeywick P, Bartlett D, Bartsch F, Baxter P, Booth N, Brown W, Christoforidis J, Clowes D, d'Adam T, Darmann F, Deura M, Harrison S, Hauser N, Horton G, Federici D, Franceschini F, Hanson P, Imamovic E, Imperia P, Jones M, Kennedy S, Kim S, Lam T, Lee WT, Lesha M, Mannicke D, Noakes T, Olsen SR, Osborn JC, Penny D, Perry M, Pullen SA, Robinson RA, Schulz JC, Xiong N, Gilbert EP. QUOKKA, the pinhole small-angle neutron scattering instrument at the OPAL Research Reactor, Australia: design, performance, operation and scientific highlights. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718002534] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
QUOKKA is a 40 m pinhole small-angle neutron scattering instrument in routine user operation at the OPAL research reactor at the Australian Nuclear Science and Technology Organisation. Operating with a neutron velocity selector enabling variable wavelength, QUOKKA has an adjustable collimation system providing source–sample distances of up to 20 m. Following the large-area sample position, a two-dimensional 1 m2position-sensitive detector measures neutrons scattered from the sample over a secondary flight path of up to 20 m. Also offering incident beam polarization and analysis capability as well as lens focusing optics, QUOKKA has been designed as a general purpose SANS instrument to conduct research across a broad range of scientific disciplines, from structural biology to magnetism. As it has recently generated its first 100 publications through serving the needs of the domestic and international user communities, it is timely to detail a description of its as-built design, performance and operation as well as its scientific highlights. Scientific examples presented here reflect the Australian context, as do the industrial applications, many combined with innovative and unique sample environments.
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4
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Krupa P, Sieradzan AK, Mozolewska MA, Li H, Liwo A, Scheraga HA. Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A. J Chem Theory Comput 2017; 13:5721-5730. [DOI: 10.1021/acs.jctc.7b00724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paweł Krupa
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Adam K. Sieradzan
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Magdalena A. Mozolewska
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Huiyu Li
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Adam Liwo
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Harold A. Scheraga
- Baker
Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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5
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Combined pressure and temperature denaturation of ribonuclease A produces alternate denatured states. Biochem Biophys Res Commun 2016; 473:834-839. [DOI: 10.1016/j.bbrc.2016.03.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 03/29/2016] [Indexed: 01/12/2023]
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6
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Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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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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8
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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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9
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Vert A, Castro J, Ruiz-Martínez S, Tubert P, Escribano D, Ribó M, Vilanova M, Benito A. Generation of new cytotoxic human ribonuclease variants directed to the nucleus. Mol Pharm 2012; 9:2894-902. [PMID: 22957849 DOI: 10.1021/mp300217b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleases are promising agents for use in anticancer therapy. Engineering a nuclear localization signal into the sequence of the human pancreatic ribonuclease has been revealed as a new strategy to endow this enzyme with cytotoxic activity against tumor cells. We previously described a cytotoxic human pancreatic ribonuclease variant, named PE5, which is able to cleave nuclear RNA, inducing the apoptosis of cancer cells and reducing the amount of P-glycoprotein in different multidrug-resistant cell lines. These results open the opportunity to use this ribonuclease in combination with other chemotherapeutics. In this work, we have investigated how to improve the properties of PE5 as an antitumor drug candidate. When attempting to develop a recombinant protein as a drug, two of the main desirable attributes are minimum immunogenicity and maximum potency. The improvements of PE5 have been designed in both senses. First, in order to reduce the potential immunogenicity of the protein, we have studied which residues mutated on PE5 can be reverted to those of the wild-type human pancreatic ribonuclease sequence without affecting its cytotoxicity. Second, we have investigated the effect of introducing an additional nuclear localization signal at different sites of PE5 in an effort to obtain a more cytotoxic enzyme. We show that the nuclear localization signal location is critical for the cytotoxicity. One of these variants, named NLSPE5, presents about a 10-fold increase in cytotoxicity respective to PE5. This variant induces apoptosis and kills the cells using the same mechanism as PE5.
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Affiliation(s)
- Anna Vert
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, M. Aurélia Campmany 69, Girona, Spain
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10
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Sanfeld A, Sefiane K, Steinchen A. Reactions of dipolar bio-molecules in nano-capsules--example of folding-unfolding process. Adv Colloid Interface Sci 2011; 169:26-39. [PMID: 21867984 DOI: 10.1016/j.cis.2011.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 07/22/2011] [Accepted: 07/24/2011] [Indexed: 11/29/2022]
Abstract
The confinement of chemical reactions in nano-capsules can lead to a dramatic effect on the equilibrium constant of these latter. Indeed, capillary effects due to the curvature and surface energy of nano-capsules can alter in a noticeable way the evolution of reactions occurring within. Nano-encapsulation of bio-materials has attracted lately wide interest from the scientific community because of the great potential of its applications in biomedical areas and targeted therapies. The present paper focuses one's attention on alterations of conformation mechanisms due to extremely confining and interacting solvated dipolar macromolecules at their isoelectric point. As a specific example studied here, the folding-unfolding reaction of proteins (particularly RNase A and creatine kinase CK) is drastically changed when encapsulated in solid inorganic hollow nano-capsules. The effects demonstrated in this work can be extended to a wide variety of nano-encapsulation situations. The design and sizing of nano-capsules can even make use of the effects shown in the present study to achieve better and more effective encapsulation.
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Affiliation(s)
- A Sanfeld
- ISM2-AD2M, UMR 6263, Universitė Paul Cezanne, Bd Escadrille Normandie Niemen, 13397, Marseille Cedex 20, France
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11
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Steinchen A, Sefiane K, Sanfeld A. Nano-encapsulation as high pressure devices for folding–unfolding proteins. J Colloid Interface Sci 2011; 355:509-11. [DOI: 10.1016/j.jcis.2010.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 11/25/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
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12
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Grigera JR, McCarthy AN. The behavior of the hydrophobic effect under pressure and protein denaturation. Biophys J 2010; 98:1626-31. [PMID: 20409483 DOI: 10.1016/j.bpj.2009.12.4298] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2009] [Revised: 11/18/2009] [Accepted: 12/07/2009] [Indexed: 11/25/2022] Open
Abstract
It is well known that proteins denature under high pressure. The mechanism that underlies such a process is still not clearly understood, however, giving way to controversial interpretations. Using molecular dynamics simulation on systems that may be regarded experimentally as limiting examples of the effect of high pressure on globular proteins, such as lysozyme and apomyoglobin, we have effectively reproduced such similarities and differences in behavior as are interpreted from experiment. From the analysis of such data, we explain the experimental evidence at hand through the effect of pressure on the change of water structure, and hence the weakening of the hydrophobic effect that is known to be the main driving force in protein folding.
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Affiliation(s)
- J Raúl Grigera
- Institute of Physics of Fluids and Biological Systems, (La Plata UNLP-CONICET) 59-789, B1900BTE, La Plata, Argentina.
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13
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Kurpiewska K, Font J, Ribó M, Vilanova M, Lewiński K. X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability. Proteins 2010; 77:658-69. [PMID: 19544568 DOI: 10.1002/prot.22480] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule.
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Affiliation(s)
- Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, Kraków 30-060, Poland
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14
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Fast JL, Cordes AA, Carpenter JF, Randolph TW. Physical instability of a therapeutic Fc fusion protein: domain contributions to conformational and colloidal stability. Biochemistry 2010; 48:11724-36. [PMID: 19899812 DOI: 10.1021/bi900853v] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein therapeutics made up of artificially combined proteins or protein domains, so-called fusion proteins, are a novel and growing class of biopharmaceuticals. We have studied abatacept (Orencia), a fusion protein that is constructed of a modified IgG Fc domain and the soluble part of the T-cell receptor CTLA-4. In accelerated degradation studies conducted at 40 degrees C, a pH shift from 7.5 to 6.0 yields significantly faster aggregation kinetics, as measured by size-exclusion chromatography. To understand how the fusion domains and their interactions contribute to this result, we considered aggregation in light of the modified Lumry-Eyring reaction pathway. Protein conformational stabilities against chaotropes and temperature were measured. The structural consequences of these perturbations were observed by a variety of experimental techniques, including differential scanning calorimetry, circular dichroism, and intrinsic fluorescence. Abatacept's colloidal stability was studied by measuring zeta potentials and osmotic second virial coefficients, as well as by modeling electrostatic potentials on the protein's surface. The domains of abatacept exhibit different conformational stabilities that are highly pH dependent, whereas abatacept was weakly colloidally unstable at pH 6 or 7.5. These results are ascribed to conformational instability of the CTLA-4 and C(H)2 domains, which unfold to form a molten globule-like structure that is aggregation-prone. We suggest the instability against aggregation is determined by the least stable domains.
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Affiliation(s)
- Jonas L Fast
- Department of Chemical and Biological Engineering, Center for Pharmaceutical Biotechnology, University of Colorado, Boulder, Colorado 80309, USA.
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15
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Vilà R, Benito A, Ribó M, Vilanova M. Mapping the stability clusters in bovine pancreatic ribonuclease A. Biopolymers 2010; 91:1038-47. [PMID: 19373927 DOI: 10.1002/bip.21204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the present work, we have thermodynamically characterized the thermally induced unfolding of 20 variants of bovine pancreatic ribonuclease A (RNase A) to experimentally describe the residues and the regions that are critical for the stability of the enzyme. The achieved results, complemented with previous studies by our group, allowed us to define the significance of the two hydrophobic nuclei present in the RNase A structure, as well as the contribution of the participating residues within each nucleus, to the global enzyme stability. We propose a structural model for the major and the minor hydrophobic nuclei of RNase A. The major nucleus is composite and located in the cavity delimited by alpha-helices 1 and 3, and the beta-sheet that is formed by strands 2, 3, 5, and 6. It consists of a central tight packed part constituted by residues Phe8, Met13, Val54, Val57, Ile106, Val108, and Phe120. This central part is surrounded by a layer formed by residues Val63, Tyr73, Met79, Ile107, Val116, and Val118. The minor nucleus, although less complex, is also constituted by a tight packing that involves the side chains of residues Tyr25, Met29, Met30, Leu35, Phe46, and Tyr97, which fill the cavity that originates the beta-sheet formed by beta-strands 1, 4, and 5 together with alpha-helix2.
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Affiliation(s)
- Roger Vilà
- Departament de Biologia, Universitat de Girona, Campus de Montilivi s/n 17071 Girona, Spain
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16
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Scirè A, Pedone E, Ausili A, Saviano M, Baldassarre M, Bertoli E, Bartolucci S, Tanfani F. High hydrostatic pressure-induced conformational changes in protein disulfide oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. A Fourier-transform infrared spectroscopic study. MOLECULAR BIOSYSTEMS 2010; 6:2015-22. [DOI: 10.1039/c005138a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Marchal S, Staiano M, Marabotti A, Vitale A, Varriale A, Lange R, D'Auria S. Pressure effects on the structure and stability of the hyperthermophilic trehalose/maltose-binding protein from Thermococcus litoralis. J Phys Chem B 2009; 113:12804-8. [PMID: 19711955 DOI: 10.1021/jp904973y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this work, we investigated the effect of pressure on the structure and stability of the recombinant D-trehalose/D-maltose-binding protein isolated from the hyperthermophilic archaeon Thermococcus litoralis (TMBP). The spectroscopic results obtained both in the absence and in the presence of maltose or trehalose revealed that the TMBP-Mal complex exhibits a larger structural stability under high pressure values than TMBP-Tre complex. In addition, the results also pointed out that pressure induces reversible denaturation transitions of the protein structure. By combining the fluorescence results obtained with 8-anilino-1-naphtalene sulfonate as extrinsic probe and the intrinsic indolic fluorescence of TMBP, it is evident that the protein structural changes above 400 MPa that involve the exposure to the solvent of a large portion of the hydrophobic protein domains are preceded by a partially unfolded protein structural state. The spectroscopic results have been interpreted and discussed by taking into account the X-ray structure of the protein and, in particular, the interactions of maltose and trehalose within the three-dimensional structure of TMBP.
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Affiliation(s)
- Stephane Marchal
- INSERM, U710, University Montpellier 2, Montpellier, F-34095, France
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18
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Marchal S, Font J, Ribó M, Vilanova M, Phillips RS, Lange R, Torrent J. Asymmetric kinetics of protein structural changes. Acc Chem Res 2009; 42:778-87. [PMID: 19378977 DOI: 10.1021/ar800266r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermodynamic and kinetic understanding of structural transformations in proteins is critical to new developments in medicine and biotechnology. These fields often require the design of mechanism-based modulators of protein function. Researchers increasingly consider these structural changes-such as folding/unfolding or shuttling between active and inactive states-within the energy landscape concept that supposes a high-dimensional, rugged conformational surface. The unevenness, or asperity, of this conformational surface results from energetic barriers and kinetic traps. However, for a large number of protein reactions, such as reversible folding/unfolding, the literature only reports simple two-state transitions, which calls into question the use of a more complex energy landscape model. The question is: are these reactions really that simple, or are we misled by a biased experimental approach? In this Account, we argue in favor of the latter possibility. Indeed, the frequently employed temperature-jump method only allows recording protein structure changes in the heating direction. Under those conditions, it might not be possible to detect other kinetic pathways that could have been taken in the cooling direction. Recently, however, we have developed bidirectional pressure- and temperature-jump methods, which can offer new insights. Here, we show the potential of these methods both for studying protein folding/unfolding reactions, taking ribonuclease A as model, and for studying functionally relevant protein conformational changes, using the open/closed allosteric transition of tryptophan synthase. For example, the heating and cooling temperature-jump induced kinetics involved in the folding/unfolding conformational surface of ribonuclease A is illustrated above. In both of our model systems, the kinetic transition states of several reaction steps were path-dependent, i.e. the rates and thermodynamic activation parameters depend on the direction of the applied pressure and temperature perturbation. This asymmetry suggests that proteins cope with external stress by adapting their structure to form different ensembles of conformational substates. These states are distinguished by their activation enthalpy and entropy barriers, which can be strongly negative in the folding direction. Based on our analysis of activation compressibility and heat capacity, hydration and packing defects of the kinetic transition states are also very important for determining the reaction path. We expect that a more generalized use of this experimental approach should allow researchers to obtain greater insight into the mechanisms of physiologically relevant protein structural changes.
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Affiliation(s)
- Stéphane Marchal
- INSERM, U710, F-34095 Montpellier, France
- Université Montpellier 2, F-34095 Montpellier, France
- EPHE, 75007 Paris, France
| | - Josep Font
- School of Molecular and Microbial Biosciences, University of Sydney, NSW, 2006 Australia
| | - Marc Ribó
- Laboratori d’Enginyeria de Proteïnes, Dept. de Biologia, Fac. de Ciències, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| | - Maria Vilanova
- Laboratori d’Enginyeria de Proteïnes, Dept. de Biologia, Fac. de Ciències, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| | | | - Reinhard Lange
- INSERM, U710, F-34095 Montpellier, France
- Université Montpellier 2, F-34095 Montpellier, France
- EPHE, 75007 Paris, France
| | - Joan Torrent
- INSERM, U710, F-34095 Montpellier, France
- Université Montpellier 2, F-34095 Montpellier, France
- EPHE, 75007 Paris, France
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19
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Torrent G, Ribó M, Benito A, Vilanova M. Bactericidal Activity Engineered on Human Pancreatic Ribonuclease and Onconase. Mol Pharm 2009; 6:531-42. [DOI: 10.1021/mp8001914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gerard Torrent
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n 17071 Girona, Spain, and Institut d’Investigació Biomèdica de Girona Josep Trueta, Girona, Spain
| | - Marc Ribó
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n 17071 Girona, Spain, and Institut d’Investigació Biomèdica de Girona Josep Trueta, Girona, Spain
| | - Antoni Benito
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n 17071 Girona, Spain, and Institut d’Investigació Biomèdica de Girona Josep Trueta, Girona, Spain
| | - Maria Vilanova
- Laboratori d’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n 17071 Girona, Spain, and Institut d’Investigació Biomèdica de Girona Josep Trueta, Girona, Spain
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20
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Bruins ME, Meersman F, Janssen AEM, Heremans K, Boom RM. Increased susceptibility of β-glucosidase from the hyperthermophile Pyrococcus furiosus to thermal inactivation at higher pressures. FEBS J 2008; 276:109-17. [DOI: 10.1111/j.1742-4658.2008.06759.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Ando N, Barstow B, Baase WA, Fields A, Matthews BW, Gruner SM. Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation. Biochemistry 2008; 47:11097-109. [PMID: 18816066 DOI: 10.1021/bi801287m] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using small-angle X-ray scattering (SAXS) and tryptophan fluorescence spectroscopy, we have identified multiple compact denatured states of a series of T4 lysozyme mutants that are stabilized by high pressures. Recent studies imply that the mechanism of pressure denaturation is the penetration of water into the protein rather than the transfer of hydrophobic residues into water. To investigate water penetration and the volume change associated with pressure denaturation, we studied the solution behavior of four T4 lysozyme mutants having different cavity volumes at low and neutral pH up to a pressure of 400 MPa (0.1 MPa = 0.9869 atm). At low pH, L99A T4 lysozyme expanded from a compact folded state to a partially unfolded state with a corresponding change in radius of gyration from 17 to 32 A. The volume change upon denaturation correlated well with the total cavity volume, indicating that all of the molecule's major cavities are hydrated with pressure. As a direct comparison to high-pressure crystal structures of L99A T4 lysozyme solved at neutral pH [Collins, M. D., Hummer, G., Quillin, M. L., Matthews, B. W., and Gruner, S. M. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 16668-16671], pressure denaturation of L99A and the structurally similar L99G/E108V mutant was studied at neutral pH. The pressure-denatured state at neutral pH is even more compact than at low pH, and the small volume changes associated with denaturation suggest that the preferential filling of large cavities is responsible for the compactness of the pressure-denatured state. These results confirm that pressure denaturation is characteristically distinct from thermal or chemical denaturation.
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Affiliation(s)
- Nozomi Ando
- Department of Physics, Cornell University, Ithaca, New York 14853, USA
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Torrent G, Benito A, Castro J, Ribó M, Vilanova M. Contribution of the C30/C75 disulfide bond to the biological properties of onconase. Biol Chem 2008. [DOI: 10.1515/bc.2008.114_bchm.just-accepted] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Torrent G, Benito A, Castro J, Ribó M, Vilanova M. Contribution of the C30/C75 disulfide bond to the biological properties of onconase. Biol Chem 2008; 389:1127-36. [DOI: 10.1515/bc.2008.114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractOnconase, a member of the pancreatic type ribonuclease family, is currently used as a chemotherapeutic agent for the treatment of different types of cancer. It is widely accepted that one of the properties that renders this enzyme cytotoxic is its ability to evade the cytosolic ribonuclease inhibitor (RI). In the present work, we produced and characterized an onconase variant that lacks the disulfide bond C30/C75. This variant mimics the stable unfolding intermediate des(30–75) produced in the reductive unfolding pathway of onconase. We found that the reduction of the C30/C75 disulfide bond does not significantly alter the cytotoxic properties of onconase, although the variant possesses a notably reduced conformational stability. Interestingly, both its catalytic activity and its ability to evade RI are comparable to wild-type onconase under mild reductive conditions in which the three disulfide containing intermediate des(30–75) is present. These results suggest that the C30/C75 disulfide bond could easily be reduced under physiological redox conditions.
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Torrent J, Marchal S, Ribó M, Vilanova M, Georges C, Dupont Y, Lange R. Distinct unfolding and refolding pathways of ribonuclease a revealed by heating and cooling temperature jumps. Biophys J 2008; 94:4056-65. [PMID: 18234832 PMCID: PMC2367170 DOI: 10.1529/biophysj.107.123893] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 12/21/2007] [Indexed: 11/18/2022] Open
Abstract
Heating and cooling temperature jumps (T-jumps) were performed using a newly developed technique to trigger unfolding and refolding of wild-type ribonuclease A and a tryptophan-containing variant (Y115W). From the linear Arrhenius plots of the microscopic folding and unfolding rate constants, activation enthalpy (DeltaH(#)), and activation entropy (DeltaS(#)) were determined to characterize the kinetic transition states (TS) for the unfolding and refolding reactions. The single TS of the wild-type protein was split into three for the Y115W variant. Two of these transition states, TS1 and TS2, characterize a slow kinetic phase, and one, TS3, a fast phase. Heating T-jumps induced protein unfolding via TS2 and TS3; cooling T-jumps induced refolding via TS1 and TS3. The observed speed of the fast phase increased at lower temperature, due to a strongly negative DeltaH(#) of the folding-rate constant. The results are consistent with a path-dependent protein folding/unfolding mechanism. TS1 and TS2 are likely to reflect X-Pro(114) isomerization in the folded and unfolded protein, respectively, and TS3 the local conformational change of the beta-hairpin comprising Trp(115). A very fast protein folding/unfolding phase appears to precede both processes. The path dependence of the observed kinetics is suggestive of a rugged energy protein folding funnel.
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Affiliation(s)
- Joan Torrent
- Université Montpellier 2, UMR-S710, and INSERM Unit 710, Montpellier, France
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25
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Abstract
The effect of strongly destabilizing mutations, I106A and V108G of Ribonuclease A (RNase A), on its structure and stability has been determined by NMR. The solution structures of these variants are essentially equivalent to RNase A. The exchange rates of the most protected amide protons in RNase A (35 degrees C), the I106A variant (35 degrees C), and the V108G variant (10 degrees C) yield stability values of 9.9, 6.0, and 6.8 kcal/mol, respectively, when analyzed assuming an EX2 exchange mechanism. Thus, the destabilization induced by these mutations is propagated throughout the protein. Simulation of RNase A hydrogen exchange indicates that the most protected protons in RNase A and the V108G variant exchange via the EX2 regime, whereas those of I106A exchange through a mixed EX1 + EX2 process. It is striking that a single point mutation can alter the overall exchange mechanism. Thus, destabilizing mutations joins high temperatures, high pH and the presence of denaturating agents as a factor that induces EX1 exchange in proteins. The calculations also indicate a shift from the EX2 to the EX1 mechanism for less protected groups within the same protein. This should be borne in mind when interpreting exchange data as a measure of local stability in less protected regions.
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26
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Kornblatt JA, Barretto TA, Chigogidze K, Chirwa B. Canine Plasminogen: Spectral Responses to Changes in 6-Aminohexanoate and Temperature. ANALYTICAL CHEMISTRY INSIGHTS 2007. [DOI: 10.4137/117739010700200009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We studied the near UV absorption spectrum of canine plasminogen. There are 19 tryptophans, 19 phenylalanines and 34 tyrosines in the protein. 4th derivative spectra optimized for either tryptophan or tyrosine give a measure of the polarity of the environments of these two aromatic amino acids. Plasminogen at temperatures between 0°C and 37°C exists as a mixture of four conformations: closed-relaxed, open-relaxed, closed-compact, and open-compact. The closed to open transition is driven by addition of ligand to a site on the protein. The relaxed to compact transition is driven by increasing temperature from 0°C to above 15-20°C. When the conformation of plasminogen is mainly closed-relaxed, the 4th derivative spectra suggest that the average tryptophan environment is similar to a solution of 20% methanol at the same temperature. Under the same conditions, 4th derivative spectra suggest that the average tyrosine environment is similar to water. These apparent polarities change as the plasminogen is forced to assume the other conformations. We try to rationalize the information based on the known portions of the plasminogen structure.
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Affiliation(s)
- Jack A. Kornblatt
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
| | - Tanya A. Barretto
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
| | - Ketevan Chigogidze
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
| | - Bahati Chirwa
- Enzyme Research Group, Department of Biology, Concordia University, Montreal, Qc., Canada H4B 1R6
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27
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Nikolovski Z, Buzón V, Ribó M, Moussaoui M, Vilanova M, Cuchillo CM, Cladera J, Nogués MV. Thermal unfolding of eosinophil cationic protein/ribonuclease 3: a nonreversible process. Protein Sci 2006; 15:2816-27. [PMID: 17088327 PMCID: PMC2242447 DOI: 10.1110/ps.062196406] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Eosinophil cationic protein (ECP)/ribonuclease 3 is a member of the RNase A superfamily involved in inflammatory processes mediated by eosinophils. ECP is bactericidal, helminthotoxic, and cytotoxic to tracheal epithelium cells and to several mammalian cell lines although its RNase activity is low. We studied the thermal stability of ECP by fourth-derivative UV absorbance spectra, circular dichroism, differential scanning calorimetry, and Fourier transform infrared spectroscopy. The T (1/2) values obtained with the different techniques were in very good agreement (T (1/2) approximately 72 degrees C), and the stability was maintained in the pH range between 5 and 7. The ECP calorimetric melting curve showed, in addition to the main transition, a pretransitional conformational change with a T (1/2) of 44 degrees C. Both calorimetric transitions disappeared after successive re-heatings, and the ratio DeltaH versus DeltaH (vH) of 2.2 indicated a significant deviation from the two-state model. It was observed that the thermal unfolding was irreversible. The unfolding process gives rise to changes in the environment of aromatic amino acids that are partially maintained in the refolded protein with the loss of secondary structure and the formation of oligomers. From the thermodynamic analysis of ECP variants, the contribution of specific amino acids, such as Trp10 and the region 115-122, to thermal stability was also determined. The high thermal stability of ECP may contribute to its resistance to degradation when the protein is secreted to the extracellular medium during the immune response.
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Affiliation(s)
- Zoran Nikolovski
- Unitat de Bioquímica, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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28
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Smith BD, Raines RT. Genetic selection for critical residues in ribonucleases. J Mol Biol 2006; 362:459-78. [PMID: 16920150 DOI: 10.1016/j.jmb.2006.07.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 07/03/2006] [Accepted: 07/11/2006] [Indexed: 11/24/2022]
Abstract
Homologous mammalian proteins were subjected to an exhaustive search for residues that are critical to their structure/function. Error-prone polymerase chain reactions were used to generate random mutations in the genes of bovine pancreatic ribonuclease (RNase A) and human angiogenin, and a genetic selection based on the intrinsic cytotoxicity of ribonucleolytic activity was used to isolate inactive variants. Twenty-three of the 124 residues in RNase A were found to be intolerant to substitution with at least one particular amino acid. Twenty-nine of the 123 residues in angiogenin were likewise intolerant. In both RNase A and angiogenin, only six residues appeared to be wholly intolerant to substitution: two histidine residues involved in general acid/base catalysis and four cysteine residues that form two disulfide bonds. With few exceptions, the remaining critical residues were buried in the hydrophobic core of the proteins. Most of these residues were found to tolerate only conservative substitutions. The importance of a particular residue as revealed by this genetic selection correlated with its sequence conservation, though several non-conserved residues were found to be critical for protein structure/function. Despite voluminous research on RNase A, the importance of many residues identified herein was unknown, and those can now serve as targets for future work. Moreover, a comparison of the critical residues in RNase A and human angiogenin, which share only 35% amino acid sequence identity, provides a unique perspective on the molecular evolution of the RNase A superfamily, as well as an impetus for applying this methodology to other ribonucleases.
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Affiliation(s)
- Bryan D Smith
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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29
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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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30
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Font J, Torrent J, Ribó M, Laurents DV, Balny C, Vilanova M, Lange R. Pressure-jump-induced kinetics reveals a hydration dependent folding/unfolding mechanism of ribonuclease A. Biophys J 2006; 91:2264-74. [PMID: 16798802 PMCID: PMC1557576 DOI: 10.1529/biophysj.106.082552] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pressure-jump (p-jump)-induced relaxation kinetics was used to explore the energy landscape of protein folding/unfolding of Y115W, a fluorescent variant of ribonuclease A. Pressure-jumps of 40 MPa amplitude (5 ms dead-time) were conducted both to higher (unfolding) and to lower (folding) pressure, in the range from 100 to 500 MPa, between 30 and 50 degrees C. Significant deviations from the expected symmetrical protein relaxation kinetics were observed. Whereas downward p-jumps resulted always in single exponential kinetics, the kinetics induced by upward p-jumps were biphasic in the low pressure range and monophasic at higher pressures. The relative amplitude of the slow phase decreased as a function of both pressure and temperature. At 50 degrees C, only the fast phase remained. These results can be interpreted within the framework of a two-dimensional energy surface containing a pressure- and temperature-dependent barrier between two unfolded states differing in the isomeric state of the Asn-113-Pro-114 bond. Analysis of the activation volume of the fast kinetic phase revealed a temperature-dependent shift of the unfolding transition state to a larger volume. The observed compensation of this effect by glycerol offers an explanation for its protein stabilizing effect.
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Affiliation(s)
- J Font
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n, 17071 Girona, Spain
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31
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Font J, Benito A, Lange R, Ribó M, Vilanova M. The contribution of the residues from the main hydrophobic core of ribonuclease A to its pressure-folding transition state. Protein Sci 2006; 15:1000-9. [PMID: 16597833 PMCID: PMC2242501 DOI: 10.1110/ps.052050306] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The role of hydrophobic interactions established by the residues that belong to the main hydrophobic core of ribonuclease A in its pressure-folding transition state was investigated using the Phi-value method. The folding kinetics was studied using pressure-jump techniques both in the pressurization and depressurization directions. The ratio between the folding activation volume and the reaction volume (beta p-value), which is an index of the compactness or degree of solvation of the transition state, was calculated. All the positions analyzed presented fractional Phi f-values, and the lowest were those corresponding to the most critical positions for the ribonuclease A stability. The structure of the transition state of the hydrophobic core of ribonuclease A, from the point of view of formed interactions, is a relatively, uniformly expanded form of the folded structure with a mean Phi f-value of 0.43. This places it halfway between the folded and unfolded states. On the other hand, for the variants, the average of beta p-values is 0.4, suggesting a transition state that is 40% native-like. Altogether the results suggest that the pressure-folding transition state of ribonuclease A looks like a collapsed globule with some secondary structure and a weakened hydrophobic core. A good correlation was found between the Phi f-values and the Deltabeta p-values. Although the nature of the transition state inferred from pressure-induced folding studies and the results of the protein engineering method have been reported to be consistent for other proteins, to the best of our knowledge this is the first direct comparison using a set of mutants.
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Affiliation(s)
- Josep Font
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, 17071 Girona, Spain
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32
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Ribó M, Font J, Benito A, Torrent J, Lange R, Vilanova M. Pressure as a tool to study protein-unfolding/refolding processes: The case of ribonuclease A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:461-9. [PMID: 16388998 DOI: 10.1016/j.bbapap.2005.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 11/09/2005] [Accepted: 11/14/2005] [Indexed: 10/25/2022]
Abstract
This paper gives an overview of the application of high-pressure to study the folding/unfolding processes of proteins using Ribonuclease A as a model protein. A particular focus is the study of pressure-equilibrium unfolding and folding kinetics using variants and the information obtained by comparing these with the wild-type enzyme.
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Affiliation(s)
- M Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n, 17071 Girona, Spain
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33
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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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34
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Font J, Benito A, Torrent J, Lange R, Ribó M, Vilanova M. Pressure- and temperature-induced unfolding studies: thermodynamics of core hydrophobicity and packing of ribonuclease A. Biol Chem 2006; 387:285-96. [PMID: 16542150 DOI: 10.1515/bc.2006.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractIn this work we demonstrate that heat and pressure induce only slightly different energetic changes in the unfolded state of RNase A. Using pressure and temperature as denaturants on a significant number of variants, and by determining the free energy of unfolding at different temperatures, we estimated the stability of variants unable to complete the unfolding transition owing to the experimental conditions required for pressure experiments. The overall set of results allowed us to map the contributions to stability of the hydrophobic core residues of RNase A, with the positions most critical for stability being V54, V57, I106 and V108. We also show that the stability differences can be attributed to both hydrophobic interactions and packing density with an equivalent energetic magnitude. The main hydrophobic core of RNase A is tightly packed, as shown by the small-to-large and isosteric substitutions. In addition, we found that large changes in the number of methylene groups have non-additive positive stability interaction energies that are consistent with exquisite tight core packing and rearrangements of van der Waals' interactions in the protein interior, even after drastic deleterious substitutions.
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Affiliation(s)
- Josep Font
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus de Montilivi s/n, E-17071 Girona, Spain
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35
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López-Alonso JP, Bruix M, Font J, Ribó M, Vilanova M, Rico M, Gotte G, Libonati M, González C, Laurents DV. Formation, structure, and dissociation of the ribonuclease S three-dimensional domain-swapped dimer. J Biol Chem 2006; 281:9400-6. [PMID: 16415350 DOI: 10.1074/jbc.m510491200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational events, such as proteolysis, are believed to play essential roles in amyloid formation in vivo. Ribonuclease A forms oligomers by the three-dimensional domain-swapping mechanism. Here, we demonstrate the ability of ribonuclease S, a proteolytically cleaved form of ribonuclease A, to oligomerize efficiently. This unexpected capacity has been investigated to study the effect of proteolysis on oligomerization and amyloid formation. The yield of the RNase S dimer was found to be significantly higher than that of RNase A dimers, which suggests that proteolysis can activate oligomerization via the three-dimensional domain-swapping mechanism. Characterization by chromatography, enzymatic assays, and NMR spectroscopy indicate that the structure of the RNase S dimer is similar to that of the RNase A C-dimer. The RNase S dimer dissociates much more readily than the RNase A C-dimer does. By measuring the dissociation rate as a function of temperature, the activation enthalpy and entropy for RNase S dimer dissociation were found to resemble those for the release of the small fragment (S-peptide) from monomeric RNase S. Excess S-peptide strongly slows RNase S dimer dissociation. These results strongly suggest that S-peptide release is the rate-limiting step of RNase S dimer dissociation.
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Affiliation(s)
- Jorge P López-Alonso
- Instituto de Química-Física "Rocasolano" CSIC, Serrano 119, E-28006 Madrid, Spain
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36
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Meersman F, Dobson CM, Heremans K. Protein unfolding, amyloid fibril formation and configurational energy landscapes under high pressure conditions. Chem Soc Rev 2006; 35:908-17. [PMID: 17003897 DOI: 10.1039/b517761h] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High hydrostatic pressure induces conformational changes in proteins ranging from compression of the molecules to loss of native structure. In this tutorial review we describe how the interplay between the volume change and the compressibility leads to pressure-induced unfolding of proteins and dissociation of amyloid fibrils. We also discuss the effect of pressure on protein folding and free energy landscapes. From a molecular viewpoint, pressure effects can be rationalised in terms of packing and hydration of proteins.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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37
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Torrent J, Alvarez-Martinez MT, Liautard JP, Balny C, Lange R. The role of the 132-160 region in prion protein conformational transitions. Protein Sci 2005; 14:956-67. [PMID: 15772306 PMCID: PMC2253438 DOI: 10.1110/ps.04989405] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The native conformation of host-encoded cellular prion protein (PrP(C)) is metastable. As a result of a post-translational event, PrP(C) can convert to the scrapie form (PrP(Sc)), which emerges as the essential constituent of infectious prions. Despite thorough research, the mechanism underlying this conformational transition remains unknown. However, several studies have highlighted the importance of the N-terminal region spanning residues 90-154 in PrP folding. In order to understand why PrP folds into two different conformational states exhibiting distinct secondary and tertiary structure, and to gain insight into the involvement of this particular region in PrP transconformation, we studied the pressure-induced unfolding/ refolding of recombinant Syrian hamster PrP expanding from residues 90-231, and compared it with heat unfolding. By using two intrinsic fluorescent variants of this protein (Y150W and F141W), conformational changes confined to the 132-160 segment were monitored. Multiple conformational states of the Trp variants, characterized by their spectroscopic properties (fluorescence and UV absorbance in the fourth derivative mode), were achieved by tuning the experimental conditions of pressure and temperature. Further insight into unexplored conformational states of the prion protein, likely to mimic the in vivo structural change, was obtained from pressure-assisted cold unfolding. Furthermore, salt-induced conformational changes suggested a structural stabilizing role of Tyr150 and Phe141 residues, slowing down the conversion to a beta-sheet form.
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Affiliation(s)
- Joan Torrent
- INSERM U710, CC 105, Université de Montpellier 2, Place Eugène Bataillon, F-34095 Montpellier cédex 5, France
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38
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Zorrilla S, Rivas G, Acuña AU, Lillo MP. Protein self-association in crowded protein solutions: a time-resolved fluorescence polarization study. Protein Sci 2004; 13:2960-9. [PMID: 15459331 PMCID: PMC2286579 DOI: 10.1110/ps.04809404] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The self-association equilibrium of a tracer protein, apomyoglobin (apoMb), in highly concentrated crowded solutions of ribonuclease A (RNase A) and human serum albumin (HSA), has been studied as a model system of protein interactions that occur in crowded macromolecular environments. The rotational diffusion of the tracer protein labeled with two different fluorescent dyes, 8-anilinonaphthalene-1-sulfonate and fluorescein isothiocyanate, was successfully recorded as a function of the two crowder concentrations in the 50-200 mg/mL range, using picosecond-resolved fluorescence anisotropy methods. It was found that apoMb molecules self-associate at high RNase A concentration to yield a flexible dimer. The apparent dimerization constant, which increases with RNase A concentration, could also be estimated from the fractional contribution of monomeric and dimeric species to the total fluorescence anisotropy of the samples. In contrast, an equivalent mass concentration of HSA does not result in tracer dimerization. This different effect of RNase A and HSA is much larger than that predicted from simple models based only on the free volume available to apoMb, indicating that additional, nonspecific interactions between tracer and crowder should come into play. The time-resolved fluorescence polarization methods described here are expected to be of general applicability to the detection and quantification of crowding effects in a variety of macromolecules of biological relevance.
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Affiliation(s)
- Silvia Zorrilla
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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39
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Ribó M, Bosch M, Torrent G, Benito A, Beaumelle B, Vilanova M. Quantitative analysis, using MALDI-TOF mass spectrometry, of the N-terminal hydrolysis and cyclization reactions of the activation process of onconase. ACTA ACUST UNITED AC 2004; 271:1163-71. [PMID: 15009195 DOI: 10.1111/j.1432-1033.2004.04020.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Onconase, a member of the ribonuclease superfamily, is a potent cytotoxic agent that is undergoing phase II/III human clinical trials as an antitumor drug. Native onconase from Rana pipiens and its amphibian homologs have an N-terminal pyroglutamyl residue that is essential for obtaining fully active enzymes with their full potential as cytotoxins. When expressed cytosolically in bacteria, Onconase is isolated with an additional methionyl (Met1) residue and glutaminyl instead of a pyroglutamyl residue at position 1 of the N-terminus and is consequently inactivated. The two reactions necessary for generating the pyroglutamyl residue have been monitored by MALDI-TOF MS. Results show that hydrolysis of Met(-1), catalyzed by Aeromonas aminopeptidase, is optimal at a concentration of >or= 3 m guanidinium-chloride, and at pH 8.0. The intramolecular cyclization of glutaminyl that renders the pyroglutamyl residue is not accelerated by increasing the concentration of denaturing agent or by strong acid or basic conditions. However, temperature clearly accelerates the formation of pyroglutamyl. Taken together, these results have allowed the characterization and optimization of the onconase activation process. This procedure may have more general applicability in optimizing the removal of undesirable N-terminal methionyl residues from recombinant proteins overexpressed in bacteria and providing them with biological and catalytic properties identical to those of the natural enzyme.
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Affiliation(s)
- Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
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40
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Marchal S, Shehi E, Harricane MC, Fusi P, Heitz F, Tortora P, Lange R. Structural instability and fibrillar aggregation of non-expanded human ataxin-3 revealed under high pressure and temperature. J Biol Chem 2003; 278:31554-63. [PMID: 12766160 DOI: 10.1074/jbc.m304205200] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein misfolding and formation of structured aggregates are considered to be the earliest events in the development of neurodegenerative diseases, but the mechanism of these biological phenomena remains to be elucidated. Here, we report a study of heat- and pressure-induced unfolding of human Q26 and murine Q6 ataxin-3 using spectroscopic methods. UV absorbance and fluorescence revealed that heat and pressure induced a structural transition of both proteins to a molten globule conformation. The unfolding pathway was partly irreversible and led to a protein conformation where tryptophans were more exposed to water. Furthermore, the use of fluorescent probes (8-anilino-1-naphthalenesulfonate and thioflavin T) allowed the identification of different intermediates during the process of pressure-induced unfolding. At high temperature and pressure, human Q26, but not murine Q6, underwent concentration-dependent aggregation. Fourier transform infrared and circular dichroism spectroscopy revealed that these aggregates are characterized by an increased beta-sheet content. As revealed by electron microscopy, heat- and pressure-induced aggregates were different; high temperature treatment led to fibrillar microaggregates (8-10-nm length), whereas high pressure induced oligomeric structures of globular shape (100 nm in diameter), which sometimes aligned to higher order suprastructures. Several intermediate structures were detected in this process. Two factors appear to govern ataxin unfolding and aggregation, the length of the polyglutamine tract and its protein context.
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Affiliation(s)
- Stéphane Marchal
- INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cédex 5, France
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41
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Ruan K, Xu C, Li T, Li J, Lange R, Balny C. The thermodynamic analysis of protein stabilization by sucrose and glycerol against pressure-induced unfolding. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1654-61. [PMID: 12694178 DOI: 10.1046/j.1432-1033.2003.03485.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have studied the reaction native left arrow over right arrow denatured for the 33-kDa protein isolated from photosystem II. Sucrose and glycerol have profound effects on pressure-induced unfolding. The additives shift the equilibrium to the left; they also cause a significant decrease in the standard volume change (DeltaV). The change in DeltaV was related to the sucrose and glycerol concentrations. The decrease in DeltaV varied with the additive: sucrose caused the largest effect, glycerol the smallest. The theoretical shift of the half-unfolding pressure (P1/2) calculated from the net increase in free energy by addition of sucrose and glycerol was lower than that obtained from experimental mea- surements. This indicates that the free energy change caused by preferential hydration of the protein is not the unique factor involved in the protein stabilization. The reduction in DeltaV showed a large contribution to the theoretical P1/2 shift, suggesting that the DeltaV change, caused by the sucrose or glycerol was associated with the protein stabilization. The origin of the DeltaV change is discussed. The rate of pressure-induced unfolding in the presence of sucrose or glycerol was slower than the refolding rate although both were significantly slower than that observed without any stabilizers.
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Affiliation(s)
- Kangcheng Ruan
- Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, China.
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42
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Alvarez-Martinez MT, Torrent J, Lange R, Verdier JM, Balny C, Liautard JP. Optimized overproduction, purification, characterization and high-pressure sensitivity of the prion protein in the native (PrP(C)-like) or amyloid (PrP(Sc)-like) conformation. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1645:228-40. [PMID: 12573253 DOI: 10.1016/s1570-9639(02)00536-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Overproduction and purification of the prion protein is a major concern for biological or biophysical analysis as are the structural specificities of this protein in relation to infectivity. We have developed a method for the effective cloning, overexpression in Escherichia coli and purification to homogeneity of Syrian golden hamster prion protein (SHaPrP(90-231)). A high level of overexpression, resulting in the formation of inclusion bodies, was obtained under the control of the T7-inducible promoter of the pET15b plasmid. The protein required denaturation, reduction and refolding steps to become soluble and attain its native conformation. Purification was carried out by differential centrifugation, gel filtration and reverse phase chromatography. An improved cysteine oxidation protocol using oxidized glutathione under denaturing conditions, resulted in the recovery of a higher yield of chromatographically pure protein. About 10 mg of PrP protein per liter of bacterial culture was obtained. The recombinant protein was identified by monoclonal antibodies and its integrity was confirmed by electrospray mass spectrometry (ES/MS), whereas correct folding was assessed by circular dichroism (CD) spectroscopy. This protein had the structural characteristics of PrP(C) and could be converted to an amyloid structure sharing biophysical and biochemical properties of the pathologic form (PrP(Sc)). The sensitivity of these two forms to high pressure was investigated. We demonstrate the potential of using pressure as a thermodynamic parameter to rescue trapped aggregated prion conformations into a soluble state, and to explore new conformational coordinates of the prion protein conformational landscape.
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Affiliation(s)
- Maria Teresa Alvarez-Martinez
- INSERM U431, CC100, Dept Biologie Sante, Université de Montpellier 2, Place Eugène Bataillon, F-34095 Montpellier Cedex 5, France
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43
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Benito A, Bosch M, Torrent G, Ribó M, Vilanova M. Stabilization of human pancreatic ribonuclease through mutation at its N-terminal edge. Protein Eng Des Sel 2002; 15:887-93. [PMID: 12538908 DOI: 10.1093/protein/15.11.887] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enzyme stability can be an important parameter in the design of recombinant toxins because unstable proteins are often degraded before they can reach their cellular target. There is great interest in the design of human pancreatic ribonuclease variants that could be cytotoxic against tumoral cells. To this end, some residues in the protein need to be substituted, but this may result in a loss of stability. Previous papers have reported the production of N- and C-terminal human pancreatic ribonuclease variants with increased thermal stability. Here, we investigated the contribution of the different amino acid changes at the N-terminus of the protein to its thermostability increase. We show that this increase correlates with the helical propensity of the first alpha-helix of the protein. On the other hand, deletion of the four last residues of the protein does not affect its thermal stability. These results set the basis for the design of a human pancreatic ribonuclease template on which amino acid substitutions can be made that could render the enzyme cytotoxic, without an important loss in its stability.
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Affiliation(s)
- A Benito
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain
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44
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Lange R, Balny C. UV-visible derivative spectroscopy under high pressure. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:80-93. [PMID: 11983388 DOI: 10.1016/s0167-4838(01)00336-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
High hydrostatic pressure affects proteins, changing their intra- or intermolecular interactions, conformation and solvation. How to detect these changes? In this paper, via some selected examples, we show the potentiality (but also the limits) of the ultraviolet derivative spectroscopy specially adapted to high pressure experiments.
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45
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Abstract
The pressure-temperature phase diagram of various biomolecules is reviewed. Special attention is focused on the elliptic phase diagram of proteins. The phenomenological thermodynamic theory describing this diagram explains the heat, cold and pressure denaturations in a unified picture. The limitations and possible developments of this theory are discussed as well. It is pointed out that a more complex diagram can be obtained when the intermolecular interactions are also taken into account. In this case metastable states appear on the pressure-temperature (p-T) diagram due to intermolecular interactions. Pressure-temperature phase diagrams of other biopolymers are also discussed. While the p-T diagrams of helix-coil transition of nucleic acids and of gel-liquid crystal transition of lipid bilayers are non-elliptical, those of gelatinization of starch and of phase separation of some synthetic polymers show an elliptic profile, similar to that of proteins. Finally, the p-T diagram of bacterial inactivation is shown to be elliptic. From the point of view of basic science, this fact shows that the key factor of inactivation should be the protein type, and from the viewpoint of practical applications, it serves as the theoretical basis of pressure treatment of biosystems.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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46
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Royer CA. Revisiting volume changes in pressure-induced protein unfolding. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:201-9. [PMID: 11983396 DOI: 10.1016/s0167-4838(01)00344-2] [Citation(s) in RCA: 351] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It has long been known that the application of hydrostatic pressure generally leads to the unfolding of proteins. Despite a relatively large number of reports in the literature over the past few decades, there has been great confusion over the sign and magnitude as well as the fundamental factors contributing to volume effects in protein conformational transitions. It is the goal of this review to present and discuss the results obtained concerning the sign and magnitude of the volume changes accompanying the unfolding of proteins. The vast majority of cases point to a significant decrease in volume upon unfolding. Nonetheless, there is evidence that, due to differences in the thermal expansivity of the folded and unfolded states of proteins reported in a half dozen manuscripts, that the sign of the volume change may become positive at higher temperatures.
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Affiliation(s)
- Catherine A Royer
- Centre de Biochimie Structurale, INSERM U554, CNRS UMR 5048, Montpellier, France.
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47
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Ribó M, Benito A, Canals A, Nogués MV, Cuchillo CM, Vilanova M. Purification of engineered human pancreatic ribonuclease. Methods Enzymol 2002; 341:221-34. [PMID: 11582779 DOI: 10.1016/s0076-6879(01)41154-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- M Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Universitat de Girona, E-17071 Girona, Spain
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48
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Scheraga HA, Wedemeyer WJ, Welker E. Bovine pancreatic ribonuclease A: oxidative and conformational folding studies. Methods Enzymol 2002; 341:189-221. [PMID: 11582778 DOI: 10.1016/s0076-6879(01)41153-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- H A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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49
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Wu Y, Jiang JH, Ozaki Y. A New Possibility of Generalized Two-Dimensional Correlation Spectroscopy: Hybrid Two-Dimensional Correlation Spectroscopy. J Phys Chem A 2002. [DOI: 10.1021/jp012140g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuqing Wu
- Department of Chemistry, School of Science, Kwansei-Gakuin University, Sanda, Hyogo 669-1337, Japan, Key Laboratory for Supramolecular Structure and Materials of the Ministry of Education, Jilin University, Changchun 130023, P. R. China, and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jian-Hui Jiang
- Department of Chemistry, School of Science, Kwansei-Gakuin University, Sanda, Hyogo 669-1337, Japan, Key Laboratory for Supramolecular Structure and Materials of the Ministry of Education, Jilin University, Changchun 130023, P. R. China, and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science, Kwansei-Gakuin University, Sanda, Hyogo 669-1337, Japan, Key Laboratory for Supramolecular Structure and Materials of the Ministry of Education, Jilin University, Changchun 130023, P. R. China, and College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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50
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Lange R, Bec N, Anzenbacher P, Munro AW, Gorren AC, Mayer B. Use of high pressure to study elementary steps in P450 and nitric oxide synthase. J Inorg Biochem 2001; 87:191-5. [PMID: 11744056 DOI: 10.1016/s0162-0134(01)00330-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chemical reactions are often highly pressure-dependent. A perturbation of the elementary steps by pressure therefore offers the possibility of a detailed characterization of enzyme mechanisms. We used this method to study distinct steps in the reaction of nitric-oxide synthase (NOS), and compared them to analogous steps in the reaction of cytochrome P450 BM3 (BM3). Our results indicate that, in BM3, electron transfer depends on electrostatic interactions. In NOS, pressure, similarly to chemical denaturants, can mimic the structural effects of Ca/calmodulin. This helps to better understand the structural basis of the regulatory effect of Ca/calmodulin. Furthermore, stopped-flow kinetics under high pressure show that CO binding to the heme iron is hindered by substrate in NOS, but not in BM3. This indicates a relatively large or flexible substrate binding site in BM3, and a more narrow and rigid binding site in NOS.
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Affiliation(s)
- R Lange
- INSERM U128, IFR24, 1919 Route de Mende, 34293, Montpellier, France.
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