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Lahfa M, Mouhand A, de Guillen K, Barthe P, Kroj T, Padilla A, Roumestand C. Does a Similar 3D Structure Mean a Similar Folding Pathway? The Presence of a C-Terminal α-Helical Extension in the 3D Structure of MAX60 Drastically Changes the Folding Pathway Described for Other MAX-Effectors from Magnaporthe oryzae. Molecules 2023; 28:6068. [PMID: 37630320 PMCID: PMC10460046 DOI: 10.3390/molecules28166068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Does a similar 3D structure mean a similar folding pathway? This question is particularly meaningful when it concerns proteins sharing a similar 3D structure, but low sequence identity or homology. MAX effectors secreted by the phytopathogenic fungus Magnaporthe oryzae present such characteristics. They share a common 3D structure, a ß-sandwich with the same topology for all the family members, but an extremely low sequence identity/homology. In a previous study, we have investigated the folding of two MAX effectors, AVR-Pia and AVR-Pib, using High-Hydrostatic-Pressure NMR and found that they display a similar folding pathway, with a common folding intermediate. In the present work, we used a similar strategy to investigate the folding conformational landscape of another MAX effector, MAX60, and found a very different folding intermediate. Our analysis strongly supports that the presence of a C-terminal α-helical extension in the 3D structure of MAX60 could be responsible for its different folding pathway.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Assia Mouhand
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Karine de Guillen
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Philippe Barthe
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Thomas Kroj
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34060 Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Christian Roumestand
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
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Wang W, Yang P, Rao L, Zhao L, Wu X, Wang Y, Liao X. Effect of high hydrostatic pressure processing on the structure, functionality, and nutritional properties of food proteins: A review. Compr Rev Food Sci Food Saf 2022; 21:4640-4682. [PMID: 36124402 DOI: 10.1111/1541-4337.13033] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 01/28/2023]
Abstract
Proteins are important food ingredients that possess both functional and nutritional properties. High hydrostatic pressure (HHP) is an emerging nonthermal food processing technology that has been subject to great advancements in the last two decades. It is well established that pressure can induce changes in protein folding and oligomerization, and consequently, HHP has the potential to modify the desired protein properties. In this review article, the research progress over the last 15 years regarding the effect of HHP on protein structures, as well as the applications of HHP in modifying protein functionalities (i.e., solubility, water/oil holding capacity, emulsification, foaming and gelation) and nutritional properties (i.e., digestibility and bioactivity) are systematically discussed. Protein unfolding generally occurs during HHP treatment, which can result in increased conformational flexibility and the exposure of interior residues. Through the optimization of HHP and environmental conditions, a balance in protein hydrophobicity and hydrophilicity may be obtained, and therefore, the desired protein functionality can be improved. Moreover, after HHP treatment, there might be greater accessibility of the interior residues to digestive enzymes or the altered conformation of specific active sites, which may lead to modified nutritional properties. However, the practical applications of HHP in developing functional protein ingredients are underutilized and require more research concerning the impact of other food components or additives during HHP treatment. Furthermore, possible negative impacts on nutritional properties of proteins and other compounds must be also considered.
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Affiliation(s)
- Wenxin Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Peiqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Lei Rao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Key laboratory for Food Non-Thermal Processing, Beijing, China
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China.,Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiaomeng Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Key laboratory for Food Non-Thermal Processing, Beijing, China
| | - Yongtao Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China.,Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Key laboratory for Food Non-Thermal Processing, Beijing, China.,National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China.,Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing, China
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3
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Puglisi R, Cioni P, Gabellieri E, Presciuttini G, Pastore A, Temussi PA. Heat and cold denaturation of yeast frataxin: The effect of pressure. Biophys J 2022; 121:1502-1511. [PMID: 35278425 PMCID: PMC9072581 DOI: 10.1016/j.bpj.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/14/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022] Open
Abstract
Yfh1 is a yeast protein with the peculiar characteristic to undergo, in the absence of salt, cold denaturation at temperatures above the water freezing point. This feature makes the protein particularly interesting for studies aiming at understanding the rules that determine protein fold stability. Here, we present the phase diagram of Yfh1 unfolding as a function of pressure (0.1-500 MPa) and temperature 278-313 K (5-40°C) both in the absence and in the presence of stabilizers using Trp fluorescence as a monitor. The protein showed a remarkable sensitivity to pressure: at 293 K, pressures around 10 MPa are sufficient to cause 50% of unfolding. Higher pressures were required for the unfolding of the protein in the presence of stabilizers. The phase diagram on the pressure-temperature plane together with a critical comparison between our results and those found in the literature allowed us to draw conclusions on the mechanism of the unfolding process under different environmental conditions.
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Affiliation(s)
- Rita Puglisi
- UK-DRI at King's College London, The Wohl Institute, London, (UK)
| | | | | | | | - Annalisa Pastore
- UK-DRI at King's College London, The Wohl Institute, London, (UK); European Synchrotron Radiation Facility, Grenoble, (France).
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Girard E, Lopes P, Spoerner M, Dhaussy AC, Prangé T, Kalbitzer HR, Colloc'h N. Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography. Chem Sci 2022; 13:2001-2010. [PMID: 35308861 PMCID: PMC8848853 DOI: 10.1039/d1sc05488k] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/12/2022] [Indexed: 01/04/2023] Open
Abstract
In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg2+·GppNHp and Ras(D33K)·Mg2+·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners. The equilibria between structural states induced by pressure within the crystal structure of Ras are illustrated with different colors corresponding to different Ras substates.![]()
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Affiliation(s)
- Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pedro Lopes
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Michael Spoerner
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | | | - Thierry Prangé
- CiTCoM UMR 8038, CNRS Université de Paris, Faculté de Pharmacie, Paris, France
| | - Hans Robert Kalbitzer
- Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Regensburg, Germany
| | - Nathalie Colloc'h
- ISTCT UMR 6030, CNRS, Université de Caen Normandie, CERVOxy Group, Centre Cyceron, Caen, France
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5
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Effects of two sterilization methods on the taste compositions of sweet and sour spare ribs flavor. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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6
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Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. BIOLOGY 2021; 10:biology10070656. [PMID: 34356511 PMCID: PMC8301334 DOI: 10.3390/biology10070656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.
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A novel ER membrane protein Ehg1/May24 plays a critical role in maintaining multiple nutrient permeases in yeast under high-pressure perturbation. Sci Rep 2019; 9:18341. [PMID: 31797992 PMCID: PMC6892922 DOI: 10.1038/s41598-019-54925-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/19/2019] [Indexed: 12/24/2022] Open
Abstract
Previously, we isolated 84 deletion mutants in Saccharomyces cerevisiae auxotrophic background that exhibited hypersensitive growth under high hydrostatic pressure and/or low temperature. Here, we observed that 24 deletion mutants were rescued by the introduction of four plasmids (LEU2, HIS3, LYS2, and URA3) together to grow at 25 MPa, thereby suggesting close links between the genes and nutrient uptake. Most of the highly ranked genes were poorly characterized, including MAY24/YPR153W. May24 appeared to be localized in the endoplasmic reticulum (ER) membrane. Therefore, we designated this gene as EHG (ER-associated high-pressure growth gene) 1. Deletion of EHG1 led to reduced nutrient transport rates and decreases in the nutrient permease levels at 25 MPa. These results suggest that Ehg1 is required for the stability and functionality of the permeases under high pressure. Ehg1 physically interacted with nutrient permeases Hip1, Bap2, and Fur4; however, alanine substitutions for Pro17, Phe19, and Pro20, which were highly conserved among Ehg1 homologues in various yeast species, eliminated interactions with the permeases as well as the high-pressure growth ability. By functioning as a novel chaperone that facilitated coping with high-pressure-induced perturbations, Ehg1 could exert a stabilizing effect on nutrient permeases when they are present in the ER.
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Roche J, Royer CA, Roumestand C. Monitoring protein folding through high pressure NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:15-31. [PMID: 29157491 DOI: 10.1016/j.pnmrs.2017.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding.
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Affiliation(s)
- Julien Roche
- Roy J. Carver 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
| | - Christian Roumestand
- Centre de Biochimie Structural INSERM U1054, CNRS UMMR 5058, Université de Montpellier, Montpellier 34090, France.
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9
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Papini CM, Pandharipande PP, Royer CA, Makhatadze GI. Putting the Piezolyte Hypothesis under Pressure. Biophys J 2017; 113:974-977. [PMID: 28803626 DOI: 10.1016/j.bpj.2017.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/15/2017] [Accepted: 07/25/2017] [Indexed: 12/01/2022] Open
Abstract
A group of small molecules that stabilize proteins against high hydrostatic pressure has been classified as piezolytes, a subset of stabilizing cosolutes. This distinction would imply that piezolytes counteract the effects of high hydrostatic pressure through effects on the volumetric properties of the protein. The purpose of this study was to determine if cosolutes proposed to be piezolytes have an effect on the volumetric properties of proteins through direct experimental measurements of volume changes upon unfolding of model proteins lysozyme and ribonuclease A, in solutions containing varying cosolute concentrations. Solutions containing the proposed piezolytes glutamate, sarcosine, and betaine were used, as well as solutions containing the denaturants guanidinium hydrochloride and urea. Changes in thermostability were monitored using differential scanning calorimetry whereas changes in volume were monitored using pressure perturbation calorimetry. Our findings indicate that increasing stabilizing cosolute concentration increases the stability and transition temperature of the protein, but does not change the temperature dependence of volume changes upon unfolding. The results suggest that the pressure stability of a protein in solution is not directly affected by the presence of these proposed piezolytes, and so they cannot be granted this distinction.
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Affiliation(s)
- Christina M Papini
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Pranav P Pandharipande
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Catherine A Royer
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.
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10
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When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches. Biochem J 2017; 473:2545-59. [PMID: 27574021 PMCID: PMC5003694 DOI: 10.1042/bcj20160107] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/18/2016] [Indexed: 11/19/2022]
Abstract
Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats.
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11
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Nguyen LM, Roche J. High-pressure NMR techniques for the study of protein dynamics, folding and aggregation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 277:179-185. [PMID: 28363306 DOI: 10.1016/j.jmr.2017.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/07/2017] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins and dissociate protein complexes or aggregates. The heterogeneity of the response to pressure offers a unique opportunity to dissect the thermodynamic contributions to protein stability. In addition, pressure perturbation is generally reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility of monitoring at an atomic resolution the structural transitions occurring upon unfolding and determining the kinetic properties of the process. The recent development of commercially available high-pressure sample cells greatly increased the potential applications for high-pressure NMR experiments that can now be routinely performed. This review summarizes the recent applications and future directions of high-pressure NMR techniques for the characterization of protein conformational fluctuations, protein folding and the stability of protein complexes and aggregates.
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Affiliation(s)
- Luan M Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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12
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Halalipour A, Duff MR, Howell EE, Reyes-De-Corcuera JI. Glucose oxidase stabilization against thermal inactivation using high hydrostatic pressure and hydrophobic modification. Biotechnol Bioeng 2016; 114:516-525. [DOI: 10.1002/bit.26185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/14/2016] [Accepted: 09/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Ali Halalipour
- Department of Food Science and Technology; University of Georgia; Food Science Building, 100 Cedar St. Athens, Georgia 30602
| | - Michael R. Duff
- Department of Biochemistry, Cellular and Molecular Biology; University of Tennessee; Knoxville Tennessee
| | - Elizabeth E. Howell
- Department of Biochemistry, Cellular and Molecular Biology; University of Tennessee; Knoxville Tennessee
| | - José I. Reyes-De-Corcuera
- Department of Food Science and Technology; University of Georgia; Food Science Building, 100 Cedar St. Athens, Georgia 30602
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