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SAXS Reveals the Stabilization Effects of Modified Sugars on Model Proteins. Life (Basel) 2022; 12:life12010123. [PMID: 35054516 PMCID: PMC8778440 DOI: 10.3390/life12010123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/31/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Many proteins are usually not stable under different stresses, such as temperature and pH variations, mechanical stresses, high concentrations, and high saline contents, and their transport is always difficult, because they need to be maintained in a cold regime, which is costly and very challenging to achieve in remote areas of the world. For this reason, it is extremely important to find stabilizing agents that are able to preserve and protect proteins against denaturation. In the present work, we investigate, by extensively using synchrotron small-angle X-ray scattering experiments, the stabilization effect of five different sugar-derived compounds developed at ExtremoChem on two model proteins: myoglobin and insulin. The data analysis, based on a novel method that combines structural and thermodynamic features, has provided details about the physical-chemical processes that regulate the stability of these proteins in the presence of stabilizing compounds. The results clearly show that some modified sugars exert a greater stabilizing effect than others, being able to maintain the active forms of proteins at temperatures higher than those in which proteins, in the absence of stabilizers, reach denatured states.
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Liu H, Li Q, Zhao D, Zhang M, Jiang S, Li C. Changes in the structure and digestibility of myoglobin treated with sodium chloride. Food Chem 2021; 363:130284. [PMID: 34120050 DOI: 10.1016/j.foodchem.2021.130284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Myoglobin is a protein not easily broken down by digestive enzymes due to its rigid structure. This study evaluated the structural characteristics of myoglobin under various sodium chloride treatments (0.4-0.8 mol/L for 5-10 h) and the impacts on its digestibility using spectroscopic and molecular dynamics simulation techniques. Myoglobin digestibility was 40% following pepsin digestion and 60% after being sequentially digested by pepsin and trypsin. The α-helix content of myoglobin did not change significantly following sodium chloride treatment but hydrophobic amino acids were exposed and the binding of phenylalanine targeted by some digestive enzymes became more stable, leading to the reduced digestibility.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Zhao
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Miao Zhang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Jiang
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, Jiangsu Collaborative Innovation Center of Meat Production, Processing and Quality Control; College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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Asami H, Kawabata R, Kawauchi N, Kohno JY. Photodissociation Spectroscopy of Hydrated Myoglobin Ions Isolated by IR-laser Ablation of a Droplet Beam: Recovery from pH-denatured Structure by Gas-phase Isolation. CHEM LETT 2019. [DOI: 10.1246/cl.180884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hiroya Asami
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Rina Kawabata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Norishi Kawauchi
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Jun-ya Kohno
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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Mukherjee S, Mukherjee M, Bandyopadhyay S, Dey A. Three phases in pH dependent heme abstraction from myoglobin. J Inorg Biochem 2017; 172:80-87. [DOI: 10.1016/j.jinorgbio.2017.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 04/04/2017] [Accepted: 04/08/2017] [Indexed: 10/19/2022]
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5
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Choi J, Yang C, Kim J, Ihee H. Protein Folding Dynamics of Cytochrome c Seen by Transient Grating and Transient Absorption Spectroscopies. J Phys Chem B 2011; 115:3127-35. [DOI: 10.1021/jp106588d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jungkweon Choi
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Cheolhee Yang
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Jeongho Kim
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
| | - Hyotcherl Ihee
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
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6
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Terazima M. Time-dependent intermolecular interaction during protein reactions. Phys Chem Chem Phys 2011; 13:16928-40. [DOI: 10.1039/c1cp21868a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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7
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Choi J, Muniyappan S, Wallis JT, Royer WE, Ihee H. Protein conformational dynamics of homodimeric hemoglobin revealed by combined time-resolved spectroscopic probes. Chemphyschem 2010; 11:109-14. [PMID: 19924759 DOI: 10.1002/cphc.200900822] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jungkweon Choi
- Center for Time-Resolved Diffraction, Department of Chemistry, Graduate School of Nanoscience & Technology (WCU), KAIST, Daejeon 305-701, Republic of Korea
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8
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Tanaka K, Nakasone Y, Okajima K, Ikeuchi M, Tokutomi S, Terazima M. Oligomeric-state-dependent conformational change of the BLUF protein TePixD (Tll0078). J Mol Biol 2009; 386:1290-300. [PMID: 19452599 DOI: 10.1016/j.jmb.2009.01.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The photochemical reaction dynamics of a BLUF (sensors of blue light using FAD) protein, PixD, from a thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePixD, Tll0078) were studied by pulsed laser-induced transient grating method. After the formation of an intermediate species with a red-shifted absorption spectrum, two new reaction phases reflecting protein conformational changes were discovered; one reaction phase manifested itself as expansion of partial molar volume with a time constant of 40 micros, whereas the other reaction phase represented a change in the diffusion coefficient D [i.e., the diffusion-sensitive conformational change (DSCC)]. D decreased from 4.9 x 10(-11) to 4.4 x 10(-11) m2 s(-1) upon the formation of the first intermediate, and subsequently showed a more pronounced decrease to 3.2 x 10(-11) m2 s(-1) upon formation of the second intermediate. From a global analysis of signals at various grating wavenumbers, the time constant of D-change was determined to be 4 ms. Although the magnitude and rate constant of the faster volume change were independent of protein concentration, the amplitude of the signal that reflects the later DSCC significantly decreased as the protein concentration decreased. This concentration dependence suggests that two species exist in solution: a reactive species exhibiting the DSCC, and a second species that is nonreactive. The fraction of these species was found to be dependent on the concentration. The difference in reactivity was attributed to the different oligomeric states of TePixD (i.e., pentamer and decamer). The equilibrium of these states in the dark was confirmed by size-exclusion chromatography at various concentrations. These results demonstrated that only the decamer state is responsible for the conformational change. The results may suggest that the oligomeric state is functionally important in the signal transduction of this photosensory protein.
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Affiliation(s)
- Keisuke Tanaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Djikaev YS, Ruckenstein E. The role of hydrogen bond networks in the barrierless thermal denaturation of a native protein. J Chem Phys 2009; 131:045105. [DOI: 10.1063/1.3179688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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10
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Effects of urea and acetic acid on the heme axial ligation structure of ferric myoglobin at very acidic pH. Arch Biochem Biophys 2009; 489:68-75. [PMID: 19622342 DOI: 10.1016/j.abb.2009.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/15/2009] [Accepted: 07/15/2009] [Indexed: 12/15/2022]
Abstract
The heme iron coordination of ferric myoglobin (Mb) in the presence of 9.0M urea and 8.0M acetic acid at acidic pH values has been probed by electronic absorption, magnetic circular dichroism and resonance Raman spectroscopic techniques. Unlike Mb at pH 2.0, where heme is not released from the protein despite the acid denaturation and the loss of the axial ligand, upon increasing the concentration of either urea or acetic acid, a spin state change is observed, and a novel, non-native six-coordinated high-spin species prevails, where heme is released from the protein.
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Choi J, Jung YO, Lee JH, Yang C, Kim B, Ihee H. Folding Dynamics of Ferrocytochrome c in a Denaturant-Free Environment Probed by Transient Grating Spectroscopy. Chemphyschem 2008; 9:2708-14. [DOI: 10.1002/cphc.200800280] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Djikaev YS, Ruckenstein E. Thermal denaturation of a native protein via spinodal decomposition in the framework of first-passage-time analysis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:011909. [PMID: 18763984 DOI: 10.1103/physreve.78.011909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Indexed: 05/26/2023]
Abstract
In this paper we present a kinetic model for the thermal unfolding of a native protein. Due to a sufficiently large temperature increase or decrease, the rate with which a cluster of native residues within a protein emits residues becomes larger than the rate of absorption of residues from the unfolded part of the protein in the whole range of cluster sizes up to the size of the whole protein. This leads to the unfolding of the protein in a barrierless way, i.e., as spinodal decomposition. Using the formalism of the first passage time analysis [previously applied also to the problem of protein folding via nucleation by the authors, J. Phys. Chem. B 111, 886 (2007); J. Chem. Phys. 126, 175103 (2007)], one can determine the temperature dependence of the rates of emission and absorption of residues by the cluster. Knowing these rates as functions of temperature and cluster size, one can find the threshold temperatures of cold and hot barrierless denaturation as well as the unfolding times at temperatures lower and higher, respectively, than those threshold values. For a numerical illustration, the method is applied to the thermal unfolding of a model protein consisting of 2500 residues.
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Affiliation(s)
- Y S Djikaev
- Department of Chemical and Biological Engineering, SUNY at Buffalo, Buffalo, New York 14260, USA.
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Eitoku T, Terazima M. Protein diffusion probed by the transient grating method with a new type of photochromic molecule. Photochem Photobiol 2008; 84:869-73. [PMID: 18346090 DOI: 10.1111/j.1751-1097.2008.00315.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new type of photochromic molecule that can be used for diffusion coefficient (D) measurements of various proteins in solution is described. The absorption spectrum of this molecule is changed upon photoexcitation by the trans-cis isomerization reaction. Target proteins were labeled by this photochromic molecule in the dark and the translational motion of the proteins was detected by the transient grating (TG) method. The TG signal was simple enough to determine D accurately and was stable even for long-time irradiation by the laser light. The TG method using this probe molecule improves many drawbacks of the other techniques.
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Affiliation(s)
- Takeshi Eitoku
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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14
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Baden N, Hirota S, Takabe T, Funasaki N, Terazima M. Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time domain. J Chem Phys 2007; 127:175103. [PMID: 17994853 DOI: 10.1063/1.2780860] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- N Baden
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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