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Li Y, Zhang Z, Abbaspourrad A. Improving solubility and functional properties of phycocyanin under acidic conditions by glutaminase deamidation and succinylation. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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2
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Del Val E, Nasser W, Abaibou H, Reverchon S. Design and comparative characterization of RecA variants. Sci Rep 2021; 11:21106. [PMID: 34702889 PMCID: PMC8548320 DOI: 10.1038/s41598-021-00589-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response. It is also used in the context of biotechnological applications in recombinase polymerase isothermal amplification (RPA). In this work, we studied the biological properties of seven RecA variants, in particular their recombinogenic activity and their ability to induce the SOS response, to better understand the structure-function relationship of RecA and the effect of combined mutations. We also investigated the biochemical properties of RecA variants that may be useful for the development of biotechnological applications. We showed that Dickeya dadantii RecA (DdRecA) had an optimum strand exchange activity at 30 °C and in the presence of a dNTP mixture that inhibited Escherichia coli RecA (EcRecA). The differences between the CTD and C-tail of the EcRecA and DdRecA domains could explain the altered behaviour of DdRecA. D. radiodurans RecA (DrRecA) was unable to perform recombination and activation of the SOS response in an E. coli context, probably due to its inability to interact with E. coli recombination accessory proteins and SOS LexA repressor. DrRecA strand exchange activity was totally inhibited in the presence of chloride ions but worked well in acetate buffer. The overproduction of Pseudomonas aeruginosa RecA (PaRecA) in an E. coli context was responsible for a higher SOS response and defects in cellular growth. PaRecA was less inhibited by the dNTP mixture than EcRecA. Finally, the study of three variants, namely, EcPa, EcRecAV1 and EcRecAV2, that contained a combination of mutations that, taken independently, are described as improving recombination, led us to raise new hypotheses on the structure-function relationship and on the monomer-monomer interactions that perturb the activity of the protein as a whole.
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Affiliation(s)
- Elsa Del Val
- UMR5240, Microbiologie, Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, 11 Avenue Jean Capelle, 69621, Villeurbanne, France
- Molecular Innovation Unit, Centre Christophe Mérieux, bioMérieux, 5 Rue des Berges, 38024, Grenoble Cedex 01, France
| | - William Nasser
- UMR5240, Microbiologie, Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, 11 Avenue Jean Capelle, 69621, Villeurbanne, France
| | - Hafid Abaibou
- Molecular Innovation Unit, Centre Christophe Mérieux, bioMérieux, 5 Rue des Berges, 38024, Grenoble Cedex 01, France.
| | - Sylvie Reverchon
- UMR5240, Microbiologie, Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, 11 Avenue Jean Capelle, 69621, Villeurbanne, France.
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3
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Rana S, Kherb J. Validation of specific cation partitioning to molecular surfaces using fluorescent carbon quantum dots. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Gong X, Li C, Zhai R, Xie J, Jiang Y, Fang X. Supercharging of Proteins by Salts during Polarity Reversed Nano-Electrospray Ionization. Anal Chem 2019; 91:1826-1837. [PMID: 30620564 DOI: 10.1021/acs.analchem.8b02759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Supercharging is beneficial in many ways to the analysis of proteins by mass spectrometry (MS). In this work, a novel supercharging method was developed. It made use of our previously developed ionization technique: namely, polarity reversed nanoelectrospray ionization (PR-nESI) for the ionization of proteins. Supercharging of proteins was achieved by just adding 1-10 mM of a salt to the sample, such as sodium chloride (NaCl). The charge state of proteins obtained by our method was significantly higher than that by nano-ESI with 1% (v/v) acetic acid (HAc). Different kinds of salts were investigated. Salts with strong acid anions were capable of supercharging proteins, including chlorides, bromides, iodides, and nitrates. The signal intensity and signal to noise ratio ( S/ N) of proteins were increased at the same time. Phosphates were also found to have a supercharging effect, due to the fact that phosphoric acid was a medium-strong acid. In comparison, salts with weak acid anions had no supercharging effect, such as carbonates, sulfides, acetates, and formates. The species of the salt anion was critical to the supercharging effect, while the species of the salt cation showed little influence on the supercharging effect. Investigations were made into the mechanism of our method. The supercharging effect was caused by interactions between protein molecules and salt anions, as well as the influence of protons. The present work offered us an alternative way for the supercharging of proteins. The use of common salts for supercharging made the procedure more convenient. The concentration of salts needed for supercharging was much lower than those conventionally used for supercharging reagents. Taking into consideration the fact that many biological samples are buffered with phosphates and chlorides, these samples could be directly supercharged by our method without any additional additives. Furthermore, as many salts are nontoxic and can easily be found in a chemical laboratory, the use of salts for supercharging would be a much more practical and economical choice. In addition, the present work also furthered our understandings about the mechanism of supercharging, as well as electrospray.
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Affiliation(s)
- Xiaoyun Gong
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Chang Li
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Rui Zhai
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Jie Xie
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - You Jiang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Xiang Fang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
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5
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Investigating the structural transitions of proteins during dissolution by mass spectrometry. Talanta 2017; 164:418-426. [DOI: 10.1016/j.talanta.2016.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022]
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6
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Borzooeian Z, Taslim ME, Borzooeian G, Ghasemi O, Aminlari M. Activity and stability analysis of covalent conjugated lysozyme-single walled carbon nanotubes: potential biomedical and industrial applications. RSC Adv 2017. [DOI: 10.1039/c7ra07189b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Analysis of covalent conjugated lysozyme-single walled carbon nanotubes.
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Affiliation(s)
- Z. Borzooeian
- Department of Mechanical and Industrial Engineering
- College of Engineering
- Northeastern University
- Boston
- USA
| | - M. E. Taslim
- Department of Mechanical and Industrial Engineering
- College of Engineering
- Northeastern University
- Boston
- USA
| | - G. Borzooeian
- Department of Biology
- Payame Noor University of Isfahan
- Iran
| | - O. Ghasemi
- Takeda Pharmaceuticals USA Inc
- Cambridge
- USA
| | - M. Aminlari
- Department of Biochemistry
- School of Veterinary Medicine
- Shiraz University
- Shiraz
- Iran
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Wu S, Wang Y, Shen T, Wang J, Zhang G. Investigation on the underlying mechanism: How fusion xylanase-ELPs self-assembles into insoluble active aggregates. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Light TP, Corbett KM, Metrick MA, MacDonald G. Hofmeister Ion-Induced Changes in Water Structure Correlate with Changes in Solvation of an Aggregated Protein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1360-1369. [PMID: 26760222 DOI: 10.1021/acs.langmuir.5b04489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RecA is a naturally aggregating Escherichia coli protein that catalyzes the strand exchange reaction utilized in DNA repair. Previous studies have shown that the presence of salts influence RecA activity, aggregation, and stability and that salts stabilize RecA in an inverse-anionic Hofmeister series. Here we utilized attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and circular dichroism (CD) to investigate how various Hofmeister salts alter the water structure and RecA solvation and aggregation. Spectroscopic studies performed in water and deuterium oxide suggest that salts alter water O-(1)H and O-(2)H stretch and bend vibrations as well as protein amide I (or I') and amide II (or II') vibrations. Anions have a much larger influence on water vibrations than cations. Water studies also show increased water-water and/or water-ion interactions in the presence of strongly hydrated SO4(2-) salts and evidence for decreased interactions with weakly hydrated Cl(-) and ClO4(-) salts. Salt-water difference infrared spectra show that kosmotropic salts are more hydrated than chaotropic salts. Interestingly, this is the opposite trend to the changes in protein solvation. Infrared spectra of RecA show that vibrations associated with protein desolvation were observed in the presence of SO4(2-) salts. Conversely, vibrations associated with protein solvation were observed in the presence of Cl(-) and ClO4(-) salts. Difference infrared studies on the dehydration of model proteins aided in identifying changes in RecA-solvent interactions. This study provides evidence that salt-induced changes in water vibrations correlate to changes in protein solvent interactions and thermal stability.
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Affiliation(s)
- Taylor P Light
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Karen M Corbett
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Michael A Metrick
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Gina MacDonald
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
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Metrick MA, Temple JE, MacDonald G. The effects of buffers and pH on the thermal stability, unfolding and substrate binding of RecA. Biophys Chem 2013; 184:29-36. [DOI: 10.1016/j.bpc.2013.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
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Bye JW, Falconer RJ. Thermal stability of lysozyme as a function of ion concentration: a reappraisal of the relationship between the Hofmeister series and protein stability. Protein Sci 2013; 22:1563-70. [PMID: 24038575 DOI: 10.1002/pro.2355] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 11/09/2022]
Abstract
Anion and cation effects on the structural stability of lysozyme were investigated using differential scanning calorimetry. At low concentrations (<5 mM) anions and cations alter the stability of lysozyme but they do not follow the Hofmeister (or inverse Hofmeister) series. At higher concentrations protein stabilization follows the well-established Hofmeister series. Our hypothesis is that there are three mechanisms at work. At low concentrations the anions interact with charged side chains where the presence of the ion can alter the structural stability of the protein. At higher concentrations the low charge density anions perchlorate and iodide interact weakly with the protein. Their presence however reduces the Gibbs free energy required to hydrate the core of the protein that is exposed during unfolding therefore destabilizing the structure. At higher concentrations the high charge density anions phosphate and sulfate compete for water with the protein as it unfolds increasing the Gibbs free energy required to hydrate the newly exposed core of the protein therefore stabilizing the structure.
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Affiliation(s)
- Jordan W Bye
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, England, United Kingdom
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