1
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Almeida DV, Ciancaglini I, Sandano ALH, Roman EKB, Andrade VB, Nunes AB, Tramontina R, da Silva VM, Gabel F, Corrêa TLR, Damasio A, Muniz JRC, Squina FM, Garcia W. Unveiling the crystal structure of thermostable dienelactone hydrolase exhibiting activity on terephthalate esters. Enzyme Microb Technol 2024; 180:110498. [PMID: 39182429 DOI: 10.1016/j.enzmictec.2024.110498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 08/06/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Dienelactone hydrolase (DLH) is one of numerous hydrolytic enzymes with an α/β-hydrolase fold, which catalyze the hydrolysis of dienelactone to maleylacetate. The DLHs share remarkably similar tertiary structures and a conserved arrangement of catalytic residues. This study presents the crystal structure and comprehensive functional characterization of a novel thermostable DLH from the bacterium Hydrogenobacter thermophilus (HtDLH). The crystal structure of the HtDLH, solved at a resolution of about 1.67 Å, exhibits a canonical α/β-hydrolase fold formed by eight β-sheet strands in the core, with one buried α-helix and six others exposed to the solvent. The structure also confirmed the conserved catalytic triad of DHLs formed by Cys121, Asp170, and His202 residues. The HtDLH forms stable homodimers in solution. Functional studies showed that HtDLH has the expected esterase activity over esters with short carbon chains, such as p-nitrophenyl acetate, reaching optimal activity at pH 7.5 and 70 °C. Furthermore, HtDLH maintains more than 50 % of its activity even after incubation at 90 °C for 16 h. Interestingly, HtDLH exhibits catalytic activity towards polyethylene terephthalate (PET) monomers, including bis-1,2-hydroxyethyl terephthalate (BHET) and 1-(2-hydroxyethyl) 4-methyl terephthalate, as well as other aliphatic and aromatic esters. These findings associated with the lack of activity on amorphous PET indicate that HtDLH has characteristic of a BHET-degrading enzyme. This work expands our understanding of enzyme families involved in PET degradation, providing novel insights for plastic biorecycling through protein engineering, which could lead to eco-friendly solutions to reduce the accumulation of plastic in landfills and natural environments.
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Affiliation(s)
- Dnane Vieira Almeida
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil
| | - Iara Ciancaglini
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Ellen K B Roman
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Viviane Brito Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil
| | - Ana Bárbara Nunes
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Robson Tramontina
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Viviam Moura da Silva
- Institut de Biologie Structurale (IBS), CEA, CNRS, UGA, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Frank Gabel
- Institut de Biologie Structurale (IBS), CEA, CNRS, UGA, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Thamy L R Corrêa
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Fabio Marcio Squina
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil.
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil.
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2
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Banerjee S, Mitra M, Roy S. Study of changes in folding/unfolding properties and stability of Arabidopsis thaliana MYB12 transcription factor following UV-B exposure in vitro. Heliyon 2024; 10:e34189. [PMID: 39071576 PMCID: PMC11279800 DOI: 10.1016/j.heliyon.2024.e34189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 06/14/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024] Open
Abstract
Flavonoids mostly protect plant cells from the harmful effects of UV-B radiation from the sun. In plants, the R2R3-subfamily of the MYB transcription factor, MYB12, is a key inducer of the biosynthesis of flavonoids. Our study involves the biophysical characterization of Arabidopsis thaliana MYB12 protein (AtMYB12) under UV-B exposure in vitro. Tryptophan fluorescence studies using recombinant full-length AtMYB12 (native) and the N-terminal truncated versions (first N-terminal MYB domain absent in AtMYB12Δ1, and both the first and second N-terminal MYB domains absent in AtMYB12Δ2) have revealed prominent alteration in the tryptophan microenvironment in AtMYB12Δ1 and AtMYB12Δ2 protein as a result of UV-B exposure as compared with the native AtMYB12. Bis-ANS binding assay and urea-mediated denaturation profiling showed an appreciable change in the structural conformation in AtMYB12Δ1 and AtMYB12Δ2 proteins as compared with the native AtMYB12 protein following UV-B irradiation. UV-B-treated AtMYB12Δ2 showed a higher predisposition of aggregate formation in vitro. CD spectral analyses revealed a decrease in α-helix percentage with a concomitant increase in random coiled structure formation in AtMYB12Δ1 and AtMYB12Δ2 as compared to native AtMYB12 following UV-B treatment. Overall, these findings highlight the critical function of the N-terminal MYB domains in maintaining the stability and structural conformation of the AtMYB12 protein under UV-B stress in vitro.
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Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Centre for Advance Study, The University of Burdwan, Golapbag Campus, Burdwan, 713104, West Bengal, India
| | | | - Sujit Roy
- Department of Botany, UGC Centre for Advance Study, The University of Burdwan, Golapbag Campus, Burdwan, 713104, West Bengal, India
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3
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Jenney FE, Wang H, George SJ, Xiong J, Guo Y, Gee LB, Marizcurrena JJ, Castro-Sowinski S, Staskiewicz A, Yoda Y, Hu MY, Tamasaku K, Nagasawa N, Li L, Matsuura H, Doukov T, Cramer SP. Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'. Sci Rep 2024; 14:12197. [PMID: 38806591 PMCID: PMC11133467 DOI: 10.1038/s41598-024-62261-2] [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: 12/15/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
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Affiliation(s)
- Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | | | | | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leland B Gee
- LCLS, SLAC National Laboratory, Stanford, CA, 94025, USA
| | | | | | - Anna Staskiewicz
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA
| | - Yoshitaka Yoda
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | | | - Nobumoto Nagasawa
- Precision Spectroscopy Division, SPring-8/JASRI, Sayo, Hyogo, 679-5198, Japan
| | - Lei Li
- Synchrotron Radiation Research Center, Hyogo, 679-5165, Japan
| | | | - Tzanko Doukov
- SSRL, SLAC National Laboratory, Stanford, CA, 94025, USA
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4
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Utzman PH, Mays VP, Miller BC, Fairbanks MC, Brazelton WJ, Horvath MP. Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field. PLoS One 2024; 19:e0284642. [PMID: 38718041 PMCID: PMC11078426 DOI: 10.1371/journal.pone.0284642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.
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Affiliation(s)
- Payton H. Utzman
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Vincent P. Mays
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary C. Fairbanks
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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5
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Kham NNN, Phovisay S, Unban K, Kanpiengjai A, Saenjum C, Lumyong S, Shetty K, Khanongnuch C. A Thermotolerant Yeast Cyberlindnera rhodanensis DK Isolated from Laphet-so Capable of Extracellular Thermostable β-Glucosidase Production. J Fungi (Basel) 2024; 10:243. [PMID: 38667914 PMCID: PMC11051217 DOI: 10.3390/jof10040243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
This study aims to utilize the microbial resources found within Laphet-so, a traditional fermented tea in Myanmar. A total of 18 isolates of thermotolerant yeasts were obtained from eight samples of Laphet-so collected from southern Shan state, Myanmar. All isolates demonstrated the tannin tolerance, and six isolates were resistant to 5% (w/v) tannin concentration. All 18 isolates were capable of carboxy-methyl cellulose (CMC) degrading, but only the isolate DK showed ethanol production at 45 °C noticed by gas formation. This ethanol producing yeast was identified to be Cyberlindnera rhodanensis based on the sequence analysis of the D1/D2 domain on rRNA gene. C. rhodanensis DK produced 1.70 ± 0.01 U of thermostable extracellular β-glucosidase when cultured at 37 °C for 24 h using 0.5% (w/v) CMC as a carbon source. The best two carbon sources for extracellular β-glucosidase production were found to be either xylose or xylan, with β-glucosidase activity of 3.07-3.08 U/mL when the yeast was cultivated in the yeast malt extract (YM) broth containing either 1% (w/v) xylose or xylan as a sole carbon source at 37 °C for 48 h. The optimal medium compositions for enzyme production predicted by Plackett-Burman design and central composite design (CCD) was composed of yeast extract 5.83 g/L, peptone 10.81 g/L and xylose 20.20 g/L, resulting in a production of 7.96 U/mL, while the medium composed (g/L) of yeast extract 5.79, peptone 13.68 and xylan 20.16 gave 9.45 ± 0.03 U/mL for 48 h cultivation at 37 °C. Crude β-glucosidase exhibited a remarkable stability of 100%, 88% and 75% stable for 3 h at 35, 45 and 55 °C, respectively.
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Affiliation(s)
- Nang Nwet Noon Kham
- Division of Biotechnology, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50100, Thailand; (N.N.N.K.); (S.P.)
| | - Somsay Phovisay
- Division of Biotechnology, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50100, Thailand; (N.N.N.K.); (S.P.)
| | - Kridsada Unban
- Division of Food Science and Technology, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50100, Thailand;
| | - Apinun Kanpiengjai
- Division of Biochemistry and Biochemical Innovation, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Chalermpong Saenjum
- Department of Pharmaceutical Science, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Kalidas Shetty
- Global Institute of Food Security and International Agriculture (GIFSIA), Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA;
| | - Chartchai Khanongnuch
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center for Multidisciplinary Approaches to Miang, Multidisciplinary Research Institute, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center for Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
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Leadbeater DR, Bruce NC. Functional characterisation of a new halotolerant seawater active glycoside hydrolase family 6 cellobiohydrolase from a salt marsh. Sci Rep 2024; 14:3205. [PMID: 38332324 PMCID: PMC10853513 DOI: 10.1038/s41598-024-53886-4] [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: 10/18/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Realising a fully circular bioeconomy requires the valorisation of lignocellulosic biomass. Cellulose is the most attractive component of lignocellulose but depolymerisation is inefficient, expensive and resource intensive requiring substantial volumes of potable water. Seawater is an attractive prospective replacement, however seawater tolerant enzymes are required for the development of seawater-based biorefineries. Here, we report a halophilic cellobiohydrolase SMECel6A, identified and isolated from a salt marsh meta-exo-proteome dataset with high sequence divergence to previously characterised cellobiohydrolases. SMECel6A contains a glycoside hydrolase family 6 (GH6) domain and a carbohydrate binding module family 2 (CBM2) domain. Characterisation of recombinant SMECel6A revealed SMECel6A to be active upon crystalline and amorphous cellulose. Mono- and oligosaccharide product profiles revealed cellobiose as the major hydrolysis product confirming SMECel6A as a cellobiohydrolase. We show SMECel6A to be halophilic with optimal activity achieved in 0.5X seawater displaying 80.6 ± 6.93% activity in 1 × seawater. Structural predictions revealed similarity to a characterised halophilic cellobiohydrolase despite sharing only 57% sequence identity. Sequential thermocycling revealed SMECel6A had the ability to partially reversibly denature exclusively in seawater retaining significant activity. Our study confirms that salt marsh ecosystems harbour enzymes with attractive traits with biotechnological potential for implementation in ionic solution based bioprocessing systems.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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Alwehaidah MS, Alsabbagh M, Al-Kafaji G. Comprehensive analysis of mitochondrial DNA variants, mitochondrial DNA copy number and oxidative damage in psoriatic arthritis. Biomed Rep 2023; 19:85. [PMID: 37881602 PMCID: PMC10594069 DOI: 10.3892/br.2023.1667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Growing evidence suggests that abnormalities in mitochondrial DNA (mtDNA) are involved in the pathogenesis of various inflammatory and immuno-mediated diseases. The present study analysed the entire mitochondrial genome by next-generation sequencing (NGS) in 23 patients with psoriatic arthritis (PsA) and 20 healthy controls to identify PsA-related variants. Changes in mtDNA copy number (mtDNAcn) were also evaluated by quantitative polymerase chain reaction (qPCR) and mtDNA oxidative damage was measured using an 8-hydroxy-2'-deoxyguanosine assay. NGS analysis revealed a total of 435 variants including 187 in patients with PsA only and 122 in controls only. Additionally, 126 common variants were found, of which 2 variants differed significantly in their frequencies among patients and controls (P<0.05), and may be associated with susceptibility to PsA. A total of 33 missense variants in mtDNA-encoded genes for complexes I, III, IV and V were identified only in patients with PsA. Of them, 25 variants were predicted to be deleterious by affecting the functions and structures of encoded proteins, and 13 variants were predicted to affect protein's stability. mtDNAcn analysis revealed decreased mtDNA content in patients with PsA compared with controls (P=0.0001) but the decrease in mtDNAcn was not correlated with patients' age or inflammatory biomarkers (P>0.05). Moreover, a higher level of oxidative damage was observed in patients with PsA compared with controls (P=0.03). The results of the present comprehensive analysis of mtDNA in PsA revealed that certain mtDNA variants may be implicated in the predisposition/pathogenesis of PsA, highlighting the importance of NGS in the identification of mtDNA variants in PsA. The current results also demonstrated that decreased mtDNAcn in PsA may be a consequence of increased oxidative stress. These data provide valuable insights into the contribution of mtDNA defects to the pathogenesis of PsA. Additional studies in larger cohorts are needed to elucidate the role of mtDNA defects in PsA.
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Affiliation(s)
- Materah Salem Alwehaidah
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, City of Kuwait 31470, State of Kuwait
| | - Manhel Alsabbagh
- Department of Molecular Medicine and Al-Jawhara Centre for Molecular Medicine, Genetics, and Inherited Disorders, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 26671, Kingdom of Bahrain
| | - Ghada Al-Kafaji
- Department of Molecular Medicine and Al-Jawhara Centre for Molecular Medicine, Genetics, and Inherited Disorders, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 26671, Kingdom of Bahrain
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8
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Pastore A, Temussi PA. Unfolding under Pressure: An NMR Perspective. Chembiochem 2023; 24:e202300164. [PMID: 37154795 DOI: 10.1002/cbic.202300164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
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Affiliation(s)
- Annalisa Pastore
- European Synchrotron Radiation Facilities, 71 Ave des Martyrs, 38000, Grenoble, France
- The Wohl Institute, King's College London, 5 Cutcombe Rd, SE59RT, London, UK
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9
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Biological role of the major AP (abasic site) endonuclease of an archaeon from geothermal environments. Extremophiles 2023; 27:1. [DOI: 10.1007/s00792-022-01286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
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10
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Ribeiro AL, Sánchez M, Bosch S, Berenguer J, Hidalgo A. Stabilization of Enzymes by Using Thermophiles. Methods Mol Biol 2023; 2704:313-328. [PMID: 37642853 DOI: 10.1007/978-1-0716-3385-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Manufactured steroid compounds have many applications in the pharmaceutical industry. Due to the chemical complexity and chirality of steroids, there is an increasing demand for enzyme-based bioconversion processes to replace those based on chemical synthesis. In this context, thermostability of the involved enzymes is a highly desirable property as both the increased half-life of the enzyme and the enhanced solubility of substrates and products will improve the yield of the reactions. Metagenomic libraries from thermal environments are potential sources of thermostable enzymes of prokaryotic origin, but the number of expected hits could be quite low for enzymes handling substrates such as steroids, rarely found in prokaryotes. An alternative to metagenome screening is the selection of thermostable variants of well-known steroid-processing enzymes. Here we review and detail a protocol for such selection, where error-prone PCR (epPCR) is used to introduce random mutations into a gene to create a variants library for further selection of thermostable variants in the thermophile Thermus thermophilus. The method involves the use of folding interference vectors where the proper folding of the enzyme of interest at high temperature is linked to the folding of a reporter encoding a selectable property such as thermostable resistance to kanamycin, leading to a life-or-death selection of variants of reinforced folding independently of the activity of the enzyme.
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Affiliation(s)
- Ana-Luisa Ribeiro
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - Mercedes Sánchez
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - Sandra Bosch
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - José Berenguer
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain
| | - Aurelio Hidalgo
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC). Facultad de Ciencias. Universidad Autónoma de Madrid, Madrid, Spain.
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11
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Röllig R, Paul CE, Duquesne K, Kara S, Alphand V. Exploring the Temperature Effect on Enantioselectivity of a Baeyer-Villiger Biooxidation by the 2,5-DKCMO Module: The SLM Approach. Chembiochem 2022; 23:e202200293. [PMID: 35648642 PMCID: PMC9400988 DOI: 10.1002/cbic.202200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Temperature is a crucial parameter for biological and chemical processes. Its effect on enzymatically catalysed reactions has been known for decades, and stereo- and enantiopreference are often temperature-dependent. For the first time, we present the temperature effect on the Baeyer-Villiger oxidation of rac-bicyclo[3.2.0]hept-2-en-6-one by the type II Bayer-Villiger monooxygenase, 2,5-DKCMO. In the absence of a reductase and driven by the hydride-donation of a synthetic nicotinamide analogue, the clear trend for a decreasing enantioselectivity at higher temperatures was observed. "Traditional" approaches such as the determination of the enantiomeric ratio (E) appeared unsuitable due to the complexity of the system. To quantify the trend, we chose to use the 'Shape Language Modelling' (SLM), a tool that allows the reaction to be described at all points in a shape prescriptive manner. Thus, without knowing the equation of the reaction, the substrate ee can be estimated that at any conversion.
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Affiliation(s)
- Robert Röllig
- Aix-Marseille UnivCNRSCentrale MarseilleiSm2 UMR CMRS 7313Aix-Marseille UniversitéPôle de l'Etoile Avenue Escadrille Normandie Niemen13397MarseilleFrance
- Biocatalysis and Bioprocessing GroupDepartment of Biological and Chemical EngineeringAarhus UniversityGustav Wieds Vej 10Aarhus8000 Aarhus CDenmark
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 9Delft2629 HZThe Netherlands
| | - Katia Duquesne
- Aix-Marseille UnivCNRSCentrale MarseilleiSm2 UMR CMRS 7313Aix-Marseille UniversitéPôle de l'Etoile Avenue Escadrille Normandie Niemen13397MarseilleFrance
| | - Selin Kara
- Biocatalysis and Bioprocessing GroupDepartment of Biological and Chemical EngineeringAarhus UniversityGustav Wieds Vej 10Aarhus8000 Aarhus CDenmark
| | - Véronique Alphand
- Aix-Marseille UnivCNRSCentrale MarseilleiSm2 UMR CMRS 7313Aix-Marseille UniversitéPôle de l'Etoile Avenue Escadrille Normandie Niemen13397MarseilleFrance
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Ahmad A, Rahamtullah, Mishra R. Structural and functional adaptation in extremophilic microbial α-amylases. Biophys Rev 2022; 14:499-515. [PMID: 35528036 PMCID: PMC9043155 DOI: 10.1007/s12551-022-00931-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rahamtullah
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
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13
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Yuan JF, Hou ZC, Wang DH, Qiu ZJ, Gong MG, Sun JR. Microwave irradiation: Effect on activities and properties of polyphenol oxidase in grape maceration stage. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Lim JS, Ha JW. Growth temperature influences the resistance of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium on lettuce to X-ray irradiation. Food Microbiol 2021; 99:103825. [PMID: 34119110 DOI: 10.1016/j.fm.2021.103825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 01/22/2023]
Abstract
This study aimed to investigate the effect of different growth temperatures on the resistance of Escherichia coli O157:H7 and Salmonella Typhimurium to low-energy X-ray irradiation. Irradiation of contaminated phosphate-buffered saline with 0.6 kGy X-ray decreased the counts of E. coli O157:H7 cultured at 37 °C to below the detection limit (<1.0 colony-forming unit (CFU)/mL) and those of E. coli O157:H7 cultured at 25 and 15 °C by 4.82 and 4.45 log CFU/mL, respectively. The viable counts of S. Typhimurium cultured at 37, 25, and 15 °C in phosphate-buffered saline decreased by 3.56, 3.08, and 2.75 log CFU/mL, respectively, after irradiation with 0.6 kGy X-ray. Irradiation of contaminated lettuce with 0.4 kGy decreased the counts of E. coli O157:H7 cultured at 37, 25, and 15 °C by 3.97, 3.45, and 3.10 log CFU/cm2, respectively, and those of S. Typhimurium by 4.41, 3.84, and 3.40 log CFU/cm2, respectively. Growth temperature influenced pathogen resistance to X-ray irradiation by modulating cellular membrane and DNA integrity, intracellular enzyme activity, and efflux pump function. The results of this study suggest that the stress resistance status of pathogenic bacteria cultured at different growth temperatures should be considered for the application of X-ray irradiation for fresh produce sterilization.
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Affiliation(s)
- Jong-Seong Lim
- Department of Food Science and Biotechnology, Global K-Food Research Center, Hankyong National University, Anseong-si, 17579, South Korea
| | - Jae-Won Ha
- Department of Food Science and Biotechnology, Global K-Food Research Center, Hankyong National University, Anseong-si, 17579, South Korea.
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15
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Penhallurick RW, Durnal MD, Harold A, Ichiye T. Adaptations for Pressure and Temperature in Dihydrofolate Reductases. Microorganisms 2021; 9:microorganisms9081706. [PMID: 34442785 PMCID: PMC8399027 DOI: 10.3390/microorganisms9081706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 11/18/2022] Open
Abstract
Enzymes from extremophilic microbes that live in extreme conditions are generally adapted so that they function under those conditions, although adaptations for extreme temperatures and pressures can be difficult to unravel. Previous studies have shown mutation of Asp27 in Escherichia coli dihydrofolate reductase (DHFR) to Glu27 in Moritella profunda (Mp). DHFR enhances activity at higher pressures, although this may be an adaptation for cold. Interestingly, MpDHFR unfolds at ~70 MPa, while Moritella yayanosii (My) was isolated at depths corresponding to ~110 MPa, indicating that MyDHFR might be adapted for higher pressures. Here, these adaptations are examined using molecular dynamics simulations of DHFR from different microbes in the context of not only experimental studies of activity and stability of the protein but also the evolutionary history of the microbe. Results suggest Tyr103 of MyDHFR may be an adaptation for high pressure since Cys103 in helix F of MpDHFR forms an intra-helix hydrogen bond with Ile99 while Tyr103 in helix F of MyDHFR forms a hydrogen bond with Leu78 in helix E. This suggests the hydrogen bond between helices F and E in MyDHFR might prevent distortion at higher pressures.
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16
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Chen Z, Fan Y, Wang L, Bian Z, Hao L. Controlling the adsorption of osteopontin for mediating cell behaviour by using self-assembled monolayers with varying surface chemistry. RSC Adv 2021; 11:36360-36366. [PMID: 35492794 PMCID: PMC9043331 DOI: 10.1039/d1ra04063d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Osteopontin (OPN) is an important protein for mediating cell behaviour on biomaterials. However, the interactions between the chemical groups on the biomaterial surface and OPN still need to be further clarified, which has restricted the application of OPN in biomaterial functionalization. In the present study, we developed different self-assembled monolayers (SAMs) with specific chemical groups, including SAMs-OH, SAMs-OEG, SAMs-COOH, SAMs-NH2, and SAMs-PO3H2, to study the behavior of OPN on these SAMs. The results showed that SAMs-NH2 could strongly adsorb OPN, and the amount of protein was highest on this material. Meanwhile, the lowest amount of OPN was present on SAMs-OEG. Interestingly, the unit-mass trend of bound OPN monoclonal antibodies (mAbs) on the SAMs was opposite to the OPN adsorption trend: lowest on SAMs-NH2 but highest on SAMs-OEG. In vitro cell assay results showed that mouse bone marrow mesenchymal stem cells (mBMSCs) on SAMs-COOH, SAMs-NH2, and SAMs-PO3H2 with pre-adsorbed OPN showed promoted behaviour, in terms of spreading, viability, and the expression levels of αv and β3 genes, compared with the other two SAMs, demonstrating the higher bioactivity of the adsorbed OPN. We believe that our findings will have great potential for developing OPN-activated biomaterials. Osteopontin (OPN) is an important protein for mediating cell behaviour on biomaterials.![]()
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Affiliation(s)
- Zhuoying Chen
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yan Fan
- National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006, China
| | - Lin Wang
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006, China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, Guangzhou 510006, China
| | - Zhengqi Bian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Key Laboratory of Biomedical Engineering of Guangdong Province, Guangzhou 510006, China
| | - Lijing Hao
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Innovation Center for Tissue Restoration and Reconstruction, Guangzhou 510006, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005 Guangzhou, China
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17
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Hjörleifsson JG, Helland R, Magnúsdóttir M, Ásgeirsson B. The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop. FEBS Open Bio 2020; 11:173-184. [PMID: 33197282 PMCID: PMC7780099 DOI: 10.1002/2211-5463.13041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium Vibrio splendidus (VAP) is characterized by an analogous large surface loop in each monomer, referred to as the large loop, that hovers over the active site of the other monomer. It presumably has a role in the high catalytic efficiency of VAP which accompanies its extremely low thermal stability. Here, we designed several different variants of VAP with the aim of removing intersubunit interactions at the dimer interface. Breaking the intersubunit contacts from one residue in particular (Arg336) reduced the temperature stability of the catalytically potent conformation and caused a 40% drop in catalytic rate. The high catalytic rates of enzymes from cold‐adapted organisms are often associated with increased dynamic flexibility. Comparison of the relative B‐factors of the R336L crystal structure to that of the wild‐type confirmed surface flexibility was increased in a loop on the opposite monomer, but not in the large loop. The increase in flexibility resulted in a reduced catalytic rate. The large loop increases the area of the interface between the subunits through its contacts and may facilitate an alternating structural cycle demanded by a half‐of‐sites reaction mechanism through stronger ties, as the dimer oscillates between high affinity (active) or low phosphoryl group affinity (inactive).
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Affiliation(s)
| | - Ronny Helland
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT, The Arctic University of Tromsø, Norway
| | - Manuela Magnúsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Bjarni Ásgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
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18
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Koko MYF, Mu W, Hassanin HAM, Zhang S, Lu H, Mohammed JK, Hussain M, Baokun Q, Yang L. Archaeal hyperthermostable mannitol dehydrogenases: A promising industrial enzymes for d-mannitol synthesis. Food Res Int 2020; 137:109638. [PMID: 33233217 DOI: 10.1016/j.foodres.2020.109638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022]
Abstract
Recently, the term healthy lifestyle connected to low-calorie diets, although it is not possible to get rid of added sugars as a source of energy, despite the close relation of added sugars to some diseases such as obesity, diabetes, etc. As a result, the sweetener market has flourished, which has led to increased demand for natural sweeteners such as polyols, including d-mannitol. Various methods have been developed to produce d-mannitol to achieve high productivity and low cost. In particular, metabolic engineering for d-mannitol considers one of the most promising approaches for d-mannitol production on the industrial scale. To date, the chemical process is not ideal for large-scale production because of its multistep mechanism involving hydrogenation and high cost. In this review, we highlight and present a comparative evaluation of the biochemical parameters that affecting d-mannitol synthesis from Thermotoga neapolitana and Thermotoga maritima mannitol dehydrogenase (MtDH) as a potential contribution for d-mannitol bio-synthesis. These species were selected because purified mannitol dehydrogenases from both strains have been reported to produce d-mannitol with no sorbitol formation under temperatures (90-120 °C).
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Affiliation(s)
- Marwa Yagoub Farag Koko
- Department of Food, Grease and Vegetable Protein Engineering, School of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | | | - Shuang Zhang
- Department of Food, Grease and Vegetable Protein Engineering, School of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Han Lu
- Department of Food, Grease and Vegetable Protein Engineering, School of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | | | - Muhammad Hussain
- Department of Food, Grease and Vegetable Protein Engineering, School of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qi Baokun
- Department of Food, Grease and Vegetable Protein Engineering, School of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Li Yang
- Department of Food, Grease and Vegetable Protein Engineering, School of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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19
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Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions of shikimate dehydrogenase in microorganisms surviving at different temperatures. Extremophiles 2020; 24:831-842. [PMID: 32975630 DOI: 10.1007/s00792-020-01198-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Hyperthermophiles, a subset of prokaryotes that thrive in adverse temperatures, potentially utilize the protein molecular biosystem for maintaining thermostability in a wide range of temperatures. Recent studies revealed that these organisms have smaller proportions of intrinsically disordered proteins. In this study, we performed sequence and structural analysis to investigate the maintenance of protein conformation and their stability at different temperatures. The sequence analysis reveals the higher proportion of charged amino acids are responsible for preventing the helix formation and, hence, become disordered regions. For structural analysis, we chose shikimate dehydrogenase from four species, namely Listeria monocytogenes, Escherichia coli, Thermus thermophilus, and Methanopyrus kandleri, and evaluated the protein adaptation at 283 K, 300 K, and 395 K temperatures. From this investigation, we found more residues of shikimate dehydrogenase prefer an order-to-disorder transition at 395 K only for hyperthermophilic species. The solvent-accessible surface area (SASA) and hydrogen-bond analysis revealed that the tertiary conformation and the number of hydrogen bonds for hyperthermophilic shikimate dehydrogenase are highly preserved at 395 K, compared to 300 K. Our simulation results conjointly provide shikimate dehydrogenase of hyperthermophile which resists high temperatures through stronger protein tertiary conformations.
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20
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Matsarskaia O, Bühl L, Beck C, Grimaldo M, Schweins R, Zhang F, Seydel T, Schreiber F, Roosen-Runge F. Evolution of the structure and dynamics of bovine serum albumin induced by thermal denaturation. Phys Chem Chem Phys 2020; 22:18507-18517. [PMID: 32780038 DOI: 10.1039/d0cp01857k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein denaturation in concentrated solutions consists of the unfolding of the native protein structure, and subsequent cross-linking into clusters or gel networks. While the kinetic evolution of structure has been studied for some cases, the underlying microscopic dynamics of proteins has so far been neglected. However, protein dynamics is essential to understand the specific nature of assembly processes, such as diffusion-limited growth, or vitrification of dense liquids. Here, we present a study on thermal denaturation of concentrated solutions of bovine serum albumin (BSA) in D2O with and without NaCl. Using small-angle scattering, we provide information on structure before, during and after denaturation. Using quasi-elastic neutron scattering, we monitor in real-time the microscopic dynamics and dynamical confinement throughout the entire denaturation process covering protein unfolding and cross-linking. After denaturation, the protein dynamics is slowed down in salty solutions compared to those in pure water, while the stability and dynamics of the native solution appears unaffected by salt. The approach presented here opens opportunities to link microscopic dynamics to emerging structural properties, with implications for assembly processes in soft and biological matter.
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Affiliation(s)
- Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France.
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21
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Wang D, Liu W, Wang L, Wang Y, Liao CK, Chen J, Hu P, Hong W, Huang M, Chen Z, Xu P. Suppression of cancer proliferation and metastasis by a versatile nanomedicine integrating photodynamic therapy, photothermal therapy, and enzyme inhibition. Acta Biomater 2020; 113:541-553. [PMID: 32562802 DOI: 10.1016/j.actbio.2020.06.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/31/2022]
Abstract
Cancer therapeutics are varied and target diverse processes in cancer progression. Photodynamic therapy (PDT), photothermal therapy (PTT), and the inhibition of pro-cancer proteases are non-invasive anticancer therapeutics that attract increasing attentions for their enhanced specificities and milder systemic toxicities compared to traditional therapeutics. These modalities offer advantages to compensate for the shortcomings of their counterparts. For instance, PDT or PTT efficiently eliminates locally confined tumor cells while exhibiting no effect on metastatic tumor cells. In contrast, the inhibition of pro-cancer proteases systemically suppresses the proliferation and metastasis of cancer cells but does not eradicate existing cancer cells. To synergize these therapeutics, we hereby report a versatile nanoparticle that integrates the effects of PDT, PTT, and enzyme-inhibition. This nanoparticle (CIKP-NP) was synthesized by covalently or non-covalently modifying a photothermal nanoparticle with a photosensitizer, a pro-cancer protease inhibitor, and an albumin-binding molecule. After confirming the PDT, PTT, albumin-binding, and enzyme-inhibition properties at the molecular level, we demonstrated that CIKP-NP killed tumor cells through PDT or PTT and suppressed tumor cell invasion through enzyme-inhibition. In addition, through a breast cancer xenograft mouse model, we demonstrated that CIKP-NP suppressed tumor growth by PDT or PTT effect. Notably, the synergism of PDT and PTT significantly enhanced its anticancer efficiency. Furthermore, CIKP-NP significantly suppressed cancer metastasis in a lung metastatic mouse model. Last, biodistribution and the in vivo retention of CIKP-NP confirmed the tumor-targeting property. Beyond demonstrating the anti-tumor and anti-metastatic efficacy of CIKP-NP, our study also suggests a new strategy to synergize multiple anticancer therapeutics.
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22
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Zhang QA, Shi FF, Yao JL, Zhang N. Effects of ultrasound irradiation on the properties of apricot kernels during accelerated debitterizing. RSC Adv 2020; 10:10624-10633. [PMID: 35492903 PMCID: PMC9050408 DOI: 10.1039/c9ra10965j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/21/2020] [Indexed: 11/21/2022] Open
Abstract
In this paper, studies were conducted to investigate the effects of ultrasonically accelerated debitterizing on the physicochemical properties of apricot kernels, such as color, texture, oil content, protein characteristics and amino acids, with UV-Vis spectroscopy, synchronous fluorescence spectroscopy, circular dichroism, electrophoresis, environmental scanning electron microscopy, and thermal property analysis. The results indicate that the novel debitterizing technique has insignificant influences on the oil and protein contents of apricot kernels; meanwhile, the color, texture and activity of beta-glucosidase were substantially improved, greatly contributing to the quality modification and shortening the debitterizing time. In addition, ultrasound greatly influenced the amino acid contents and compositions, the fluorescence spectra and the thermal properties of the apricot kernel proteins. In a word, all these results greatly contribute to our understanding of the debitterizing mechanism mediated by ultrasound irradiation and further prove the feasibility of this novel debitterizing technique in the practical processing of apricot kernels.
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Affiliation(s)
- Qing-An Zhang
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University Xi'an 710062 Shaanxi Province PR China
- Shaanxi International Science and Technology Cooperation Bases: Cereal Science International Joint Research Center Xi'an 710062 Shaanxi Province PR China
| | - Fang-Fang Shi
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University Xi'an 710062 Shaanxi Province PR China
| | - Jian-Li Yao
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University Xi'an 710062 Shaanxi Province PR China
| | - Ning Zhang
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University Xi'an 710062 Shaanxi Province PR China
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23
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Evans TG, Kültz D. The cellular stress response in fish exposed to salinity fluctuations. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 333:421-435. [DOI: 10.1002/jez.2350] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Tyler G. Evans
- Department of Biological Sciences California State University East Bay Hayward California
| | - Dietmar Kültz
- Department of Animal Sciences University of California Davis Meyer Hall Davis California
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24
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Wang L, Peng R, Tian Y, Gao J, Wang B, Yao Q. A thermostable 5-enolpyruvylshikimate-3-phosphate synthase from Thermotoga maritima enhances glyphosate tolerance in Escherichia coli and transgenic Arabidopsis. Extremophiles 2019; 23:659-667. [PMID: 31338597 DOI: 10.1007/s00792-019-01118-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) overexpression, attempting to provide excess EPSPS to combine with glyphosate, is one way to improve glyphosate resistance of plants. The EPSPS in extremophiles which is selected by nature to withstand the evolutionary pressure may possess some potential-specific biological functions. In this study, we reported the cloning, expression and enzymatic characterization of a novel Class II EPSPS AroAT. maritima from Thermotoga maritima MSB8. The enzyme showed low sequence identities with other EPSPSs, and was one of the most thermostable EPSPSs so far, which showed the optimum enzyme activity at 80 °C. The enzyme maintains the activity below 50 °C and in a wide range of pH 4.0-10, which indicated its stability under rough environment, especially in tropical regions and alkaline soil. Excellent Ki/Km value of AroAT. maritima suggested that the enzyme showed powerful competitive binding capacity of PEP over glyphosate and high glyphosate tolerance. Furthermore, aroAT. maritima gene was transformed into Arabidopsis thaliana. The transgenic lines were resistant to 15 mM glyphosate, which proved the application value in the cultivation of glyphosate-tolerant plants.
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Affiliation(s)
- Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Jianjie Gao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
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25
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Higher peptide nonplanarity (ω) close to protein carboxy-terminal and its positive correlation with ψ dihedral-angle is evolved conferring protein thermostability. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:1-9. [DOI: 10.1016/j.pbiomolbio.2018.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/08/2018] [Accepted: 10/21/2018] [Indexed: 11/24/2022]
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26
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Uralcan B, Debenedetti PG. Computational Investigation of the Effect of Pressure on Protein Stability. J Phys Chem Lett 2019; 10:1894-1899. [PMID: 30939023 DOI: 10.1021/acs.jpclett.9b00545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previous studies show parabolic or elliptical regions of protein stability in the pressure-temperature ( P, T) plane. The construction of stability diagrams requires accessing a sufficiently broad ( P, T) range, which is often frustrated by ice formation in experiments and sampling challenges in simulations. We perform a fully atomistic computational study of the miniprotein Trp-cage over the range of temperatures 210 ≤ T ≤ 420 K and pressures P ≤ 5 kbar and construct the corresponding stability diagram. At ambient temperature, pressure shifts the conformational states toward unfolding. Below 250 K, the native fold's stability depends nonmonotonically on pressure. While cold unfolding and thermal denaturation differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures. At ambient pressure, cold denaturation is an enthalpically driven process that preserves significant elements of Trp-cage's secondary structure. In contrast, cold unfolding at elevated pressures involves a more substantial loss of secondary and tertiary structure, similar to thermal denaturation.
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Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
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27
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Fan XH, Zhang XY, Zhang QA, Zhao WQ, Shi FF. Optimization of ultrasound parameters and its effect on the properties of the activity of beta-glucosidase in apricot kernels. ULTRASONICS SONOCHEMISTRY 2019; 52:468-476. [PMID: 30594520 DOI: 10.1016/j.ultsonch.2018.12.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/05/2018] [Accepted: 12/14/2018] [Indexed: 05/25/2023]
Abstract
In this paper, ultrasound was used as an auxiliary tool to activate the activity of beta-glucosidase (beta-GC) in apricot kernels, and its parameters were optimized to evaluate the effects on the beta-GC activity with the response surface methodology (RSM), variables including ultrasonic time, temperature, power and frequency. The results indicate that the obtained quadratic regression model could simulate the actual conditions, and the optimum conditions were as follows: exposure time of 31 min, temperature 50 °C, power 225 W and frequency 28 kHz, and the activity of beta-GC achieved 3.64 × 105 U/g·apricot kernel (dry weight), having an increase of 34.67% compared to the untreated beta-GC. In addition, the changes of the beta-GC properties demonstrated that ultrasound did improve the activity of beta-GC by influencing the beta-GC's properties of fluorescence, circular dichroism, thermal property, etc. All these results would contribute to understand the mechanism of the rapid debitterizing of apricot kernels accelerated by ultrasound.
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Affiliation(s)
- Xue-Hui Fan
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, PR China
| | - Xin-Yun Zhang
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, PR China
| | - Qing-An Zhang
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, PR China.
| | - Wu-Qi Zhao
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, PR China
| | - Fang-Fang Shi
- Institute of Food & Physical Field Processing, School of Food Engineering and Nutrition Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, PR China
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Luhtanen AM, Eronen-Rasimus E, Oksanen HM, Tison JL, Delille B, Dieckmann GS, Rintala JM, Bamford DH. The first known virus isolates from Antarctic sea ice have complex infection patterns. FEMS Microbiol Ecol 2019; 94:4898008. [PMID: 29481638 DOI: 10.1093/femsec/fiy028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 01/21/2023] Open
Abstract
Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original host at 0°C and 4°C, but not at higher temperatures. The results showed that virus-host interactions can be very complex and that the viral community can also be dynamic in the winter-sea ice.
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Affiliation(s)
- Anne-Mari Luhtanen
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jean-Louis Tison
- Laboratoire de Glaciologie, DGES, Université Libre de Bruxelles, Belgium
| | - Bruno Delille
- Unité d'Océanographie Chimique, Université de Liège, Belgium
| | - Gerhard S Dieckmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Janne-Markus Rintala
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland.,Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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29
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Enhanced dynamics of conformationally heterogeneous T7 bacteriophage lysozyme native state attenuates its stability and activity. Biochem J 2019; 476:613-628. [DOI: 10.1042/bcj20180703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Proteins are dynamic in nature and exist in a set of equilibrium conformations on various timescale motions. The flexibility of proteins governs various biological functions, and therefore elucidation of such functional dynamics is essential. In this context, we have studied the structure–dynamics–stability–activity relationship of bacteriophage T7 lysozyme/endolysin (T7L) native-state ensemble in the pH range of 6–8. Our studies established that T7L native state is conformationally heterogeneous, as several residues of its C-terminal half are present in two conformations (major and minor) in the slow exchange time scale of nuclear magnetic resonance (NMR). Structural and dynamic studies suggested that the residues belonging to minor conformations do exhibit native-like structural and dynamic features. Furthermore, the NMR relaxation experiments unraveled that the native state is highly dynamic and the dynamic behavior is regulated by the pH, as the pH 6 conformation exhibited enhanced dynamics compared with pH 7 and 8. The stability measurements and cell-based activity studies on T7L indicated that the native protein at pH 6 is ∼2 kcal less stable and is ∼50% less active than those of pH 7 and 8. A comprehensive analysis of the T7L active site, unfolding initiation sites and the residues with altered dynamics outlined that the attenuation of stability and activity is a resultant of its enhanced dynamic properties, which, in turn, can be attributed to the protonation/deprotonation of its partially buried His residues. Our study on T7L structure–dynamics–activity paradigm could assist in engineering novel amidase-based endolysins with enhanced activity and stability over a broad pH range.
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30
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Susceptibility of Escherichia coli O157:H7 grown at low temperatures to the krypton-chlorine excilamp. Sci Rep 2019; 9:563. [PMID: 30679621 PMCID: PMC6346039 DOI: 10.1038/s41598-018-37060-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/27/2018] [Indexed: 11/28/2022] Open
Abstract
This study was conducted to investigate the resistance of Escherichia coli O157:H7 to 222-nm krypton-chlorine(KrCl) excilamp and 254-nm low-pressure Hg lamp (LP lamp) treatment according to growth temperature. As growth temperature decreased, lag time of E. coli O157:H7 significantly increased while the growth rate significantly decreased. Regardless of growth temperature, the KrCl excilamp showed higher disinfection capacity compared to the LP lamp at stationary growth phase. KrCl excilamp treatment showed significantly higher reduction as growth temperature decreased. Conversely, reduction levels according to growth temperature were not significantly different when the pathogen was subjected to LP lamp treatment. Inactivation mechanisms were evaluated by the thiobarbituric acid reactive substances (TBARS) assay and SYBR green assay, and we confirmed that lipid oxdiation capacity following KrCl excilamp treatment increased as growth temperature decreased, which was significantly higher than that of LP lamp treated samples regardless of growth temperature. DNA damage level was significantly higher for LP Hg lamp treated samples compared to those subjected to the KrCl excilamp, but no significant difference pursuant to growth temperature was observed. At the transcriptional level, gene expression related to several metabolic pathways was significantly higher for the pathogen grown at 15 °C compared that of 37 °C, enabling it to adapt and survive at low temperature, and membrane lipid composition became altered to ensure membrane fluidity. Consequently, resistance of E. coli O157:H7 to the KrCl excilamp decreased as growth temperature decreased because the ratio of unsaturated fatty acid composition increased at low growth temperature resulting in higher lipid oxidation levels. These results indicate that KrCl excilamp treatment should be determined carefully considering the growth temperature of E. coli O157:H7.
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31
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Do thermal treatments influence the ultrafast opto-thermal processes of eumelanin? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:153-160. [DOI: 10.1007/s00249-018-1342-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/12/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
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32
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Julió Plana L, Nadra AD, Estrin DA, Luque FJ, Capece L. Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. J Chem Inf Model 2018; 59:441-452. [PMID: 30516994 DOI: 10.1021/acs.jcim.8b00840] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins are sensitive to temperature, and abrupt changes in the normal temperature conditions can have a profound impact on both structure and function, leading to protein unfolding. However, the adaptation of certain organisms to extreme conditions raises questions about the structural features that permit the structure and function of proteins to be preserved under these adverse conditions. To gain insight into the molecular basis of protein thermostability in the globin family, we have examined three representative examples: human neuroglobin, horse heart myoglobin, and Drosophila hemoglobin, which differ in their melting temperatures and coordination states of the heme iron in the absence of external ligands. In order to elucidate the possible mechanisms that govern the thermostability of these proteins, microsecond-scale classical molecular dynamics simulations were performed at different temperatures. Structural fluctuations and essential dynamics were analyzed, indicating that the flexibility of the CD region, which includes the two short C and D helixes and the connecting CD loop, is directly related to the thermostability. We observed that a larger inherent flexibility of the protein produces higher thermostability, probably concentrating the thermal fluctuations observed at high temperature in flexible regions, preventing unfolding. Globally, the results of this work improve our understanding of thermostability in the globin family.
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Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - Alejandro D Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/IQUIBICEN-CONICET , C1428EGA Buenos Aires , Argentina
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences , University of Barcelona , Campus Torribera , 08921 Santa Coloma de Gramenet , Spain.,Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB) , University of Barcelona , 08028 Barcelona , Spain
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
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33
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Proteomic evaluation of the freshly isolated cyanobionts from Azolla microphylla exposed to salinity stress. Symbiosis 2018. [DOI: 10.1007/s13199-018-0586-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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34
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Wang M, Li Y, Srinivasan P, Hu Z, Wang R, Saragih A, Repka MA, Murthy SN. Interactions Between Biological Products and Product Packaging and Potential Approaches to Overcome Them. AAPS PharmSciTech 2018; 19:3681-3686. [PMID: 30280349 DOI: 10.1208/s12249-018-1184-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/11/2018] [Indexed: 12/20/2022] Open
Abstract
Biological products such as protein-based biopharmaceuticals are playing an important role in the healthcare and pharmaceutical industry. The interaction between biological products and packaging materials has become the focus of many studies since it can reduce the effectiveness of biological products. These interactions are heavily influenced by the surface properties and physicochemical nature of the therapeutic agents and the packaging materials. Therefore, it is critical to understand the interactions between packaging materials and biological products in order to design biocompatible packaging materials and develop approaches to minimize adverse interactions. We describe the interactions that occur when using several common packaging materials, including glass and polymer. We discuss the interaction between these materials and biological products such as blood, blood derivatives, recombinant proteins, monoclonal antibodies, and gene therapeutics. We also summarize approaches for overcoming these interactions. Understanding the interactions between biological materials and packaging materials is critical for the development of novel packaging materials that improve the safety of pharmaceutical products.
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35
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Moosa MM, Ferreon JC, Ferreon ACM. Ligand interactions and the protein order-disorder energetic continuum. Semin Cell Dev Biol 2018; 99:78-85. [PMID: 29753880 DOI: 10.1016/j.semcdb.2018.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 04/05/2018] [Accepted: 05/04/2018] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins as computationally predicted account for ∼1/3 of eukaryotic proteomes, are involved in a plethora of biological functions, and have been linked to several human diseases as a result of their dysfunctions. Here, we present a picture wherein an energetic continuum describes protein structural and conformational propensities, ranging from the hyperstable folded proteins on one end to the hyperdestabilized and sometimes functionally disordered proteins on the other. We distinguish between proteins that are folding-competent but disordered because of marginal stability and those that are disordered due mainly to the absence of folding code-completing structure-determining interactions, and postulate that disordered proteins that are unstructured by way of partial population of protein denatured states represent a sizable proportion of the proteome.
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Affiliation(s)
- Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
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36
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Borgohain G, Paul S. Atomistic level understanding of the stabilization of protein Trp cage in denaturing and mixed osmolyte solutions. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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37
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Yik LY, Chin GJWL, Budiman C, Joseph CG, Musta B, Rodrigues KF. Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia. Indian J Microbiol 2018; 58:165-173. [PMID: 29651175 DOI: 10.1007/s12088-017-0701-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/26/2017] [Indexed: 11/29/2022] Open
Abstract
The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage.
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Affiliation(s)
- Low Yi Yik
- 1Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | | | - Cahyo Budiman
- 1Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Collin Glenn Joseph
- 2Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Baba Musta
- 2Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
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38
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Establishment of Aromatic Pairs at the Surface of Chondroitinase ABC I: the Effect on Activity and Stability. Appl Biochem Biotechnol 2018; 186:358-370. [DOI: 10.1007/s12010-018-2741-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/18/2018] [Indexed: 10/17/2022]
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39
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The role of supercritical fluids in the fractionation pretreatments of a wheat bran-based biorefinery. J Supercrit Fluids 2018. [DOI: 10.1016/j.supflu.2017.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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40
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Hendriks A, van Lier J, de Kreuk M. Growth media in anaerobic fermentative processes: The underestimated potential of thermophilic fermentation and anaerobic digestion. Biotechnol Adv 2018; 36:1-13. [DOI: 10.1016/j.biotechadv.2017.08.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/08/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022]
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41
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Purification, Characterization, and Mode of Action of Pentocin JL-1, a Novel Bacteriocin Isolated from Lactobacillus pentosus, against Drug-Resistant Staphylococcus aureus. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7657190. [PMID: 29333451 PMCID: PMC5733122 DOI: 10.1155/2017/7657190] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/21/2017] [Accepted: 10/18/2017] [Indexed: 12/16/2022]
Abstract
Staphylococcus aureus and its drug-resistant strains, which threaten public health and food safety, are in need of effective control by biopreservatives. A novel bacteriocin, pentocin JL-1, produced by Lactobacillus pentosus that was isolated from the intestinal tract of Chiloscyllium punctatum, was purified by a four-step chromatographic process. Mass spectrometry based on MALDI-TOF indicated that pentocin JL-1 has a molecular mass of 2987.23 Da. Only six of the twenty-five amino acids could be identified by Edman degradation. This bacteriocin is thermostable and tolerates a pH range of 5–7. Also, it is sensitive to proteinase K, trypsin, pepsin, and alkaline protease. This bacteriocin has a broad inhibitory spectrum against both Gram-positive and Gram-negative strains and in particular is effective against multidrug-resistant S. aureus. Additionally, we showed that the cell membrane is the target of pentocin JL-1 against methicillin-resistant S. aureus (MRSA), causing a loss of proton motive force. Furthermore, pentocin JL-1 has a drastic impact on the structure and integrity of MRSA cells. These results suggest that pentocin JL-1 has potential as a biopreservative in the food industry.
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42
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Gao L, Wang H, Liu Z, Liu S, Zhao G, Xu B, Guo X. The initial analysis of a serine proteinase gene (AccSp10) from Apis cerana cerana: possible involvement in pupal development, innate immunity and abiotic stress responses. Cell Stress Chaperones 2017; 22:867-877. [PMID: 28695333 PMCID: PMC5655375 DOI: 10.1007/s12192-017-0818-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 05/31/2017] [Accepted: 06/05/2017] [Indexed: 12/15/2022] Open
Abstract
Serine proteinases play important roles in innate immunity and insect development. We isolated a serine proteinase gene, designated AccSp10, from the Chinese honeybees (Apis cerana cerana). RT-qPCR and a Western blot analysis at different pupal development stages indicated that AccSp10 might be involved in melanin formation in pupae and promote pupal development. In adult workers, the expression of AccSp10 was upregulated by treatments mimicking harmful environments such as the presence of Bacillus bombysepticus, different temperatures (4, 24 and 42 °C), HgCl2, H2O2 and paraquat; the exception was treatment with VC (vitamin C), which did not upregulate AccSp10 expression. Western blot confirmed the results. A disc diffusion assay indicated that recombinant AccSp10 accelerated E. coli cell death during stimulation with harmful substances (HgCl2, paraquat and cumene hydroperoxide). These findings suggest that AccSp10 may be involved in the pupal development of Chinese honeybees and protection against microorganisms and abiotic harms.
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Affiliation(s)
- Lijun Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
- College of Life Sciences, Taishan Medical University, Taian, Shandong, 271016, People's Republic of China
| | - Hongfang Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Zhenguo Liu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuchang Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Guangdong Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
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43
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Evolved Aztreonam Resistance Is Multifactorial and Can Produce Hypervirulence in Pseudomonas aeruginosa. mBio 2017; 8:mBio.00517-17. [PMID: 29089424 PMCID: PMC5666152 DOI: 10.1128/mbio.00517-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
While much attention has been focused on acquired antibiotic resistance genes, chromosomal mutations may be most important in chronic infections where isolated, persistently infecting lineages experience repeated antibiotic exposure. Here, we used experimental evolution and whole-genome sequencing to investigate chromosomally encoded mutations causing aztreonam resistance in Pseudomonas aeruginosa and characterized the secondary consequences of resistance development. We identified 19 recurrently mutated genes associated with aztreonam resistance. The most frequently observed mutations affected negative transcriptional regulators of the mexAB-oprM efflux system and the target of aztreonam, ftsI. While individual mutations conferred modest resistance gains, high-level resistance (1,024 µg/ml) was achieved through the accumulation of multiple variants. Despite being largely stable when strains were passaged in the absence of antibiotics, aztreonam resistance was associated with decreased in vitro growth rates, indicating an associated fitness cost. In some instances, evolved aztreonam-resistant strains exhibited increased resistance to structurally unrelated antipseudomonal antibiotics. Surprisingly, strains carrying evolved mutations which affected negative regulators of mexAB-oprM (mexR and nalD) demonstrated enhanced virulence in a murine pneumonia infection model. Mutations in these genes, and other genes that we associated with aztreonam resistance, were common in P. aeruginosa isolates from chronically infected patients with cystic fibrosis. These findings illuminate mechanisms of P. aeruginosa aztreonam resistance and raise the possibility that antibiotic treatment could inadvertently select for hypervirulence phenotypes. Inhaled aztreonam is a relatively new antibiotic which is being increasingly used to treat cystic fibrosis patients with Pseudomonas aeruginosa airway infections. As for all antimicrobial agents, bacteria can evolve resistance that decreases the effectiveness of the drug; however, the mechanisms and consequences of aztreonam resistance are incompletely understood. Here, using experimental evolution, we have cataloged spontaneous mutations conferring aztreonam resistance and have explored their effects. We found that a diverse collection of genes contributes to aztreonam resistance, each with a small but cumulative effect. Surprisingly, we found that selection for aztreonam resistance mutations could confer increased resistance to other antibiotics and promote hypervirulence in a mouse infection model. Our study reveals inherent mechanisms of aztreonam resistance and indicates that aztreonam exposure can have unintended secondary effects.
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44
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Naderi N, House JD, Pouliot Y, Doyen A. Effects of High Hydrostatic Pressure Processing on Hen Egg Compounds and Egg Products. Compr Rev Food Sci Food Saf 2017; 16:707-720. [DOI: 10.1111/1541-4337.12273] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Nassim Naderi
- Inst. of Nutrition and Functional Foods (INAF), Dept. of Food Science; Univ. Laval; Québec QC Canada G1V 0A6
- Dept. of Human Nutritional Sciences; Univ. of Manitoba; Winnipeg MB Canada R3T 2N2
| | - James D. House
- Inst. of Nutrition and Functional Foods (INAF), Dept. of Food Science; Univ. Laval; Québec QC Canada G1V 0A6
- Dept. of Human Nutritional Sciences; Univ. of Manitoba; Winnipeg MB Canada R3T 2N2
| | - Yves Pouliot
- Inst. of Nutrition and Functional Foods (INAF), Dept. of Food Science; Univ. Laval; Québec QC Canada G1V 0A6
| | - Alain Doyen
- Inst. of Nutrition and Functional Foods (INAF), Dept. of Food Science; Univ. Laval; Québec QC Canada G1V 0A6
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45
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Miller SR. An appraisal of the enzyme stability‐activity trade‐off. Evolution 2017; 71:1876-1887. [DOI: 10.1111/evo.13275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Scott R. Miller
- Division of Biological SciencesThe University of Montana Missoula Montana 59812
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46
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Zaak H, Siar EH, Kornecki JF, Fernandez-Lopez L, Pedrero SG, Virgen-Ortíz JJ, Fernandez-Lafuente R. Effect of immobilization rate and enzyme crowding on enzyme stability under different conditions. The case of lipase from Thermomyces lanuginosus immobilized on octyl agarose beads. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.02.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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47
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NADP +-dependent isocitrate dehydrogenase from a psychrophilic bacterium, Psychromonas marina. Extremophiles 2017; 21:711-721. [PMID: 28447265 DOI: 10.1007/s00792-017-0936-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 04/17/2017] [Indexed: 10/19/2022]
Abstract
The gene encoding NADP+-dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) of a psychrophilic bacterium, Psychromonas marina, was cloned and sequenced. The open reading frame of the gene encoding IDH of P. marina (PmIDH) was 2229 bp in length and corresponded to a polypeptide composed of 742 amino acids. The molecular mass of IDH was calculated as 80,426 Da. The deduced amino acid sequence of PmIDH exhibited high degrees of homology with the monomeric IDH from other bacteria such as Colwellia maris (62% identity) and Azotobacter vinelandii (AvIDH) (64%). His-tagged PmIDH overexpressed in Escherichia coli cells was purified and characterized. The optimum temperature of PmIDH activity was about 35 °C; however, the enzyme lost 74% of the activity after incubation for 10 min at 30 °C, indicating that this enzyme is thermolabile. Chimeric enzymes produced through domain swapping between PmIDH and mesophilic AvIDH were constructed and their optimum temperatures and thermostability were determined. The results suggest that regions 2 and 3, especially region 3, of the two IDHs are involved in their catalytic activities and optimum temperature and thermostability for activity.
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Pica A, Graziano G. Shedding light on the extra thermal stability of thermophilic proteins. Biopolymers 2017; 105:856-63. [PMID: 27449333 DOI: 10.1002/bip.22923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 11/08/2022]
Abstract
An entropic stabilization mechanism has recently gained attention and credibility as the physical ground for the extra thermal stability of globular proteins from thermophilic microorganisms. An empirical result, obtained from the analysis of thermodynamic data for a large set of proteins, strengthens the general reliability of the theoretical approach originally devised to rationalize the occurrence of cold denaturation [Graziano, PCCP 2014, 16, 21755-21767]. It is shown that this theoretical approach can readily account for the entropic stabilization mechanism. On decreasing the conformational entropy gain associated with denaturation, the thermal stability of a model globular protein increases markedly.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, Napoli, 80126, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, Benevento, 82100, Italy.
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Novikova OD, Chistyulin DK, Khomenko VA, Sidorin EV, Kim NY, Sanina NM, Portnyagina OY, Solov'eva TF, Uversky VN, Shnyrov VL. Peculiarities of thermal denaturation of OmpF porin from Yersinia ruckeri. MOLECULAR BIOSYSTEMS 2017; 13:1854-1862. [DOI: 10.1039/c7mb00239d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Irreversible denaturation of membrane proteins in detergent solutions is similar to unfolding of water-soluble multidomain proteins and represents a complex, multistage process.
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Affiliation(s)
- Olga D. Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | - Dmitry K. Chistyulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | - Valentina A. Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | - Evgeny V. Sidorin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | - Natalya Yu. Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | | | - Olga Yu. Portnyagina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | - Tamara F. Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry
- Far East Branch
- Russian Academy of Sciences
- Vladivostok
- Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Valery L. Shnyrov
- Departamento de Bioquimica y Biologia Molecular
- Universidad de Salamanca
- 37007 Salamanca
- Spain
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