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Duan R, Wang S, Li Z, Zhang W, Wu J, Jiang Y, Lin Q, Yuan P, Yue X, Yao Y, Xiao X, Xiao Y, Wang Z. Computer-assisted semi-rational design enhanced the enzymatic activity and protein stability of Proteinase K in calcium-free conditions. Biochem Biophys Res Commun 2024; 721:150109. [PMID: 38762932 DOI: 10.1016/j.bbrc.2024.150109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Wild-type Proteinase K binds to two Ca2+ ions, which play an important role in regulating enzymaticactivity and maintaining protein stability. Therefore, a predetermined concentration of Ca2+ must be added during the use of Proteinase K, which increases its commercial cost. Herein, we addressed this challenge using a computational strategy to engineer a Proteinase K mutant that does not require Ca2+ and exhibits high enzymatic activity and protein stability. In the absence of Ca2+, the best mutant, MT24 (S17W-S176N-D260F), displayed an activity approximately 9.2-fold higher than that of wild-type Proteinase K. It also exhibited excellent protein stability, retaining 56.2 % of its enzymatic activity after storage at 4 °C for 5 days. The residual enzymatic activity was 65-fold higher than that of the wild-type Proteinase K under the same storage conditions. Structural analysis and molecular dynamics simulations suggest that the introduction of new hydrogen bond and π-π stacking at the Ca2+ binding sites due to the mutation may be the reasons for the increased enzymatic activity and stability of MT24.
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Affiliation(s)
- Rongdi Duan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Shen Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Zhetao Li
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Wenjun Zhang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Junteng Wu
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yifei Jiang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Qinting Lin
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Peixiong Yuan
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Xiaoyan Yue
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yunxiao Yao
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Xiaoyue Xiao
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yunjie Xiao
- School of Life Sciences, Tianjin University, Tianjin, 300072, China.
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China.
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Castagnini D, Palma K, Jara-Wilde J, Navarro N, González MJ, Toledo J, Canales-Huerta N, Scavone P, Härtel S. Proteus mirabilis biofilm expansion microscopy yields over 4-fold magnification for super-resolution of biofilm structure and subcellular DNA organization. J Microbiol Methods 2024; 220:106927. [PMID: 38561125 DOI: 10.1016/j.mimet.2024.106927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Bacterial biofilms form when bacteria attach to surfaces and generate an extracellular matrix that embeds and stabilizes a growing community. Detailed visualization and quantitative analysis of biofilm architecture by optical microscopy are limited by the law of diffraction. Expansion Microscopy (ExM) is a novel Super-Resolution technique where specimens are physically enlarged by a factor of ∼4, prior to observation by conventional fluorescence microscopy. ExM requires homogenization of rigid constituents of biological components by enzymatic digestion. We developed an ExM approach capable of expanding 48-h old Proteus mirabilis biofilms 4.3-fold (termed PmbExM), close to the theoretic maximum expansion factor without gross shape distortions. Our protocol, based on lytic and glycoside-hydrolase enzymatic treatments, degrades rigid components in bacteria and extracellular matrix. Our results prove PmbExM to be a versatile and easy-to-use Super-Resolution approach for enabling studies of P. mirabilis biofilm architecture, assembly, and even intracellular features, such as DNA organization.
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Affiliation(s)
- Dante Castagnini
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile
| | - Karina Palma
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Jorge Jara-Wilde
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicolás Navarro
- Advanced Center for Chronic Diseases ACCDiS, Santiago, Chile.; Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - María José González
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Jorge Toledo
- Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicole Canales-Huerta
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile
| | - Paola Scavone
- Laboratorio de Biofilms Microbianos, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Steffen Härtel
- Laboratory for Scientific Image Analysis SCIAN-Lab, Integrative Biology Program, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Biomedical Neuroscience Institute BNI, Independencia, Santiago, Chile; Centro de Informática Médica y Telemedicina CIMT, Faculty of Medicine, University of Chile, Santiago, Chile; National Center for Health Information Systems CENS, Santiago, Chile.; Red de Equipamiento Científico Avanzado REDECA, Institute of Biomedical Sciences ICBM, Faculty of Medicine, University of Chile, Santiago, Chile; Centro de Modelamiento Matemático, Universidad de Chile, Beauchef 851, Casilla 170-3, Santiago, Chile.
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Kim MJ, Park PG, Hwang SJ, Bang SJ, Jung JH, Kown EB, Sul EK, Song KC, Choi JS, Han KR, Lee HY, Kim DH, Lee JM. Saliva-based Proteinase K method: A rapid and reliable diagnostic tool for the detection of SARS-COV-2 in children. J Med Virol 2024; 96:e29361. [PMID: 38178612 DOI: 10.1002/jmv.29361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Early and accurate detection of viruses in children might help prevent transmission and severe diseases. In this study, the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) detection in children was evaluated using saliva specimens with a Proteinase K (PTK)-based RNA preparation, as saliva collection is a simple and noninvasive procedure, even in young children, with fewer concerns about sample contamination. The saliva-based PTK and the conventional paired nasopharyngeal aspiration (NPA)-based detection methods were compared between COVID-19-positive and -negative children. In addition, the detection rate for SARS-COV-2 and the difference between admission and discharge by the saliva-based PTK method was tested in COVID-19 patients. The diagnostic accuracy of the saliva-based PTK method was 98.8% compared to NP swab-based reverse transcriptase polymerase chain reaction. Saliva samples showed high sensitivity (94.1%) and specificity (100%) when using the PTK method. Furthermore, the saliva-based PTK method significantly reduced the test processing time by 2 h. Notably, Ct values at discharge increased in saliva samples compared with those at admission, which might indicate patients' clinical conditions or virus activity. In conclusion, the saliva-based PTK implemented in this study streamlines RNA extraction, making the process faster, safer, and more cost-effective, demonstrating that this method is a rapid and reliable diagnostic tool for SARS-CoV-2 detection in children.
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Affiliation(s)
- Min Jung Kim
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Pil-Gu Park
- Department of Microbiology, Gachon University, Incheon, Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Jun Bang
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Jae Hwa Jung
- Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Bin Kown
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Eun Kyung Sul
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Kyung Chul Song
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Joon-Sik Choi
- Department of Pediatrics, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin-si, Korea
| | - Kyeo Re Han
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Young Lee
- Department of Biomedical Laboratory Science, College of Software and Digital Healthcare Convergence, Yonsei University, Wonju, Korea
| | - Dong Hyun Kim
- Department of Pediatrics, Inha University Hospital, Inha University College of Medicine, Incheon, Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
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Chabalier M, Doan T, Cascales E. Probing Protein Topology and Conformation by Limited Proteolysis. Methods Mol Biol 2024; 2715:111-119. [PMID: 37930525 DOI: 10.1007/978-1-0716-3445-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Proteases are enzymes that catalyze the hydrolytic degradation of other proteins into peptides or amino acids through the digestion of the peptide bond. Promiscuous proteases that target a wide range of proteins are distinguished from specific proteases that have a narrow range of substrates. In terms of activity, endoproteases cleave their substrates at specific residues within the target proteins, whereas exoproteases cleave from one extremity and may have processive activities. Proteases are therefore very useful tools to study proteins, notably their structure or conformation. In addition, proteases can be used to probe the topology of bacterial membrane proteins. Here, we describe limited protease accessibility assays to define inner membrane protein topology and conformational changes based on digestion profiles.
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Affiliation(s)
- Maïalène Chabalier
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ - CNRS, Marseille, France.
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Weng Y, Dunn CB, Qiang Z, Ren J. Immobilization of Protease K with ZIF-8 for Enhanced Stability in Polylactic Acid Melt Processing and Catalytic Degradation. ACS Appl Mater Interfaces 2023. [PMID: 37971900 DOI: 10.1021/acsami.3c11979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Polylactic acid (PLA) is a biodegradable alternative to petroleum-based polymers for improving environmental sustainability of our society. However, the limited degradation rate and environmental conditions for PLA-based products remain significant challenges for their broader use in various applications. While Proteinase K (Pro K) from Tritirachium album has been demonstrated to efficiently degrade PLA, its autocatalytic degradation function in composite films is underexplored. Here, this work reports a strategy that encapsulates Pro K with zeolitic imidazole framework-8 (ZIF-8) in situ, combining a PLA matrix to prepare Pro K@ZIF-8/PLA films through solvent casting. The method is scalable and commercially viable, and the pH and thermal stability of the Pro K enzyme are significantly enhanced after immobilization. The enzyme can retain 61.8% of its initial activity after annealing at 160 °C for 10 min, allowing for its use in the melt processing of filler-containing PLA films. As a result, Pro K@ZIF-8/PLA films in buffer solutions exhibit stable degradation rates, which can be extended to PLA decomposition in acidic environments. Moreover, the enzyme in Pro K@ZIF-8/PLA films prepared by thermoforming remains active sufficiently to degrade PLA with a weight loss of up to 15% in 2 weeks. These results further indicate that our strategy can be broadly applicable for melt processing and controlled degradation of PLA materials with immobilized enzymes, allowing for its transformative impact for promoting environmental sustainability.
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Affiliation(s)
- Yiming Weng
- Institute of Nano and Biopolymeric Materials, School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
| | - Carmen B Dunn
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Zhe Qiang
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jie Ren
- Institute of Nano and Biopolymeric Materials, School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
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Schactler SA, Scheuerman SJ, Lius A, Altemeier WA, An D, Matula TJ, Mikula M, Kulecka M, Denisenko O, Mar D, Bomsztyk K. CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis. BMC Genomics 2023; 24:446. [PMID: 37553584 PMCID: PMC10408117 DOI: 10.1186/s12864-023-09527-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/20/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Disease molecular complexity requires high throughput workflows to map disease pathways through analysis of vast tissue repositories. Great progress has been made in tissue multiomics analytical technologies. To match the high throughput of these advanced analytical platforms, we have previously developed a multipurpose 96-well microplate sonicator, PIXUL, that can be used in multiple workflows to extract analytes from cultured cells and tissue fragments for various downstream molecular assays. And yet, the sample preparation devices, such as PIXUL, along with the downstream multiomics analytical capabilities have not been fully exploited to interrogate tissues because storing and sampling of such biospecimens remain, in comparison, inefficient. RESULTS To mitigate this tissue interrogation bottleneck, we have developed a low-cost user-friendly system, CryoGrid, to catalog, cryostore and sample tissue fragments. TRIzol is widely used to isolate RNA but it is labor-intensive, hazardous, requires fume-hoods, and is an expensive reagent. Columns are also commonly used to extract RNA but they involve many steps, are prone to human errors, and are also expensive. Both TRIzol and column protocols use test tubes. We developed a microplate PIXUL-based TRIzol-free and column-free RNA isolation protocol that uses a buffer containing proteinase K (PK buffer). We have integrated the CryoGrid system with PIXUL-based PK buffer, TRIzol, and PureLink column methods to isolate RNA for gene-specific qPCR and genome-wide transcript analyses. CryoGrid-PIXUL, when integrated with either PK buffer, TRIzol or PureLink column RNA isolation protocols, yielded similar transcript profiles in frozen organs (brain, heart, kidney and liver) from a mouse model of sepsis. CONCLUSIONS RNA isolation using the CryoGrid-PIXUL system combined with the 96-well microplate PK buffer method offers an inexpensive user-friendly high throughput workflow to study transcriptional responses in tissues in health and disease as well as in therapeutic interventions.
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Affiliation(s)
- Scott A Schactler
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Stephen J Scheuerman
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Andrea Lius
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - William A Altemeier
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Center for Lung Biology, University of Washington, Seattle, WA, 98109, USA
| | - Dowon An
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Center for Lung Biology, University of Washington, Seattle, WA, 98109, USA
| | - Thomas J Matula
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA, 98195, USA
- Matchstick Technologies, Inc, Kirkland, WA, 98033, USA
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, 01-813, Warsaw, Poland
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
| | - Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, WA, 98109, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA.
- Matchstick Technologies, Inc, Kirkland, WA, 98033, USA.
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Chalifoux A, Hadioui M, Amiri N, Wilkinson KJ. Analysis of Silver Nanoparticles in Ground Beef by Single Particle Inductively Coupled Plasma Mass Spectrometry (SP-ICP-MS). Molecules 2023; 28:molecules28114442. [PMID: 37298916 DOI: 10.3390/molecules28114442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The regulation and characterization of nanomaterials in foods are of great interest due to the potential risks associated with their exposure and the increasing number of applications where they are used within the food industry. One factor limiting the scientifically rigorous regulation of nanoparticles in foods is the lack of standardized procedures for the extraction of nanoparticles (NPs) from complex matrices without alteration of their physico-chemical properties. To this end, we tested and optimized two sample preparation approaches (enzymatic- and alkaline-based hydrolyses) in order to extract 40 nm of Ag NP, following their equilibration with a fatty ground beef matrix. NPs were characterized using single particle inductively coupled plasma mass spectrometry (SP-ICP-MS). Fast sample processing times (<20 min) were achieved using ultrasonication to accelerate the matrix degradation. NP losses during the sample preparation were minimized by optimizing the choice of enzymes/chemicals, the use of surfactants, and the product concentration and sonication. The alkaline approach using TMAH (tetramethylammonium hydroxide) was found to have the highest recoveries (over 90%); however, processed samples were found to be less stable than the samples processed using an enzymatic digestion based upon pork pancreatin and lipase (≈60 % recovery). Low method detection limits (MDLs) of 4.8 × 106 particles g-1 with a size detection limit (SDL) of 10.9 nm were achieved for the enzymatic extraction whereas an MDL of 5.7 × 107 particles g-1 and an SDL of 10.5 nm were obtained for the alkaline hydrolysis.
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Affiliation(s)
- Alexandre Chalifoux
- Department of Chemistry, Université de Montréal, 1375 Ave. Thérèse-Lavoie-Roux, Montreal, QC H2V 0B3, Canada
| | - Madjid Hadioui
- Department of Chemistry, Université de Montréal, 1375 Ave. Thérèse-Lavoie-Roux, Montreal, QC H2V 0B3, Canada
| | - Nesrine Amiri
- Department of Chemistry, Université de Montréal, 1375 Ave. Thérèse-Lavoie-Roux, Montreal, QC H2V 0B3, Canada
| | - Kevin J Wilkinson
- Department of Chemistry, Université de Montréal, 1375 Ave. Thérèse-Lavoie-Roux, Montreal, QC H2V 0B3, Canada
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Saretia S, Folikumah MY, Liu Y, Machatschek R. Understanding the (dis)-assembly of in situ forming hydrogel coatings in a 2D model system. J Colloid Interface Sci 2023; 636:176-83. [PMID: 36630855 DOI: 10.1016/j.jcis.2022.12.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/07/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
HYPOTHESIS Injectable hydrogels are important in situ forming implants for tissue regeneration at damaged sites. Understanding the behavior of these systems in a complex in vivo environment remains a challenge. Ultrathin films as 2D model systems are expected to provide fundamental insights into formation and (bio)degradation at material-liquid interfaces, and are also applicable as bioresponsive coatings. EXPERIMENTS Hydrogel ultrathin films are prepared by covalently cross-linking four-arm PEG macromers with maleimide end-groups (PEG4MAL) at alkaline pH using two different types of dithiol-bearing cross-linkers - thio-depsipeptide (TDP) or 3,6-Dioxa-1,8-octanedithiol (DODT). This thiol-Michael addition "click" reaction is carried out at the air-water interface using the Langmuir technique. Morphological observation in real time is carried out by Brewster angle microscopy (BAM) and in coatings using atomic force microscopy (AFM). Stability against enzymatic and oxidative degradation is evaluated in the same setup. FINDINGS Non-cross-linked PEG or PEG incubated with cross-linkers at slightly acidic pH desorbs from the interface over time. Cross-linking of PEG at alkaline pH renders 2D hydrogel networks (thickness <1 nm) that are stable against desorption. They are easily transferrable onto solid mica surfaces, forming homogenous coatings as revealed by AFM. The type of dithiol cross-linker used to form the branching centers influences the degradability of these 2D hydrogel networks in the presence of lipase, peroxides, or bases. For example, enzymatic degradation of the 2D hydrogel networks can be switched "on" or "off" depending on the cleavable sites in the cross-linkers.
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Baboo S, Diedrich JK, Martínez-Bartolomé S, Wang X, Schiffner T, Groschel B, Schief WR, Paulson JC, Yates JR. DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins. Methods Enzymol 2022; 682:137-185. [PMID: 36948700 PMCID: PMC11032187 DOI: 10.1016/bs.mie.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditional mass spectrometry-based glycoproteomic approaches have been widely used for site-specific N-glycoform analysis, but a large amount of starting material is needed to obtain sampling that is representative of the vast diversity of N-glycans on glycoproteins. These methods also often include a complicated workflow and very challenging data analysis. These limitations have prevented glycoproteomics from being adapted to high-throughput platforms, and the sensitivity of the analysis is currently inadequate for elucidating N-glycan heterogeneity in clinical samples. Heavily glycosylated spike proteins of enveloped viruses, recombinantly expressed as potential vaccines, are prime targets for glycoproteomic analysis. Since the immunogenicity of spike proteins may be impacted by their glycosylation patterns, site-specific analysis of N-glycoforms provides critical information for vaccine design. Using recombinantly expressed soluble HIV Env trimer, we describe DeGlyPHER, a modification of our previously reported sequential deglycosylation strategy to yield a "single-pot" process. DeGlyPHER is an ultrasensitive, simple, rapid, robust, and efficient approach for site-specific analysis of protein N-glycoforms, that we developed for analysis of limited quantities of glycoproteins.
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Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | | | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - Bettina Groschel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
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10
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Yu KH, Jheng CP, Lee CI. Quercetin binding accelerates prion fibrillation into proteinase sensitive and loosely structured amyloids. Biomed Pharmacother 2022; 151:113177. [PMID: 35676783 DOI: 10.1016/j.biopha.2022.113177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/18/2022] [Accepted: 05/22/2022] [Indexed: 11/23/2022] Open
Abstract
Amyloidoses are caused by the deposition of amyloid fibrils ascribed to protein misfolding. In this study, we examined the antiamyloidogenic and antioxidative activities of quercetin, a plant flavonol from the flavonoid group of polyphenols, on mouse prion protein (moPrP) with biophysical approaches. As the results show, quercetin binds to the C-terminal region of moPrP, and quercetin binding does not affect the structure of moPrP. However, quercetin binding accelerates moPrP fibrillation and changes the structure of moPrP fibrils. Unlike typical prion fibrils, quercetin-bound fibrils are sensitive to proteinase K and are loosely structured. Moreover, due to high antioxidant activity of flavonoid, quercetin-bound fibrils lack imbalance of free radicals and, therefore, they are nontoxic towards neuroblastoma cells. The quercetin shows its uniqueness from typical antiamyloidogenic drugs which either suppress the development of amyloid or eliminate formed amyloids. Quercetin binding converts moPrP into protease-sensitive and non-cytotoxic fibrils. This work provides a powerful resolution in the advancement of antiamyloidogenic treatment.
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Cui L, Wang X, Szarka G, Hegyesi N, Wang Y, Sui X, Pukánszky B. Quantitative analysis of factors determining the enzymatic degradation of poly(lactic acid). Int J Biol Macromol 2022; 209:1703-9. [PMID: 35487382 DOI: 10.1016/j.ijbiomac.2022.04.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 11/22/2022]
Abstract
The enzymatic degradation of poly(lactic acid) was catalyzed with Proteinase K and the effect of various factors on the rate of degradation was analyzed quantitatively with the help of appropriate kinetic models. The Michaelis-Menten model was modified for the purpose by considering the heterogeneous nature of the reaction and the denaturation of the enzyme. The results proved that Proteinase K degrades the polymer very efficiently. The rate of degradation increases considerably up to 0.1 mg/ml enzyme concentration, but remains constant at larger values. Temperature has an optimum at around 50 °C that is somewhat higher than the 37 °C extensively used in the literature as the most advantageous temperature. If degradation occurs in the same medium throughout the process, the formation of lactic acid results in the rapid decrease of pH and finally in the denaturation of the enzyme. The dropping of pH below 5 slows down and finally stops degradation completely. The daily change of the medium results in degradation with a constant rate and the entire amount of the polymer can be decomposed mainly into monomer or smaller oligomer fragments. Degradation rate decreases slightly with increasing molecular weight and increasing d-lactide content. The use of appropriate kinetic models allows quantitative analysis and the prediction of the rate of enzymatic degradation of PLA.
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Paudyal S, Sigdel G, Shah SK, Sharma SK, Grubb JD, Micic M, Caseli L, Leblanc RM. Interfacial behavior of Proteinase K enzyme at air-saline subphase. J Colloid Interface Sci 2022; 616:701-708. [PMID: 35247808 DOI: 10.1016/j.jcis.2022.02.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/19/2022] [Indexed: 10/19/2022]
Abstract
This study investigates the interfacial behavior of the proteinase K enzyme at air-water interface. Adsorption of enzyme on the surface was induced using saline subphase. The surface packing and stability of the enzyme was investigated using of surface pressure-area (π-A) and surface potential-area (ΔV-A) isotherms. Proteinase K enzyme forms film at air-aqueous interface and demonstrates good stability as shown through compression-decompression cycle experiments. To characterize the surface assembly morphology of the interfacial enzymes UV-vis and fluorescence spectroscopic techniques were used. The data revealed that the enzyme Langmuir monolayer has good homogeneity with no evidence of aggregates during compression. The secondary structure of the enzyme at interface was determined to be α-helix using p-polarized infrared-reflection absorption spectroscopy. This was confirmed through Circular dichroism spectra of the enzyme Langmuir-Blodgett (LB) film which showed that the major conformation present were α-helices.
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Affiliation(s)
- Suraj Paudyal
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Ganesh Sigdel
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Sujit K Shah
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA; Department of Chemistry, Mahendra Morang Adarsh Multiple Campus, Tribhuvan University, Biratnagar 56613, Nepal
| | - Shiv K Sharma
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - John D Grubb
- Gojira Fine Chemicals LLC, 5386 Majestic Pkwy , Suite #7, Bedford Heights, OH 44146, USA
| | - Miodrag Micic
- Gojira Fine Chemicals LLC, 5386 Majestic Pkwy , Suite #7, Bedford Heights, OH 44146, USA; Department of Engineering Design Technology, Cerritos College, 11110, Alondra Blvd, Norwalk, CA 90650, USA
| | - Luciano Caseli
- Department of Chemistry, Federal University of São Paulo, Diadema, Sao Paulo, Brazil
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA.
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Peña-Rico MA, Bravo-D HR, Roldan-Sabino C, Castro-Cerritos KV, Huerta-Heredia A, Navarro-Mtz AK. Addition of proteinase K during the culture alter the physiology of Bacillus thuringiensis culture and the cry1Ac, nprX, nprA, and spo0A gene transcription. Antonie Van Leeuwenhoek 2021; 115:89-102. [PMID: 34797466 DOI: 10.1007/s10482-021-01683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022]
Abstract
Bacillus thuringiensis is the major bioinsecticide worldwide produced due to the Cry protein activity. Several studies have been done to improve the cost-productivity relation. The neutral protease A (NprA) is the major extracellular protein massively produced during the stationary phase by this bacterium, contributing to the Cry proteins' degradation. Also, the deletion of aprA and nprA genes enhanced the yield of Cry protein, stabilizing it. Therefore, to increase Cry production, one possibility is to degrade the NprA protease in the culture media. In the present study, proteinase K was used to hydrolyze the NprA to increase Cry production. Proteinase K was added during the exponential growth of B. thuringiensis culture. The bacilli and endospores were measured along all culture, while the Cry protein was measured at the end of the culture. The addition of PK affects the bacilli and spore kinetics positively but negatively to the Cry protein (there is no Cry protein detection). Therefore, the gene expression of the cry1Ac, nprX, nprA, and spo0A was measured. The expression of each gene was followed along all culture. Results demonstrated that PK alters both the transcriptional levels and the expression order of the genes.
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Affiliation(s)
- Miguel A Peña-Rico
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Humberto R Bravo-D
- División de Estudios de Posgrado, Doctorado en Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Crisanto Roldan-Sabino
- Ingeniería en Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Karla V Castro-Cerritos
- Instituto de Química Aplicada, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - Ariana Huerta-Heredia
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México.,CONACyT-UNPA, Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México
| | - A Karin Navarro-Mtz
- Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central 200, Parque Industrial, 68301, Tuxtepec, Oaxaca, México.
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Shukla A, Gangwar M, Sharma G, Prakash P, Nath G. Vitality of Proteinase K in rRTPCR Detection of SARS-CoV2 Bypassing RNA Extraction. Front Cell Infect Microbiol 2021; 11:717068. [PMID: 34804989 PMCID: PMC8595283 DOI: 10.3389/fcimb.2021.717068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
This study aimed to detect the SARS-COV2 viral component directly from inoculated VTM without RNA extraction. Inoculated VTMs of already tested 50 positive and 50 negative samples were divided into three groups. Group I was treated with Proteinase K (PK) followed by 3-step-heat treatment at different temperatures (25°C, 60°C, and 98°C) and stored at 4°C. Group II was directly subjected to 3-step-heat treatment without PK exposure and stored at 4°C. And group III was set-up as standard group; it was processed using Qiagen's column based QIAamp Nucleic Acid kit and the obtained nucleic acids were stored at 4°C. These stored samples were used as a template to execute real-time polymerase chain reaction, and results were noted. Group I demonstrated 96% and 88% sensitivity for N and ORF1ab genes respectively, whereas group II demonstrated 78% and 60% when compared to the results of standard group III. Overall group I showed better results than group II when compared to group III. Thus, in situations where gold-standard reagents are not available, PK exposure and heat treatment can be employed to carry out molecular detection of SARS-CoV2 viral component.
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Affiliation(s)
- Alka Shukla
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Mayank Gangwar
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gaurav Sharma
- Department of Public Health Dentistry, SriRama Chandra Bhanj Dental College & Hospital, Cuttack, India
| | - Pradyot Prakash
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal Nath
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Dou Z, Chau M, Muder D, Vedung T, Nilsson O. Optimized protocols for in situ hybridization, immunohistochemistry, and immunofluorescence on skeletal tissue. Acta Histochem 2021; 123:151747. [PMID: 34217048 DOI: 10.1016/j.acthis.2021.151747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022]
Abstract
Assessment of gene and protein expression in tissue sections is instrumental in medical research. However, this is often challenging to perform on skeletal tissues that require prolonged decalcification and have poor adhesion to slides. In this study, we optimized selected steps of in situ hybridization (ISH), immunohistochemistry (IHC), and immunofluorescence (IF) for formalin fixed and decalcified skeletal tissues. Sections from distal femur of 6-, 8- and 14- week-old rats injected with BrdU with or without a hemizygous eGFP transgene expressed under the control of a ubiquitous promotor were used. We report that proteinase K digestion is critical for the sensitivity of ISH, as concentrations that were too strong and too mild both resulted in loss of signal. In addition, intensified RNase A digestion removed nonspecific riboprobe-mRNA hybrids. Furthermore, enzymatic antigen retrieval using proteinase K provided more consistent results in IHC and can therefore be a useful alternative to heat induced epitope retrieval (HIER) for skeletal tissues where such treatment often damages the morphology. A mild proteinase K digestion also improved IF detection of GFP and worked well for double labeling IF of GFP and osteocalcin on frozen sections of formalin fixed and decalcified rat bones while maintaining morphology. In summary, this study provides strategies to improve protocols for enzymatic digestion in ISH, IHC, and IF for skeletal tissues and also demonstrates the importance of careful optimization and validation with the use of these techniques.
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Yan L, Ke Y, Kan Y, Lin D, Yang J, He Y, Wu L. New insight into enzymatic hydrolysis of peptides with site-specific amino acid d-isomerization. Bioorg Chem 2020; 105:104389. [PMID: 33120320 DOI: 10.1016/j.bioorg.2020.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 10/11/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
The isomerization of l-amino acids in peptides and proteins into d-configuration under physiological conditions would affect the physiological dysfunction and caused protein conformational diseases. The presence of d-amino acids might change the higher-order structure of proteins and triggered abnormal aggregation. In order to better understand this phenomenon and promote degradation, we systematically studied the enzymatic hydrolysis of a series of peptides obtained by replacing l-amino acids in different positions of template peptide KYNETWRSED with d-amino acids under the action of Protease K. The results showed that, compared with normal peptide, isomerization of different amino acids had different effects on the anti-enzymatic hydrolysis of the peptides, especially d-tryptophan at position 6, which significantly inhibited enzymatic hydrolysis. The analysis of the peptide cleavage site revealed that the efficiency of enzymatic hydrolysis mainly depended on the isomerization of the amino acids at a specific site of the peptide cleavage. Further studies showed that the enzymatic hydrolysis of substrates could be facilitated by optimized reaction conditions such as temperature, pH, addition of metal ions, and change of buffer. In this way the accumulation of disease-associated d-amino acid containing polypeptides/proteins could be prevented.
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Affiliation(s)
- Liang Yan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhe Kan
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dao Lin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingkui Yang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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17
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Zhu L, Bu G, Jing L, Shi D, Lee MY, Gonen T, Liu W, Nannenga BL. Structure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroED. Structure 2020; 28:1149-1159.e4. [PMID: 32735770 PMCID: PMC7544639 DOI: 10.1016/j.str.2020.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023]
Abstract
The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.
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Affiliation(s)
- Lan Zhu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Guanhong Bu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Liang Jing
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ming-Yue Lee
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Liu
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, 551 East University Drive, Tempe, AZ 85287, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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Michel D, Danzer KM, Groß R, Conzelmann C, Müller JA, Freischmidt A, Weishaupt JH, Heller S, Münch J, Michel M, Stamminger T, Kleger A, Otto M. Rapid, convenient and efficient kit-independent detection of SARS-CoV-2 RNA. J Virol Methods 2020; 286:113965. [PMID: 32891677 DOI: 10.1016/j.jviromet.2020.113965] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
Simplified SARS-CoV-2 RNA isolation is possible without commercial RNA isolation kits. The method is rapid, reliable and cost-effective, works best on nasopharyngeal swabs. Tracheal secretion appears unsuitable most likely due to high mucus/protein content. Detection threshold is slightly higher compared to kit-based RNA extraction methods. Method could bypass or temporally bridge shortage of resources.
Pandemic SARS-CoV-2 infection has rapidly developed into a socioeconomic and humanitarian catastrophe. Basic principles to prevent SARS-CoV-2 transmission are social distancing, face masks, contact tracing and early detection of SARS-CoV-2. To meet these requirements, virtually unlimited test capacities delivering results in a rapid and reliable manner are a prerequisite. Here, we provide and validate such a rapid, convenient and efficient kit-independent detection of SARS-CoV-2 RNA, termed COVID-quick-DET. This straightforward method operates with simple proteinase K treatment and repetitive heating steps with a sensitivity of 94.6% in head-to-head comparisons with kit-based isolation methods. This result is supported by data obtained from serially diluted SARS-CoV-2 virus stocks. Given its cost- and time-effective operation, COVID-quick-DET might be best suited for countries with general shortage or temporary acute scarcity of resources and equipment.
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Skowron PM, Krefft D, Brodzik R, Kasperkiewicz P, Drag M, Koller KP. An alternative for proteinase K-heat-sensitive protease from fungus Onygena corvina for biotechnology: cloning, engineering, expression, characterization and special application for protein sequencing. Microb Cell Fact 2020; 19:135. [PMID: 32580707 PMCID: PMC7313183 DOI: 10.1186/s12934-020-01392-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Background A neutral, heat-sensitive serine protease (NHSSP) originating from the feather-degrading fungus Onygena corvina (O. corvina) was described and defined as an alkaline serine protease of the subtilisin type S8 family, exhibiting an enzymatic activity at neutral pH. Generally, broad specificity proteases, such as proteinase K or trypsin, have found numerous applications in research and biotechnology. Results We report the cloning and expression in the yeast PichiaPink™ system, as well as purification, and characterization of the NHSSP. Recombinant, His6-tagged NHSSP was efficiently expressed from an optimized, synthetic gene and purified using a simple protocol based on ammonium sulfate fractionation and hydrophobic interaction chromatography. The enzyme shows atypical C-terminal processing, the coded preproprotein undergoes signal peptide removal and maturation through the clipping of a propeptide section and 10 amino acids (aa) from the C-terminus, including the His6-tag. The deletion variant has been constructed, devoid of the C-terminal ORF segment, thus eliminating the need for C-terminal processing. Both NHSSP variants exhibit very similar enzymatic characteristics. The purified enzymes were characterized to determine the optimal proteolytic conditions. We revealed that the mature NHSSP is reproducibly active over a wide pH range from neutral to mild acidic (pH of 5.0 to 8.5), with an optimum at pH 6.8, and at temperatures of 15 to 50 °C with an optimum at 38–42 °C. Interestingly, we demonstrated that the protease can be fully deactivated by a moderate increase in temperature of about 15 °C from the optimum to over 50 °C. The protease was partially sensitive to serine protease inhibitors, and not inhibited by chelating or reducing agents and detergents. SDS induced autolysis of NHSSP, which points to a high stimulation of its proteolytic activity. Conclusions The NHSSP was produced as a recombinant protein with high efficiency. Compared to proteinase K, the most common serine protease used, NHSSP shows an approx. twofold higher specific activity. Protein sequencing can be a valuable technical application for the protease. The protein coverage is significantly higher in comparison to trypsin and reaches about 84–100% for β-lactoglobulin (BLG), antibody (mAb) light and heavy chains. Furthermore, the option to perform digestions at neutral to slightly acidic pH-values down to pH 5.0 avoids modification of peptides, e.g. due to deamidation.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, 80-308, Gdansk, Poland.
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, 80-308, Gdansk, Poland
| | - Robert Brodzik
- BLIRT S.A., Trzy Lipy 3/1.38 Street, 80-172, Gdansk, Poland
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27 Street, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27 Street, 50-370, Wroclaw, Poland
| | - Klaus-Peter Koller
- Institute for Molecular Bio Science, University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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Chu AWH, Chan WM, Ip JD, Yip CCY, Chan JFW, Yuen KY, To KKW. Evaluation of simple nucleic acid extraction methods for the detection of SARS-CoV-2 in nasopharyngeal and saliva specimens during global shortage of extraction kits. J Clin Virol 2020; 129:104519. [PMID: 32629187 PMCID: PMC7309780 DOI: 10.1016/j.jcv.2020.104519] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/16/2020] [Accepted: 06/21/2020] [Indexed: 01/13/2023]
Abstract
Proteinase K-heat method improves nucleic acid extraction from respiratory specimens. Proteinase K-heat method is most useful during shortage of nucleic acid extraction kits. Proteinase-K-heat method is inexpensive.
Background The severe shortage of nucleic acid extraction kits during the current COVID-19 pandemic represents a key limiting factor in testing capacity. Objectives This study compared the results of SARS-CoV-2 RT-PCR using different simple nucleic acid extraction methods on nasopharyngeal and saliva specimens. Study design Fifty nasopharyngeal swab and saliva specimens previously tested positive for SARS-CoV-2 were retrieved. Three different methods of nucleic acid extraction were compared. The first method involves incubating the specimen with proteinase K, and then heat treatment at 98 °C for 5 min (PKH); the second method involves heat treatment at 98 °C for 5 min without proteinase K pre-incubation (heat only); the third method involves no pre-processing steps (direct). The products from all 3 methods were tested by SARS-CoV-2 RT-PCR. Results PKH had significantly higher positive rate in SARS-CoV-2 RT-PCR (80 %) than those of heat only (58 %; P = 0.001) or direct (56 %; P = 0.002). The median Ct value was significantly earlier for PKH (median Ct: 37.0, IQR 31.7–40) than that of heat only (median Ct: 40, IQR 36.2–41; P < 0.0001) and direct (median Ct, 37.5; IQR 33.9–41.0; P = 0.0049). Subgroup analysis showed that PKH had higher detection rate, lower limit of detection and earlier Ct values than the other two groups for both NPS and saliva specimens. Conclusions PKH pre-processing resulted in the highest detection rate of SARS-CoV-2 by RT-PCR, and represents an alternative method for nucleic acid extraction when commercial extraction kits are not available.
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Affiliation(s)
- Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China.
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Abstract
Leptospira species are one of the few spirochetes to possess a lipopolysaccharide (LPS) embedded in their outer membrane. Two protocols are currently available to extract and/or purify the leptospiral lipopolysaccharides: the rapid proteinase K method and the classical hot water/phenol extraction. The first method allows to get a quick overview of the LPS O antigen structure, whereas the second method is fitted to study the immunological properties of the leptospiral LPS. These two methods will be detailed in this chapter. Methodologies to assess the quality of the purification, such as the modified silver staining coloration, will also be reviewed. Both advantages and limitations of the different analyses will be described.
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22
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Ahmad MS, Akbar Z, Choudhary MI. Insight into the binding affinity of thiourea in the calcium binding pocket of proteinase K, through high resolution X-ray crystallography. Bioorg Chem 2019; 94:103443. [PMID: 31812259 DOI: 10.1016/j.bioorg.2019.103443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/20/2019] [Accepted: 11/13/2019] [Indexed: 12/01/2022]
Abstract
Proteinase K is a stable serine protease, crystallized and extensively used in the study of molecular interactions at the atomic level. During the current study, crystal structure of proteinase K with thiourea (TU) was solved at 1.45 Å (angstrom) resolution. Proteinase K showed its binding affinity with thiourea after soaking with 200 mM (millimolar) concentration of thiourea solution for 6 h. The binding affinity of proteinase K was evaluated with three different molecules i.e., thiourea, acetamide, and thiosemicarbazide. Interestingly, only the thiourea went into the calcium-binding region, and showed interactions with those amino acids which have also displayed interactions with calcium previously. Pro175 (proline 175), Ser197 (Serine 197), Val198 (valine 198), and Asp200 (aspartic acid 200) were the key amino acids involved in the binding of thiourea with proteinase K. Thiourea showed strong hydrogen bondings with Pro175 (2.85 Å), Ser197 (2.88 Å), and Asp200 (2.90 Å, and 3.30 Å), as the key interactions involved in the binding of thiourea with proteinase K. This study provides an insight into the binding mechanism of thiourea with calcium-binding pocket of proteinase K, and thus can be extrapolated to other calcium-binding proteins.
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Affiliation(s)
- Malik Shoaib Ahmad
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Zeeshan Akbar
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21412, Saudi Arabia
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23
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Ren Y, Luo H, Huang H, Hakulinen N, Wang Y, Wang Y, Su X, Bai Y, Zhang J, Yao B, Wang G, Tu T. Improving the catalytic performance of Proteinase K from Parengyodontium album for use in feather degradation. Int J Biol Macromol 2020; 154:1586-95. [PMID: 31706815 DOI: 10.1016/j.ijbiomac.2019.11.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/06/2019] [Accepted: 11/06/2019] [Indexed: 01/14/2023]
Abstract
Proteinase K (PROK) from Parengyodontium album hydrolyzes keratin, a major protein component of poultry feathers, which are an inexpensive and renewable protein resource. Based on structural studies for analysis of amino acid flexibility near the catalytic center, identification of highly conserved residues, and experimental screening, we obtained a mutant R218S with residual activity 1.6-fold higher than that of PROK after incubation at 60 °C for 1 h. Molecular dynamics simulation indicated that substitution of Arg218 with Ser leads to three hydrogen bonds being introduced into the structure, stabilizing the β-sheet in which Ser218 is located, and thus improvement of thermostability. Additionally, the mutant R218S had a 15% increase in specific activity compared to PROK and improvement in the rate and thoroughness of feather degradation compared with PROK. We confirmed the positive effects of enhancing catalytic center rigidity on enzyme thermostability, a finding which may have broad applications.
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24
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Jiang L, Li L, Kang P, Yu H, Nie SP, Xie MY, Gong J. Inappropriateness of RNAlater to preserve Caenorhabditis elegans for RNA extraction. MethodsX 2019; 6:2460-2467. [PMID: 31720236 PMCID: PMC6838534 DOI: 10.1016/j.mex.2019.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2019] [Indexed: 01/04/2023] Open
Abstract
Caenorhabditis elegans is a well-established laboratory animal model and has been widely used in biological research. However, it is still a challenge to obtain a good amount of quality RNA from a limited number of C. elegans for gene expression studies. To address this issue, the present study has compared different conditions to preserve C. elegans for RNA extraction after the failure of an initial effort to use RNAlater-preserved worms for RNA extraction. The effects of different concentrations of proteinase K, different worm life stages, and different worm numbers on RNA extraction were also investigated. The best results were achieved under the following conditions: 1) adult worms that were either freshly prepared or quickly frozen in liquid nitrogen followed by storage at −80 °C; 2) disruption of C. elegans with proteinase K (1 mg/mL) in a lysis buffer (65 °C for 10 min) prior to extraction with Trizol agent. This method can provide a stable, rapid, and effective means to extract RNA from C. elegans with variable worm numbers from 20 to 200. RNAlater was inappropriate for preserving C. elegans for effective RNA extraction. Proteinase K was verified for lysing a limited number of C. elegans for RNA extraction.
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Affiliation(s)
- Leming Jiang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, 330047, China.,Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, N1G 5C9, Canada
| | - Linyan Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, 330047, China.,Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, N1G 5C9, Canada
| | - Ping Kang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, N1G 5C9, Canada.,Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Hai Yu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, N1G 5C9, Canada
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, 330047, China
| | - Ming-Yong Xie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, 330047, China
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, N1G 5C9, Canada
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25
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Boos GS, Nobach D, Failing K, Eickmann M, Herden C. Optimization of RNA extraction protocol for long-term archived formalin-fixed paraffin-embedded tissues of horses. Exp Mol Pathol 2019; 110:104289. [PMID: 31348903 DOI: 10.1016/j.yexmp.2019.104289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/24/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022]
Abstract
A suitable RNA extraction protocol was established to gain high quality RNA from formalin-fixed paraffin-embedded tissues to perform reliable molecular assays either applicable for using FFPE tissue archives or tissues with harsh formalin-fixation. Eighteen FFPE samples from the central nervous system of horses, stored up to 11 years, were used as archive cases. To test the influence of the fixation period, brain, liver, kidney, and skeletal muscle tissue fragments from another horse, were treated either with water or tris-acetate-EDTA buffer after fixation under different timepoints with 10% unbuffered formalin. Two deparaffinization methods and three proteinase K-based lysis step were tested and translated into three protocols. After detailed statistical analysis it was determined that a longer period and increase in volume of proteinase K incubation provide higher yields and purity of RNA (P < 0.01) of archived samples. Alongside, amplification of equid-housekeeping gene up to 298 bp was successful with the protocol adaptations. For different formalin-fixation timepoints, it was demonstrated that the right choice for treatment and formalin-fixation period is organ-related (P ≤ 0.05). Essentially, little alterations to pre-existing extraction protocols unwound the RNA of up to 11-year-old samples, enabling the use of FFPE tissue archives or e.g. harshly fixed material needed in infection research under high biosafety levels for a variety of molecular analysis.
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Affiliation(s)
- Gisele Silva Boos
- Institute of Veterinary Pathology, Justus-Liebig-University, Gießen 35392, Germany.
| | - Daniel Nobach
- Institute of Veterinary Pathology, Justus-Liebig-University, Gießen 35392, Germany
| | - Klaus Failing
- Unit for Biomathematics and Data Processing, Justus-Liebig-Universität, Gießen 35392, Germany
| | - Markus Eickmann
- Institute of Virology, Philipps-University, Marburg 35043, Germany
| | - Christiane Herden
- Institute of Veterinary Pathology, Justus-Liebig-University, Gießen 35392, Germany; Center of Mind, Brain and Behavior, Justus-Liebig-University Gießen, Gießen, Germany
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Abstract
This study investigated the effects of enzyme application on biofilms of bacterial isolates from a cafeteria kitchen and foodborne pathogens and the susceptibility of Salmonella biofilms to proteinase K combined with chlorine treatment. For four isolates from a cafeteria kitchen ( Acinetobacter, Enterobacter, and Kocuria) and six strains of foodborne pathogens ( Salmonella enterica, Staphylococcus aureus, and Vibrio parahaemolyticus), the inhibitory effect of enzymes on biofilm formation at 25°C for 24 h or the degradative efficacy of enzymes on 24-h mature biofilm at 37°C for 1 h in tryptic soy broth (TSB) was examined in a polystyrene microtiter plate. The effect of enzymes was also evaluated on a subset of these strains in 20 times diluted TSB (1/20 TSB) at 25°C. The working concentrations of five enzymes were 1 U/100 μL for α-amylase, amyloglucosidase, cellulase, and DNase and 1 milli-Anson unit/100 μL for proteinase K. In addition, 24-h mature Salmonella Typhimurium biofilm on a stainless steel coupon was treated with proteinase K for 1 h at 25°C followed by 20 ppm of chlorine for 1 min at 25°C. The results showed that certain enzymes inhibited biofilm formation by the kitchen-originated bacteria; however, the enzymatic effect was diminished on the mature biofilms. Biofilm formation of V. parahaemolyticus was suppressed by all tested enzymes, whereas the mature biofilm was degraded by α-amylase, DNase I, and proteinase K. Proteinase K was effective in controlling Salmonella biofilms, whereas a strain-dependent variation was observed in S. aureus biofilms. In 1/20 TSB, Enterobacter cancerogenus and Kocuria varians were more susceptible to certain enzymes during biofilm formation than those in TSB, whereas the enzymatic effect was much decreased on 24-h mature biofilms, regardless of nutrient conditions. Furthermore, synergistic inactivation of Salmonella Typhimurium in biofilms was observed in the combined treatment of proteinase K followed by chlorine. Live/Dead assays also revealed a decrease in density and loss of membrane integrity in Salmonella Typhimurium biofilms exposed to the combined treatment. Therefore, certain enzymes can control biofilms of isolates residing in a cafeteria kitchen and foodborne pathogens. This study demonstrates the potential of enzymes for the sanitation of food processing environments and of proteinase K combined with chlorine to control Salmonella biofilms on food contact surfaces.
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Affiliation(s)
- Min-Jeong Kim
- 1 Research Group of Consumer Safety, Research Division of Strategic Food Technology, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Eun Seob Lim
- 2 Department of Food Biotechnology, Korea University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Joo-Sung Kim
- 1 Research Group of Consumer Safety, Research Division of Strategic Food Technology, Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do 55365, Republic of Korea.,2 Department of Food Biotechnology, Korea University of Science and Technology, 217, Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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27
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Schroeder H, de Barros Damgaard P, Allentoft ME. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step. Methods Mol Biol 2019; 1963:21-4. [PMID: 30875040 DOI: 10.1007/978-1-4939-9176-1_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.
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28
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Kakizaki E, Sonoda A, Shinkawa N, Yukawa N. A new enzymatic method for extracting diatoms from organs of suspected drowning cases using papain: Optimal digestion and first practical application. Forensic Sci Int 2019; 297:204-16. [PMID: 30831412 DOI: 10.1016/j.forsciint.2019.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/13/2019] [Accepted: 02/05/2019] [Indexed: 12/12/2022]
Abstract
Diatom analysis is very effective for positive diagnosis of water inhalation in drowning. However, conventional strong acid diatom testing is laborious and potentially dangerous. We propose a simple, fast, and safe protocol using inexpensive reagents such as papain, SDS, and 5 N HCl for extracting diatoms from lung, kidney, and liver tissues. First, we determined optimal conditions for papain digestion using porcine tissues. Papain digestion was clearly superior to Proteinase K digestion. Next, for assessing the assay effectiveness in practical cases, the papain digestion protocol was applied to 80 tissue samples from 20 suspected drowning victims. Left and right lung tissues (1 g each) were digested in 15-mL conical centrifuge tubes. Kidney and liver tissues (10 g each) were extracted in 175-mL conical centrifuge bottles. Papain dissolved all organs sufficiently and permitted clear visualization of diatoms, although papain's solubilization activity was still inferior to strong acid digestion. The proposed enzymatic method requires only a low-speed centrifuge and water bath. Diatoms typically can be extracted from tissue samples within 3-5 h. The cost of protease is reduced some 6-fold by using papain in place of Proteinase K. Thus, the proposed method can be useful as a less-laborious, less-hazardous, and less-costly minimal test when the conventional strong acid digestion method is not performed due to personnel, equipment, budgetary limitation, or environmental and safety considerations.
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29
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Klingelfus T, Disner GR, Voigt CL, Alle LF, Cestari MM, Leme DM. Nanomaterials induce DNA-protein crosslink and DNA oxidation: A mechanistic study with RTG-2 fish cell line and Comet assay modifications. Chemosphere 2019; 215:703-709. [PMID: 30347365 DOI: 10.1016/j.chemosphere.2018.10.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 06/08/2023]
Abstract
Genotoxic effects of nanomaterials (NMs) have been controversially reported in literature, and the mode of action (MoA) via DNA oxidation is cited as the main damage caused by them. Evidence of nano-silver as a crosslinker has been previously reported by the present research team in an in vivo fish genotoxicity study. Thus, aiming to confirm the evidence about NMs as crosslinker agent, the present investigation elucidated the genotoxic potential of NMs and their genotoxic MoA through in vitro assay with RTG-2 cells line (rainbow trout gonadal) by exposure to nano-silver (PVP-coated) and nano-titanium. The types and levels of DNA damage were assessed by the Comet assay (standard alkaline, hOGG1-modified alkaline, and two crosslink-modified alkaline versions). It was demonstrated that the use of the standard alkaline Comet assay alone may inaccurately predict the genotoxicity of NMs since oxidative and crosslink DNA damages were also verified in RTG-2 cells when assessed by the modified versions of the alkaline protocol. More importantly, it was confirmed that both nano-silver and nano-titanium acted as DNA-protein crosslinkers through the Comet assay version with proteinase K. As both nano-silver and nano-titanium present a great risk to aquatic life, these findings reinforce the need of genotoxicity testing strategies that encompass the assessment of different types of DNA damage, in order to ensure an accurate prediction of the genotoxic potential of NMs.
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Affiliation(s)
- T Klingelfus
- Genetics Department, Federal University of Paraná, Curitiba, Paraná State, Brazil.
| | - G R Disner
- Genetics Department, Federal University of Paraná, Curitiba, Paraná State, Brazil.
| | - C L Voigt
- Chemistry Department, State University of Ponta Grossa, Ponta Grossa, Paraná State, Brazil.
| | - L F Alle
- Genetics Department, Federal University of Paraná, Curitiba, Paraná State, Brazil.
| | - M M Cestari
- Genetics Department, Federal University of Paraná, Curitiba, Paraná State, Brazil.
| | - D M Leme
- Genetics Department, Federal University of Paraná, Curitiba, Paraná State, Brazil.
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30
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Abstract
The infectious virion of hepatitis C virus (HCV) is made up of the viral nucleocapsid surrounded by an envelope that contains an ER-derived membrane bilayer, cellular lipids, and the viral E1 and E2 glycoproteins. Because the infectious HCV particle contains both protein and lipid layers, selective disruption of these layers and analysis for the presence or absence of resulting virion components can be used to study the virion assembly process. This chapter describes an experimental method to measure HCV virion envelopment, which can reveal the mechanisms of how specific viral protein-protein interactions and host factors contribute to the process of HCV envelopment.
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Affiliation(s)
- Allison E Roder
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
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31
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Dun Y, Li Y, Xu J, Hu Y, Zhang C, Liang Y, Zhao S. Simultaneous fermentation and hydrolysis to extract chitin from crayfish shell waste. Int J Biol Macromol 2018; 123:420-426. [PMID: 30439435 DOI: 10.1016/j.ijbiomac.2018.11.088] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 10/09/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022]
Abstract
Chitin is the second-most abundant bioresource and widely used in the food, agricultural, textile, biomedical, and pharmaceutical industries. However, an efficient, environmentally friendly, and economically feasible process for chitin extraction from shellfish waste remains to be explored. This study aimed to extract chitin from crayfish shell waste powder (CSP) by removing Ca2+ and protein, using Bacillus coagulans LA204 and proteinase K. A simultaneous enzymatic hydrolysis and fermentation process was conducted at 50 °C with 5% (w/v) CSP, 5% (w/v) glucose, 1000 U proteinase k g-1 CSP, and 10% inoculation of B. coagulans LA204 in a 5-L bioreactor under non-sterile conditions. After 48 h of fermentation, the deproteinization efficiency, demineralization efficiency, and chitin recovery reached 93%, 91%, and 94%, respectively. 1 mol additional glucose efficiently removed 0.91 mol calcium carbonate and 93% of the removed protein was hydrolyzed to acid-soluble protein. Simultaneous enzymatic hydrolysis and fermentation was a new strategy and a competitive biological method for chitin extraction.
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Affiliation(s)
- Yaohao Dun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongqiang Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiahui Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanliang Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Collaborative Innovation Center for Industrial Fermentation, Wuhan 430068, China; Hubei Key Laboratory of Edible Wild Plants Conservation & Utilization, College of Life Sciences, Hubei Normal University, Huangshi 435002, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Collaborative Innovation Center for Industrial Fermentation, Wuhan 430068, China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Collaborative Innovation Center for Industrial Fermentation, Wuhan 430068, China.
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32
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Hosseini-Koupaei M, Shareghi B, Saboury AA, Davar F, Sirotkin VA, Hosseini-Koupaei MH, Enteshari Z. Catalytic activity, structure and stability of proteinase K in the presence of biosynthesized CuO nanoparticles. Int J Biol Macromol 2018; 122:732-744. [PMID: 30408449 DOI: 10.1016/j.ijbiomac.2018.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/14/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022]
Abstract
Here, CuO nanoparticles were synthesized using Sambucus nigra (elderberry) fruit extract. Further, the binding of proteinase K, as a model enzyme with green synthesized nanoparticles was investigated. The results demonstrated that the structural changes in enzyme were induced by the binding of nanoparticles. These changes were accompanied by the decrease in the Michaelis-Menten constant at 298 K. This means that the enzyme affinity for the substrate was increased. Thermodynamic parameters of protein stability and protein-ligand binding were estimated from the spectroscopic measurements at 298-333 K. Depending on the temperature, CuO nanoparticles showed a dual effect on the thermodynamic stability and binding affinity of enzyme. Nanoparticles increase the stability of the native state of enzyme at room temperature. On the other hand, nanoparticles stabilize the unfolded state of enzyme at 310-333 K. An overall favorable Gibbs energy change was observed for the binding process at 298-333 K. The enzyme-nanoparticle binding is enthalpically driven at room temperature. It was concluded that hydrogen bonding plays a key role in the interaction of enzyme with nanoparticles at 298-310 K. At higher temperatures, the protein-ligand binding is entropically driven. This means that hydrophobic association plays a major role in the proteinase K-CuO binding at 310-333 K.
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Affiliation(s)
- Mansoore Hosseini-Koupaei
- Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box .115, Iran; Department of Biology, Naghshe Jahan Institute of Higher Education, Isfahan, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, P. O. Box .115, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Fatemeh Davar
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
| | - Vladimir A Sirotkin
- Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kremlevskaya str., 18, Kazan 420008, Russia
| | | | - Zahra Enteshari
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
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33
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Yang RS, Tang W, Sheng H, Meng F. Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS. J Am Soc Mass Spectrom 2018; 29:853-858. [PMID: 29380268 DOI: 10.1007/s13361-017-1887-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/06/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. Graphical Abstract ᅟ.
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Affiliation(s)
- Rong-Sheng Yang
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA.
| | - Weijuan Tang
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Huaming Sheng
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA
| | - Fanyu Meng
- Analytical Research and Development, Merck and Co., Inc., Rahway, NJ, 07065, USA.
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Ge Y, Gu Y, Wang J, Zhang Z. Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2). Biochim Biophys Acta Biomembr 2018; 1860:1460-1469. [PMID: 29678469 DOI: 10.1016/j.bbamem.2018.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/24/2018] [Accepted: 04/15/2018] [Indexed: 11/19/2022]
Abstract
Sodium-coupled neutral amino acid transporter 2 (SNAT2) is a subtype of the amino acid transport system A that is widely expressed in mammalian tissues. It plays critical roles in glutamic acid-glutamine circulation, liver gluconeogenesis and other biological pathway. However, the topology of the SNAT2 amino acid transporter is unknown. Here we identified the topological structure of SNAT2 using bioinformatics analysis, Methoxy-polyethylene glycol maleimide (mPEG-Mal) chemical modification, protease cleavage assays, immunofluorescence and examination of glycosylation. Our results show that SNAT2 contains 11 transmembrane domains (TMDs) with an intracellular N terminus and an extracellular C terminus. Three N-glycosylation sites were verified at the largest extracellular loop. This model is consistent with the previous model of SNAT2 with the exception of a difference in number of glycosylation sites. This is the first time to confirm the SNAT2 membrane topology using experimental methods. Our study on SNAT2 topology provides valuable structural information of one of the solute carrier family 38 (SLC38) members.
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Affiliation(s)
- Yudan Ge
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Yanting Gu
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Jiahong Wang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China
| | - Zhou Zhang
- College of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang City 110016, China.
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Voitechovič E, Korepanov A, Kirsanov D, Legin A. Quantification of immobilized protein in pharmaceutical production by bio-assisted potentiometric multisensor system. J Pharm Biomed Anal 2018; 150:67-71. [PMID: 29216587 DOI: 10.1016/j.jpba.2017.11.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 11/20/2022]
Abstract
Quantification of proteins is a key biochemical assay in molecular biology, biotechnology, medicine and pharmacology. Protein quantification protocols can be based on spectrophotometry, enzyme-linked immunosorbent assay, mass spectrometry or quantitative immunoblotting depending on analyte. In case of immobilized protein these methods require suitable sample preparation. Thus, sophisticated analysis becomes even more complex, expensive and time-consuming. Such drawbacks are highly undesirable in industry. In this study we propose a new approach for evaluation of immobilized protein concentration based on application of bio-assisted potentiometric multisensor system. Surface-immobilized recombinant protein A from Staphylococcus aureus (SpA, expressed in Escherichia coli), which is commonly used as affinity ligand immobilized to stationary phase (сhromatography media) for monoclonal antibody purification was employed as the model object. Chromatography media samples containing different amounts of immobilized SpA were analyzed. Proteinase K from Tritirachium album was employed as a bio-transducer. We demonstrated that the suggested approach provides information about immobilized SpA concentration with 0.8mg/ml accuracy in the range 1-6.7mg/ml and within just 16min. Moreover, the proposed procedure requires no expensive materials and equipment and no bio-transducer immobilization. This method has potential of application for fast monitoring of other immobilized proteins in different tasks.
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Affiliation(s)
- Edita Voitechovič
- St. Petersburg State University, St. Petersburg, Russia; Institute of Microelectronics of Barcelona, Barcelona, Spain.
| | | | - Dmitry Kirsanov
- St. Petersburg State University, St. Petersburg, Russia; Laboratory of Artificial Sensory Systems, ITMO University, St. Petersburg, Russia.
| | - Andrey Legin
- St. Petersburg State University, St. Petersburg, Russia; Laboratory of Artificial Sensory Systems, ITMO University, St. Petersburg, Russia
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Vincent MS, Cascales E. Probing Inner Membrane Protein Topology by Proteolysis. Methods Mol Biol 2017; 1615:97-103. [PMID: 28667606 DOI: 10.1007/978-1-4939-7033-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Inner membrane proteins are inserted into the membrane via α-helices. These helices do not only constitute membrane anchors but may mediate specific interactions with membrane protein partners or participate in energetic processes. The number, location, and orientation of these helices is referred to as topology. Bitopic membrane proteins that consist of a single membrane-embedded domain connecting two soluble domains are distinguished from polytopic ones that consist of multiple membrane-spanning helices connected by extramembrane domains. Defining inner membrane protein topology could be achieved by different methods. Here we describe a protease accessibility assay that makes it possible to define topology based on digestion profiles.
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Abstract
Dendronized polymer-enzyme conjugates are large, water-soluble macromolecular structures built from a linear, fully synthetic, dendronized polymer (denpol), and several copies of enzyme molecules covalently bound to the peripheral functional groups of the denpol. Since denpol chains comprise repeating units with regularly branched side chains (dendrons), denpols have a cylindrical shape and are much thicker than conventional linear polymers. Depending on the dendron generation and chemical structure, denpols may have a large number of functional groups on their surface, exposed to the aqueous medium in which they are dissolved. Enzymes (and also other molecules) can be attached to these functional groups, for example, via a stable bis-aryl hydrazone (BAH) bond. The dendronized polymer scaffold might also serve as a nanoarmor and stabilize the delicate enzymes. One of the denpols which can be used for the preparation of denpol-enzyme conjugates is de-PG2. It has a poly(methacrylate) backbone and consists of second-generation dendrons with four peripheral amino groups in each repeating unit. The synthesis of de-PG2 and the preparation of a de-PG2 conjugate carrying BAH-linked proteinase K (proK), as an example, are described here for applications in the field of enzyme immobilization on solid surfaces. The nanoarmored enzyme-polymer conjugate indicated high stability and retention of enzymatic activity.
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Sung H, Yong D, Ki CS, Kim JS, Seong MW, Lee H, Kim MN. Comparative Evaluation of Three Homogenization Methods for Isolating Middle East Respiratory Syndrome Coronavirus Nucleic Acids From Sputum Samples for Real-Time Reverse Transcription PCR. Ann Lab Med 2017; 36:457-62. [PMID: 27374711 PMCID: PMC4940489 DOI: 10.3343/alm.2016.36.5.457] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. METHODS We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). RESULTS While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1-35.4 with the PK-DNase method, 34.7-39.0 with the PBS method, and 33.9-38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). CONCLUSIONS The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction.
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Affiliation(s)
- Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea.
| | - Dongeun Yong
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon, Korea
| | - Mi Na Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea.
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Francisco T, Dias AF, Pedrosa AG, Grou CP, Rodrigues TA, Azevedo JE. Determining the Topology of Peroxisomal Proteins Using Protease Protection Assays. Methods Mol Biol 2017; 1595:27-35. [PMID: 28409448 DOI: 10.1007/978-1-4939-6937-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protease protection assays are powerful tools to determine the topology of organelle proteins. Their simplicity, together with the fact that they are particularly suited to characterize endogenous proteins, are their major advantages and the reason why these assays have been in use for so many years. Here, we provide a detailed protocol to use with mammalian peroxisomes. Suggestions on how these assays can be controlled, and how to identify some technical pitfalls, are also presented.
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Affiliation(s)
- Tânia Francisco
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Ana F Dias
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Cláudia P Grou
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- Organelle Biogenesis and Function Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
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Singh G, Singh L, Ghosh R, Nath D, Dinda AK. Immunofluorescence on paraffin embedded renal biopsies: Experience of a tertiary care center with review of literature. World J Nephrol 2016; 5:461-470. [PMID: 27648410 PMCID: PMC5011253 DOI: 10.5527/wjn.v5.i5.461] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/11/2016] [Accepted: 08/18/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To describe the technique of immunofluorescence on paraffin embedded tissue sections and discuss the potential pitfalls with an in depth review of literature.
METHODS Immunofluorescence is integral to diagnostic renal pathology. Immunofluorescence on paraffin embedded renal biopsies (IF-P) after enzyme treatment has been described in literature, however has not found widespread use in renal pathology laboratories. In our laboratory proteinase K digestion of paraffin embedded renal biopsy material was standardized and applied prospectively in cases where immunofluorescence on fresh frozen tissue was non contributory or not possible. Diagnostic utility was assessed and in a cohort of cases comparison of intensity of staining with routine immunofluorescence was performed.
RESULTS Over the 5-year study period, of the 3141 renal biopsies received IF-P was performed on 246 cases (7.7%) and was interpretable with optimal digestion in 214 cases (6.8%). It was of diagnostic utility in the majority of cases, which predominantly included glomerular disease. Non-diagnostic IF-P was found in membranous nephropathy (2 of 11 cases), membranoproliferative glomerulonephritis (2 of 32 cases), lupus nephritis (1 of 25 cases), post infectious glomerulonephritis (1 of 11 cases) and chronic glomerulonephritis (3 of 8 cases). Comparing cases with both routine IF and IF-P, 35 of 37 showed either equal intensity or a minor difference in intensity of staining (1+) for the diagnostic immunoglobulin/complement. Technically assessment of immunofluorescence on the paraffin embedded tissue was found to be easier with clearly observed morphology, however a false positive staining pattern was observed in under-digested tissue.
CONCLUSION As a “salvage” technique, immunofluorescence on paraffin embedded renal biopsies is of great diagnostic utility, however not without pitfalls.
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Yang H, Zhai C, Yu X, Li Z, Tang W, Liu Y, Ma X, Zhong X, Li G, Wu D, Ma L. High-level expression of Proteinase K from Tritirachium album Limber in Pichia pastoris using multi-copy expression strains. Protein Expr Purif 2016; 122:38-44. [PMID: 26892536 DOI: 10.1016/j.pep.2016.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 01/26/2023]
Abstract
Proteinase K is widely used in scientific research and industries. This report was aimed to achieve high-level expression of proteinase K using Pichia pastoris GS115 as the host strain. The coding sequence of a variant of proteinase K that has higher activity than the wild type protein was chosen and optimized based on the codon usage preference of P. pastoris. The novel open reading frame was synthesized and a series of multi-copy expression vectors were constructed based on the pHBM905BDM plasmid, allowing for the tandem integration of multiple copies of the target gene into the genome of P. pastoris with a single recombination. These strains were used to study the correlation between the gene copy number and the expression level of proteinase K. The results of quantitative polymerase chain reaction (qPCR) indicated that the tandem expression cassettes were integrated into the host genome stably. Meanwhile, the results of qPCR and enzyme activity assays indicated that the mRNA and protein expression levels of the target gene increased as the gene copy number increased. Moreover, the effect of gene dosage on the expression level of the recombinant protein was more obvious using high-density fermentation. The maximum expression level and enzyme activity of proteinase K, which were obtained from the recombinant yeast strain bearing 5 copies of the target gene after an 84-h induction, were approximately 8.069 mg/mL and 108,295 U/mL, respectively. The recombinant proteinase was purified and characterized. The optimum pH and temperature for the activity of this protease were approximately pH 11 and 55 °C, respectively.
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Affiliation(s)
- Hu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Chao Zhai
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xianhong Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China; Institute of Molecular Medicine, Peking University, Beijing 100871, People's Republic of China
| | - Zhezhe Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Wei Tang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Yunyun Liu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xiaojian Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xing Zhong
- Department of Bioengineering, Zhixing College of Hubei University, Wuhan, People's Republic of China
| | - Guolong Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Di Wu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China.
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Piercey MJ, Hingston PA, Truelstrup Hansen L. Genes involved in Listeria monocytogenes biofilm formation at a simulated food processing plant temperature of 15 °C. Int J Food Microbiol 2016; 223:63-74. [PMID: 26900648 DOI: 10.1016/j.ijfoodmicro.2016.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 12/30/2022]
Abstract
Listeria monocytogenes is a pathogenic foodborne bacterium whose persistence in food processing environments is in part attributed to its biofilm formation. Most biofilm studies have been carried out at 30-37 °C rather than at temperatures found in the food processing plants (i.e., 10-20 °C). The objective of the present study was to mine for novel genes that contribute to L. monocytogenes biofilm formation at 15 °C using the random insertional mutagenesis approach. A library of 11,024 L. monocytogenes 568 (serotype 1/2a) Himar1 insertional mutants was created. Mutants with reduced or enhanced biofilm formation at 15 °C were detected in microtiter plate assays with crystal violet and safranin staining. Fourteen mutants expressed enhanced biofilm phenotypes, and harbored transposon insertions in genes encoding cell wall biosynthesis, motility, metabolism, stress response, and cell surface associated proteins. Deficient mutants (n=5) contained interruptions in genes related to peptidoglycan, teichoic acid, or lipoproteins. Enhanced mutants produced significantly (p<0.05) higher cell densities in biofilm formed on stainless steel (SS) coupons at 15 °C (48 h) than deficient mutants, which were also more sensitive to benzalkonium chloride. All biofilm deficient mutants and four enhanced mutants in the microtiter plate assay (flaA, cheR, lmo2563 and lmo2488) formed no biofilm in a peg lid assay (Calgary biofilm device) while insertions in lmo1224 and lmo0543 led to excess biofilm in all assays. Two enhanced biofilm formers were more resistant to enzymatic removal with DNase, proteinase K or pectinase than the parent strain. Scanning electron microscopy of individual biofilms made by five mutants and the parent on SS surfaces showed formation of heterogeneous biofilm with dense zones by immotile mutants, while deficient mutants exhibited sparse growth. In conclusion, interruptions of 9 genes not previously linked to biofilm formation in L. monocytogenes (lmo2572, lmo2488 (uvrA), lmo1224, lmo0434 (inlB), lmo0263 (inlH), lmo0543, lmo0057 (EsaA), lmo2563, lmo0453), caused enhanced biofilm formation in the bacterium at 15 °C. The remaining mutants harbored interruptions in 10 genetic loci previously associated with biofilm formation at higher temperatures, indicating some temperature driven differences in the formation of biofilm by L. monocytogenes.
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Affiliation(s)
- Marta J Piercey
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax B3H 4R2, Canada.
| | - Patricia A Hingston
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax B3H 4R2, Canada.
| | - Lisbeth Truelstrup Hansen
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax B3H 4R2, Canada.
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Kuszak AJ, Noinaj N, Buchanan SK. Methods to Characterize Folding and Function of BamA Cross-Link Mutants. Methods Mol Biol 2015; 1329:137-47. [PMID: 26427681 DOI: 10.1007/978-1-4939-2871-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The utility of protein engineering, both the mutation and deletion of specific amino acids, to investigate protein structure and function has been demonstrated time and time again, and intermolecular and intramolecular interactions within the BAM complex and its individual components are no exception. Extensive efforts have probed conserved and unique amino acid sequences of the Bam proteins to define their functional roles. This chapter summarizes efforts as applied to the disulfide cross-link mutants of BamA and describes experimental methods used in our studies to determine that lateral opening of the barrel domain is required for function.
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44
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Silva CJ, Vázquez-Fernández E, Onisko B, Requena JR. Proteinase K and the structure of PrPSc: The good, the bad and the ugly. Virus Res 2015; 207:120-6. [PMID: 25816779 DOI: 10.1016/j.virusres.2015.03.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/14/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
Abstract
Infectious proteins (prions) are, ironically, defined by their resistance to proteolytic digestion. A defining characteristic of the transmissible isoform of the prion protein (PrP(Sc)) is its partial resistance to proteinase K (PK) digestion. Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrP(Sc) by Western blot, ELISA or immunohistochemical detection. PK digestion has also been used to detect differences in prion strains. Thus, PK has been a crucial tool to detect and, thereby, control the spread of prions. PK has also been used as a tool to probe the structure of PrP(Sc). Mass spectrometry and antibodies have been used to identify PK cleavage sites in PrP(Sc). These results have been used to identify the more accessible, flexible stretches connecting the β-strand components in PrP(Sc). These data, combined with physical constraints imposed by spectroscopic results, were used to propose a qualitative model for the structure of PrP(Sc). Assuming that PrP(Sc) is a four rung β-solenoid, we have threaded the PrP sequence to satisfy the PK proteolysis data and other experimental constraints.
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45
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Kiselev KV, Dubrovina AS, Tyunin AP. The methylation status of plant genomic DNA influences PCR efficiency. J Plant Physiol 2015; 175:59-67. [PMID: 25506767 DOI: 10.1016/j.jplph.2014.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 10/11/2014] [Accepted: 10/12/2014] [Indexed: 05/20/2023]
Abstract
During the polymerase chain reaction (PCR), which is a versatile and widely used method, certain DNA sequences are rapidly amplified through thermocycling. Although there are numerous protocols of PCR optimization for different applications, little is known about the effect of DNA modifications, such as DNA methylation, on PCR efficiency. Recent studies show that cytosine methylation alters DNA mechanical properties and suggest that DNA methylation may directly or indirectly influence the effectiveness of DNA amplification during PCR. In the present study, using plant DNA, we found that highly methylated plant DNA genomic regions were amplified with lower efficiencies compared to that for the regions methylated at a lower level. The correlation was observed when amplifying stilbene synthase (STS1, STS10) genes of Vitis amurensis, the Actin2 gene of Arabidopsis thaliana, the internal transcribed spacer (AtITS), and tRNAPro of A. thaliana. The level of DNA methylation within the analyzed DNA regions has been analyzed with bisulfite sequencing. The obtained data show that efficient PCRs of highly methylated plant DNA regions can be hampered. Proteinase K treatment of the plant DNA prior to PCR and using HotTaq DNA polymerase improved amplification of the highly methylated plant DNA regions. We suggest that increased DNA denaturation temperatures of the highly methylated DNA and contamination with DNA-binding proteins contribute to the hampered PCR amplification of highly methylated DNA. The data show that it is necessary to use current DNA purification protocols and commercial kits with caution to ensure appropriate PCR product yield and prevent bias toward unmethylated DNA amplification in PCRs.
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Affiliation(s)
- K V Kiselev
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok 690022, Russia; Department of Biochemistry, Microbiology and Biotechnology, The School of Natural Sciences, Far Eastern Federal University, 690090, Vladivostok, Russia.
| | - A S Dubrovina
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok 690022, Russia
| | - A P Tyunin
- Laboratory of Biotechnology, Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok 690022, Russia
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Fränzel B, Fischer F, Steegborn C, Wolters DA. Proteinase K improves quantitative acylation studies. Proteomics 2014; 15:44-7. [PMID: 25332194 DOI: 10.1002/pmic.201400015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 08/10/2014] [Accepted: 10/15/2014] [Indexed: 11/08/2022]
Abstract
Acetylation is a common PTM of proteins but is still challenging to analyze. Only few acetylome studies have been performed to tackle this issue. Yet, the detection of acetylated proteins in complex cell lysates remains to be improved. Here, we present a proteomic approach with proteinase K as a suitable protease to identify acetylated peptides quantitatively. We first optimized the digestion conditions using an artificial system of purified bovine histones to find the optimal protease. Subsequently, the capability of proteinase K was demonstrated in complex HEK293 cell lysates. Finally, SILAC in combination with MudPIT was used to show that quantification with proteinase K is possible. In this study, we identified a sheer number of 557 unique acetylated peptides originating from 633 acetylation sites.
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Affiliation(s)
- Benjamin Fränzel
- Department of Analytical Chemistry, Biomolecular Mass Spectrometry, Institute of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
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Shishova KV, Lavrentyeva EA, Dobrucki JW, Zatsepina OV. Nucleolus-like bodies of fully-grown mouse oocytes contain key nucleolar proteins but are impoverished for rRNA. Dev Biol 2014; 397:267-81. [PMID: 25481757 DOI: 10.1016/j.ydbio.2014.11.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 11/20/2014] [Accepted: 11/22/2014] [Indexed: 11/26/2022]
Abstract
It is well known that fully-grown mammalian oocytes, rather than typical nucleoli, contain prominent but structurally homogenous bodies called "nucleolus-like bodies" (NLBs). NLBs accumulate a vast amount of material, but their biochemical composition and functions remain uncertain. To clarify the composition of the NLB material in mouse GV oocytes, we devised an assay to detect internal oocyte proteins with fluorescein-5-isothiocyanate (FITC) and applied the fluorescent RNA-binding dye acridine orange to examine whether NLBs contain RNA. Our results unequivocally show that, similarly to typical nucleoli, proteins and RNA are major constituents of transcriptionally active (or non-surrounded) NLBs as well as of transcriptionally silent (or surrounded) NLBs. We also show, by exposing fixed oocytes to a mild proteinase K treatment, that the NLB mass in oocytes of both types contains nucleolar proteins that are involved in all major steps of ribosome biogenesis, including rDNA transcription (UBF), early rRNA processing (fibrillarin), and late rRNA processing (NPM1/nucleophosmin/B23, nucleolin/C23), but none of the nuclear proteins tested, including SC35, NOBOX, topoisomerase II beta, HP1α, and H3. The ribosomal RPL26 protein was detected within the NLBs of NSN-type oocytes but is virtually absent from NLBs of SN-type oocytes. Taking into account that the major class of nucleolar RNA is ribosomal RNA (rRNA), we applied fluorescence in situ hybridization with oligonucleotide probes targeting 18S and 28S rRNAs. The results show that, in contrast to active nucleoli, NLBs of fully-grown oocytes are impoverished for the rRNAs, which is consistent with the absence of transcribed ribosomal genes in the NLB mass. Overall, the results of this study suggest that NLBs of fully-grown mammalian oocytes serve for storing major nucleolar proteins but not rRNA.
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Affiliation(s)
- Kseniya V Shishova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russian Federation.
| | - Elena A Lavrentyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russian Federation; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, Office, Moscow 119991, Russian Federation.
| | - Jurek W Dobrucki
- Laboratory of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Gronostajowa Street, 30-387 Krakow, Poland.
| | - Olga V Zatsepina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russian Federation.
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48
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Changotra H, Sehajpal PK. An improved method for the isolation of hepatitis B virus DNA from human serum. Indian J Virol 2013; 24:174-9. [PMID: 24426273 DOI: 10.1007/s13337-013-0155-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
Abstract
Studies show that hepatitis B virus (HBV) DNA isolation methods vary in their efficiency to extract DNA from serum samples. The purpose of the present study was to develop an improved method for isolation of HBV DNA and compare it with commonly used HBV DNA isolation protocols. In order to develop HBV DNA isolation protocol, serum samples were collected from patients and screened for the presence of hepatitis B surface antigen, hepatitis B e antigen and HBV DNA. Highly viremic samples were pooled and used to compare commonly used HBV DNA isolation methods; namely alkaline lysis, microwave treatment, organic, inorganic with modified inorganic method. DNA isolated by these methods was detected qualitatively by polymerase chain reaction and quantitatively with competitive polymerase chain reaction (cPCR). The modified inorganic method gave maximum yield of HBV DNA followed by inorganic, organic, microwave treatment and alkaline lysis method. Our data also demonstrated a critical role of proteinase K in HBV DNA isolation. DNA isolation method described here, in combination with a reproducible and sensitive quantitative technique would further help in accurate classification of HBV infected patients, designing suitable drug regimen for treatment and monitoring antiviral treatment as well as emergence of drug resistant mutants.
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Affiliation(s)
- Harish Changotra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234 Himachal Pradesh India
| | - Prabodh K Sehajpal
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, 143005 India
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Febbraro F, Andersen KJ, Sanchez-Guajardo V, Tentillier N, Romero-Ramos M. Chronic intranasal deferoxamine ameliorates motor defects and pathology in the α-synuclein rAAV Parkinson's model. Exp Neurol 2013; 247:45-58. [PMID: 23531432 DOI: 10.1016/j.expneurol.2013.03.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/10/2013] [Accepted: 03/14/2013] [Indexed: 10/27/2022]
Abstract
Parkinson's disease is characterized by neuronal death in the substantia nigra and the presence of intracellular inclusions of α-synuclein in the Lewy bodies. Several lines of data support a role for iron in Parkinson's disease: iron is present in Lewy bodies, iron accumulates in the dopaminergic neurons in the substantia nigra, and Parkinson's disease is correlated with polymorphisms of several genes implicated in iron metabolism. Furthermore, iron can compromise the solubility of α-synuclein through direct interaction and can induce neurotoxicity in vitro. Here, we investigate the possible neuroprotective effect of the iron chelator deferoxamine in vivo to elucidate whether iron chelation can provide meaningful therapy for Parkinson's disease. Hence, we used a Parkinson's disease animal model based on unilateral injection of a recombinant adeno-associated viral vector encoding α-synuclein in the rat midbrain. Rats were treated with a novel deferoxamine delivery approach: 6 mg of the compound was administered intranasally three times a week for 3 or 7 weeks. The behavior of the animals and histopathological changes in the brain were analyzed. Our data show that although intranasal administration of deferoxamine in rats did not protect them from dopaminergic cell death, it did decrease the number of the pathological α-synuclein formations at the terminal level. In addition, this treatment resulted in changes in the immune response and an overall partial improvement in motor behavior. Taken together, our data show that in vivo iron chelation can modulate α-synuclein-induced pathology in the central nervous system. Our data suggest that chronic administration of intranasal deferoxamine may be a valid approach to limiting the mishandling of α-synuclein in the central nervous system observed in Parkinson's disease and slowing disease progression.
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Affiliation(s)
- Fabia Febbraro
- CNS Disease Modeling Group, Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark.
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