1
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Versmessen N, Van Simaey L, Negash AA, Vandekerckhove M, Hulpiau P, Vaneechoutte M, Cools P. Comparison of DeNovix, NanoDrop and Qubit for DNA quantification and impurity detection of bacterial DNA extracts. PLoS One 2024; 19:e0305650. [PMID: 38885212 PMCID: PMC11182499 DOI: 10.1371/journal.pone.0305650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
Accurate DNA quantification is key for downstream application including library preparations for whole genome sequencing (WGS) and the quantification of standards for quantitative PCR. Two commonly used technologies for nucleic acid quantification are based on spectrometry, such as NanoDrop, and fluorometry, such as Qubit. The DS-11+ Series spectrophotometer/fluorometer (DeNovix) is a UV spectrophotometry-based instrument and is a relatively new spectrophotometric method but has not yet been compared to established platforms. Here, we compared three DNA quantification platforms, including two UV spectrophotometry-based techniques (DeNovix and NanoDrop) and one fluorometry-based approach (Qubit). We used genomic prokaryotic DNA extracted from Streptococcus pneumoniae using a Roche DNA extraction kit. We also evaluated purity assessment and effect of a single freeze-thaw cycle. Spectrophotometry-based methods reported 3 to 4-fold higher mean DNA concentrations compared to Qubit, both before and after freezing. The ratio of DNA concentrations assessed by spectrophotometry on the one hand, and Qubit on the other hand, was function of the A260/280. In case DNA was pure (A260/280 between 1.7 and 2.0), the ratio DeNovix or Nanodrop vs. Qubit was close or equal to 2, while this ratio showed an incline for DNA with increasing A260/280 values > 2.0. The A260/280 and A260/230 purity ratios exhibited negligible variation across spectrophotometric methods and freezing conditions. The comparison of DNA concentrations from before and after freezing revealed no statistically significant disparities for each technique. DeNovix exhibited the highest Spearman correlation coefficient (0.999), followed by NanoDrop (0.81), and Qubit (0.77). In summary, there is no difference between DeNovix and NanoDrop in estimated gDNA concentrations of S. pneumoniae, and the spectrophotometry methods estimated close or equal to 2 times higher concentrations compared to Qubit for pure DNA.
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Affiliation(s)
- Nick Versmessen
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Abel Abera Negash
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Paco Hulpiau
- HOWEST University of Applied Sciences, Bruges, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Piet Cools
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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2
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Elmer-Dixon MM, Fawcett LP, Sorensen EN, Maurer-Jones MA. Bovine Serum Albumin Bends Over Backward to Interact with Aged Plastics: A Model for Understanding Protein Attachment to Plastic Debris. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10207-10215. [PMID: 38809092 PMCID: PMC11171446 DOI: 10.1021/acs.est.3c10028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plastic pollution, a major environmental crisis, has a variety of consequences for various organisms within aquatic systems. Beyond the direct toxicity, plastic pollution has the potential to absorb biological toxins and invasive microbial species. To better understand the capability of environmental plastic debris to adsorb these species, we investigated the binding of the model protein bovine serum albumin (BSA) to polyethylene (PE) films at various stages of photodegradation. Circular dichroism and fluorescence studies revealed that BSA undergoes structural rearrangement to accommodate changes to the polymer's surface characteristics (i.e., crystallinity and oxidation state) that occur as the result of photodegradation. To understand how protein structure may inform docking of whole organisms, we studied biofilm formation of bacteriaShewanella oneidensison the photodegraded PE. Interestingly, biofilms preferentially formed on the photodegraded PE that correlated with the state of weathering that induced the most significant structural rearrangement of BSA. Taken together, our work suggests that there are optimal physical and chemical properties of photodegraded polymers that predict which plastic debris will carry biochemical or microbial hitchhikers.
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Affiliation(s)
- Margaret M. Elmer-Dixon
- Department
of Physics & Astronomy, University of
Minnesota, Duluth, Duluth, Minnesota 55812, United States
- Department
of Mechanical and Industrial Engineering, University of Minnesota, Duluth, Duluth, Minnesota 55812, United States
| | - Liam P. Fawcett
- Department
of Chemistry and Biochemistry, University
of Minnesota, Duluth, Duluth, Minnesota 55812, United States
| | - Emma N. Sorensen
- Department
of Chemistry and Biochemistry, University
of Minnesota, Duluth, Duluth, Minnesota 55812, United States
| | - Melissa A. Maurer-Jones
- Department
of Chemistry and Biochemistry, University
of Minnesota, Duluth, Duluth, Minnesota 55812, United States
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3
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Qiu Y, Huang T, Cai YD. Review of predicting protein stability changes upon variations. Proteomics 2024; 24:e2300371. [PMID: 38643379 DOI: 10.1002/pmic.202300371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/22/2024]
Abstract
Forecasting alterations in protein stability caused by variations holds immense importance. Improving the thermal stability of proteins is important for biomedical and industrial applications. This review discusses the latest methods for predicting the effects of mutations on protein stability, databases containing protein mutations and thermodynamic parameters, and experimental techniques for efficiently assessing protein stability in high-throughput settings. Various publicly available databases for protein stability prediction are introduced. Furthermore, state-of-the-art computational approaches for anticipating protein stability changes due to variants are reviewed. Each method's types of features, base algorithm, and prediction results are also detailed. Additionally, some experimental approaches for verifying the prediction results of computational methods are introduced. Finally, the review summarizes the progress and challenges of protein stability prediction and discusses potential models for future research directions.
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Affiliation(s)
- Yiling Qiu
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Mathematics and Statistics, Guangdong University of Technology, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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4
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Guan H, Zhang W, Liu H, Jiang Y, Li F, Wang D, Liu Y, He F, Wu M, Ivan Neil Waterhouse G, Sun-Waterhouse D, Li D. Simultaneous binding of quercetin and catechin to FOXO3 enhances IKKα transcription inhibition and suppression of oxidative stress-induced acute alcoholic liver injury in rats. J Adv Res 2024:S2090-1232(24)00043-2. [PMID: 38286301 DOI: 10.1016/j.jare.2024.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024] Open
Abstract
INTRODUCTION Oxidative stress is one of the major contributors to acute alcoholic liver injury (AALI), which is a common alcoholic liver disease. Quercetin and catechin are flavonoid antioxidants present in plant foods and possess chemopreventive and chemotherapeutic activities. Quercetin and catechin are often included in the same meal and ingested together. While they show cooperative actions against oxidative damage, the underlying mechanisms behind their counteracting effects against oxidative stress-induced AALI remain poorly understood. OBJECTIVES The aim of this study was to understand the mechanism underlying the enhanced antioxidant effect of quercetin-catechin combination to alleviate AALI in rats. METHODS The ethanol (EtOH)-treated rats and H2O2-treated liver cells were used to demonstrate the enhanced antioxidant effect of quercetin and catechin. Then we used RNA-sequencing to compare quercetin alone, catechin alone and quercetin-catechin combination and then identified the critical role of IKKα combining with gene silencing and overexpression techniques. Its transcription factor, FOXO3 was found through yeast one-hybrid assay, luciferase reporter assay, EMSA and ChIP assay. Finally, the interaction between quercetin, catechin and FOXO3 was verified through molecular docking, UV-Vis absorption spectroscopy, fluorescence spectroscopy, and CD spectroscopy. RESULTS The study demonstrated the enhanced antioxidant effect of a quercetin-catechin combination in EtOH-treated rats and in H2O2-treated liver cells. Quercetin and catechin cooperatively inhibited IKKα/p53 pathway and activated Nrf2 signaling pathway. IKKα was a critical negative regulator in their joint action. FOXO3 bound to IKKα promoter to regulate IKKα transcription. Quercetin and catechin influenced FOXO3-IKKα binding through attaching directly to FOXO3 at different sites and altering FOXO3's secondary structures. CONCLUSION Our study revealed the mechanism of quercetin and catechin against oxidative stress-induced AALI through jointly interacting with transcription factor. This research opens new vistas for examining the joint effect of therapeutics towards functional proteins and confirms the chemopreventive effects of multiple flavonoids via co-regulation.
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Affiliation(s)
- Hui Guan
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Wenyuan Zhang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Hui Liu
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Yang Jiang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Feng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Dan Wang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Yang Liu
- College of Life Sciences, Shandong Agricultural University, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China
| | - Fatao He
- Jinan Fruit Research Institute of All China Federation of Supply & Marketing Cooperatives, 16001 East Road Jingshi, Jinan 250220, Shandong, People's Republic of China
| | - Maoyu Wu
- Jinan Fruit Research Institute of All China Federation of Supply & Marketing Cooperatives, 16001 East Road Jingshi, Jinan 250220, Shandong, People's Republic of China
| | | | - Dongxiao Sun-Waterhouse
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China; School of Chemical Sciences, The University of Auckland, Auckland, New Zealand.
| | - Dapeng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, 61 Dai Zong Street, Tai'an 271018, Shandong, People's Republic of China.
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5
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Devitt G, Johnson PB, Hanrahan N, Lane SIR, Vidale MC, Sheth B, Allen JD, Humbert MV, Spalluto CM, Hervé RC, Staples K, West JJ, Forster R, Divecha N, McCormick CJ, Crispin M, Hempler N, Malcolm GPA, Mahajan S. Mechanisms of SARS-CoV-2 Inactivation Using UVC Laser Radiation. ACS PHOTONICS 2024; 11:42-52. [PMID: 38249683 PMCID: PMC10797618 DOI: 10.1021/acsphotonics.3c00828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 01/23/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) has had a tremendous impact on humanity. Prevention of transmission by disinfection of surfaces and aerosols through a chemical-free method is highly desirable. Ultraviolet C (UVC) light is uniquely positioned to achieve inactivation of pathogens. We report the inactivation of SARS-CoV-2 virus by UVC radiation and explore its mechanisms. A dose of 50 mJ/cm2 using a UVC laser at 266 nm achieved an inactivation efficiency of 99.89%, while infectious virions were undetectable at 75 mJ/cm2 indicating >99.99% inactivation. Infection by SARS-CoV-2 involves viral entry mediated by the spike glycoprotein (S), and viral reproduction, reliant on translation of its genome. We demonstrate that UVC radiation damages ribonucleic acid (RNA) and provide in-depth characterization of UVC-induced damage of the S protein. We find that UVC severely impacts SARS-CoV- 2 spike protein's ability to bind human angiotensin-converting enzyme 2 (hACE2) and this correlates with loss of native protein conformation and aromatic amino acid integrity. This report has important implications for the design and development of rapid and effective disinfection systems against the SARS-CoV-2 virus and other pathogens.
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Affiliation(s)
- George Devitt
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Peter B. Johnson
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Niall Hanrahan
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Simon I. R. Lane
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Magdalena C. Vidale
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Bhavwanti Sheth
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Joel D. Allen
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Maria V. Humbert
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
- University
of Cambridge, MRC Toxicology Unit, Cambridge, CB2 1QR, United Kingdom
| | - Cosma M. Spalluto
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
- Southampton
NIHR Biomedical Research Centre, Southampton
General Hospital, Southampton SO16 6YD, United
Kingdom
| | - Rodolphe C. Hervé
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Karl Staples
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
- Wessex Investigational
Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
- Southampton
NIHR Biomedical Research Centre, Southampton
General Hospital, Southampton SO16 6YD, United
Kingdom
| | - Jonathan J. West
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Cancer
Sciences, Faculty of Medicine, University
of Southampton, Southampton SO16 6YD, United
Kingdom
| | - Robert Forster
- M Squared
Lasers, Limited, 1 K
Campus, West of Scotland Science Park, Glasgow, G20 0SP, United
Kingdom
| | - Nullin Divecha
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Christopher J. McCormick
- Clinical
and Experimental Sciences, Faculty of Medicine, University of Southampton,
Sir Henry Wellcome Laboratories, University
Hospital Southampton, Southampton SO16 6YD, United
Kingdom
| | - Max Crispin
- School
of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Nils Hempler
- M Squared
Lasers, Limited, 1 K
Campus, West of Scotland Science Park, Glasgow, G20 0SP, United
Kingdom
| | - Graeme P. A. Malcolm
- M Squared
Lasers, Limited, 1 K
Campus, West of Scotland Science Park, Glasgow, G20 0SP, United
Kingdom
| | - Sumeet Mahajan
- School
of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Institute
for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Department
of Biotechnology, Inland Norway University
of Applied Sciences, Holsetgata 22, N-2317 Hamar, Norway
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6
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Waters LJ, Whiteley J, Small W, Mellor S. Determining suitable surfactant concentration ranges to avoid protein unfolding in pharmaceutical formulations using UV analysis. Heliyon 2023; 9:e21712. [PMID: 37954313 PMCID: PMC10632529 DOI: 10.1016/j.heliyon.2023.e21712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023] Open
Abstract
Protein stability is fundamental to maintain pharmaceutical efficacy in the nascent field of biologics. One particular property that is essential for therapeutic effect is retention of the folded 3-dimensional conformation, i.e. once unfolding has occurred the biologic is often rendered inactive. In this work we propose a modified form of a recently published UV spectroscopic method that identifies protein unfolding. In this study we determine concentration limits to avoid protein unfolding of two model surfactants, namely polysorbate 20 and polysorbate 80, by correlating surfactant concentration with percentage 'unfolded' for three model proteins. For each scenario two distinct regions were observed, firstly surfactant concentrations at which no unfolding had occurred, followed by a second region whereby unfolding steadily increased with surfactant concentration. In general for the combinations analysed in this study, this second region began to appear around ten times below the critical micellar concentration of each surfactant, regardless of the protein or polysorbate chosen. It is therefore proposed that this adapted method could be used by researchers in the early stages of formulation development as a convenient and simple screening tool to confirm the 'onset of unfolding' concentration for protein-surfactant formulations, thus helping to optimise surfactant concentration selection in pharmaceutical formulations to maintain the benefits of surfactants yet avoid inadvertent unfolding.
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Affiliation(s)
- Laura J. Waters
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Joseph Whiteley
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - William Small
- Croda Europe Ltd, Cowick Hall, Snaith, Goole, DN14 9AA, UK
| | - Steve Mellor
- Croda Europe Ltd, Cowick Hall, Snaith, Goole, DN14 9AA, UK
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7
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Ortega-Pinazo J, Pacheco-Rodríguez MJ, Serrano-Castro PJ, Martínez B, Pinto-Medel MJ, Gómez-Zumaquero JM, Lago-Sampedro A, García-Díaz B, Estivill-Torrús G, Emilio Ferro Gallego P. Comparing RNA extraction methods to face the variations in RNA quality using two human biological matrices. Mol Biol Rep 2023; 50:9263-9271. [PMID: 37812354 DOI: 10.1007/s11033-023-08761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Nucleic acids, RNA among them, are widely used in biomedicine and Biotechnology. Because of their susceptibility to degradation by RNases, the handling and extraction process of RNA from cells and tissues require specialized personnel and standardized methods to guarantee high purity and integrity. Due to the diversity of techniques found in the market, a comparative study between different RNA extraction methods is useful to facilitate the best choice for the researcher or in research service platforms such as biobanks to see the traceability of the samples. METHODS AND RESULTS In this study, we have compared seven different RNA extraction methods: manual (TRIzol™), semiautomated (QIAGEN™, Bio-Rad, Monarch®, and Canvax™), and fully automated (QIAcube™ and Maxwell®) processes, from two biological matrices: human Jurkat T cells and peripheral blood mononuclear cells (PBMC). Results showed marked differences in the RNA quality and functionality according to the method employed for RNA extraction and the matrix used. DISCUSSION QIAcube™ and semi-automated extraction methods were perceived as the best options because of their lower variability, good functionality, and lower cost (P < 0.001). These data contribute to facilitating researchers or research service platforms (Biobanks) in decision-making practices and emphasize the relevance of the selection of the RNA extraction method in each experimental procedure or traceability study to guarantee both quality standards and its reproducibility.
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Affiliation(s)
- J Ortega-Pinazo
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - M J Pacheco-Rodríguez
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - P J Serrano-Castro
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - B Martínez
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Intercentros de Oncología Médica, Hospitales Universitarios Regional de Málaga y Virgen de la Victoria, Málaga, Spain
| | - M J Pinto-Medel
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - J M Gómez-Zumaquero
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - A Lago-Sampedro
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - B García-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Guillermo Estivill-Torrús
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain.
| | - Pedro Emilio Ferro Gallego
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Biobank ECAI, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Unidad Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain.
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8
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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9
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Kiewlicz J, Kwaśniewska D. Study of the properties of binary systems: selected derivatives of B-vitamins-cationic surfactant. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Whey protein isolate nanofibrils formed with phosphoric acid: Formation, structural characteristics, and emulsion stability. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Nanostructures self-assembled from food-grade molecules with pH-cycle as functional food ingredients. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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12
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Dolores-Hernández M, Morales-Hipólito EA, Villaseñor A, López-Arellano R. Determination of zilpaterol in a residue depletion study using LC-MS/MS in cattle plasma, muscle, liver and kidney. Food Chem 2022; 382:132287. [PMID: 35139465 DOI: 10.1016/j.foodchem.2022.132287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/30/2021] [Accepted: 01/26/2022] [Indexed: 11/04/2022]
Abstract
Zilpaterol is a β-agonist compound which promotes fat loss and muscle gain in cattle, providing economic benefits. However, zilpaterol residues in the animal might introduce a significant risk to humans after consumption. In the present manuscript, a highly specific, sensitive method using Selected Reaction Monitoring (SRM) in positive electrospray ionization (ESI +) mode by liquid chromatography coupled to triple quadrupole mass spectrometry (LC-MS/MS) for plasma, muscle, liver and kidney is presented. For method development, composition of the aqueous mobile phase, precipitation agent, and solid phase extraction (SPE) conditions were optimized. The method was fully validated showing a good linearity and recovery average greater than or equal to 97 % for all matrices. The method was applied to residue depletion studies in cattle after withdrawal of zilpaterol supplementation at 3, 4, 5 and 6 days showing that tissues can be consumed by humans after 4th day of zilpaterol withdrawal.
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Affiliation(s)
- Mariana Dolores-Hernández
- Laboratory of Pharmaceutical Development Tests, Multidisciplinary Research Unit (UIM), Faculty of Higher Education Cuautitlán, National Autonomous University of Mexico, Carr. Cuautitlán-Teoloyucan Km 2.5, San Sebastián Xhala, 54714 Cuautitlán Izcalli, Mexico
| | - Elvia A Morales-Hipólito
- Laboratory of Pharmaceutical Development Tests, Multidisciplinary Research Unit (UIM), Faculty of Higher Education Cuautitlán, National Autonomous University of Mexico, Carr. Cuautitlán-Teoloyucan Km 2.5, San Sebastián Xhala, 54714 Cuautitlán Izcalli, Mexico
| | - Alma Villaseñor
- IMMA, Instituto de Medicina Molecular Aplicada, Facultad de Medicina, San Pablo CEU Universities, Madrid, España
| | - Raquel López-Arellano
- Laboratory of Pharmaceutical Development Tests, Multidisciplinary Research Unit (UIM), Faculty of Higher Education Cuautitlán, National Autonomous University of Mexico, Carr. Cuautitlán-Teoloyucan Km 2.5, San Sebastián Xhala, 54714 Cuautitlán Izcalli, Mexico.
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13
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Alrosan M, Tan TC, Easa AM, Gammoh S, Alu'datt MH. Mechanism of the structural interaction between whey and lentil proteins in the unique creation of a protein structure. J Food Sci 2021; 86:5282-5294. [PMID: 34796499 DOI: 10.1111/1750-3841.15974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Poor solubility is a substantial factor that restricts the production of high value-added lentil proteins (LPs). In this study, whey protein isolates (WPIs), which have high solubility and are used in various food industries, were mixed with LPs at pH 12 to create LP-WPI protein complexes with improved water solubility properties using pH-recycling approach (maintained at pH 12.0 for 60 min and then readjusting to pH 7.0). LP-WPI protein complexes produced in this study have gained high surface charge, increased in the solubilization of protein complexes to ≈92%, as well as improved resistance against protein aggregation. The ratio of LPs to WPIs has a significant effect on the generation of unique tertiary and secondary protein structures based on the protein-protein interaction (PPI) technique via pH-recycling. The protein interaction between LPs and WPIs resulted in alteration on the surface morphology of the produced protein complexes. This study showed that electrostatic interaction, hydrophobic force, and hydrogen bond appear as major molecular forces in this PPI. The efficacy of the pH-recycling method used in this research indicates that this approach could be a robust approach to enhance the functional properties of food proteins. PRACTICAL APPLICATION: The pH-recycling technique is a proven technique for protein complexation in creating novel protein complexes with improved functional properties. Even though lentils are a rich source of plant-based protein, its utilization by food industries is restricted due to the poor water solubility of lentil proteins (LPs). However, by using complexing lentil proteins with whey protein isolates (WPIs), that is, LP-WPI protein complex, was developed. The water solubility of LP-WPI protein complex was significantly higher than LPs, up to approximately 92%. In addition, this could improve the utilization of lentil seeds in food application as an alternative for animal-based proteins.
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Affiliation(s)
- Mohammad Alrosan
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia.,Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Thuan-Chew Tan
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
| | - Azhar Mat Easa
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
| | - Sana Gammoh
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Muhammad H Alu'datt
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
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14
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Alrosan M, Tan T, Easa AM, Gammoh S, Kubow S, Alu'datt MH. Mechanisms of molecular and structural interactions between lentil and quinoa proteins in aqueous solutions induced by pH recycling. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mohammad Alrosan
- Food Technology Division School of Industrial Technology Universiti Sains Malaysia Penang 11800 USM Malaysia
- Department of Nutrition and Food Technology Faculty of Agriculture Jordan University of Science and Technology P.O. Box 3030 Irbid 22110 Jordan
| | - Thuan‐Chew Tan
- Food Technology Division School of Industrial Technology Universiti Sains Malaysia Penang 11800 USM Malaysia
| | - Azhar Mat Easa
- Food Technology Division School of Industrial Technology Universiti Sains Malaysia Penang 11800 USM Malaysia
| | - Sana Gammoh
- Department of Nutrition and Food Technology Faculty of Agriculture Jordan University of Science and Technology P.O. Box 3030 Irbid 22110 Jordan
| | - Stan Kubow
- School of Human Nutrition Macdonald Campus McGill University 21,111 Lakeshore Road Ste‐Anne‐De‐Bellevue QC H9X 3V9 Canada
| | - Muhammad H. Alu'datt
- Department of Nutrition and Food Technology Faculty of Agriculture Jordan University of Science and Technology P.O. Box 3030 Irbid 22110 Jordan
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15
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Bjedov D, Mikuška A, Lackmann C, Begović L, Mikuška T, Velki M. Application of Non-Destructive Methods: Biomarker Assays in Blood of White Stork ( Ciconia ciconia) Nestlings. Animals (Basel) 2021; 11:2341. [PMID: 34438798 PMCID: PMC8388685 DOI: 10.3390/ani11082341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/06/2021] [Indexed: 01/31/2023] Open
Abstract
White stork (Ciconia ciconia) nestlings can provide quantitative information on the quality of the surrounding environment by indicating the presence of pollutants, as they depend on locally foraged food. This study represents the first comparison of biomarkers in two fractions of white stork nestling blood: plasma and S9 (the post-mitochondrial fraction). The aim of this study was to evaluate acetylcholinesterase (AChE), carboxylesterase (CES), glutathione S-transferase (GST), and glutathione reductase (GR), as well as to establish a novel fluorescence-based method for glutathione (GSH) and reactive oxygen species (ROS) detection in plasma and S9. Considering the enzymatic biomarkers, lower variability in plasma was detected only for AChE, as CES, GST, and GR had lower variability in S9. Enzyme activity was higher in plasma for AChE, CES, and GST, while GR had higher activity in S9. Regarding the fluorescence-based method, lower variability was detected in plasma for GSH and ROS, although higher GSH detection was reported in S9, and higher ROS was detected in plasma. The present study indicated valuable differences by successfully establishing protocols for biomarker measurement in plasma and S9 based on variability, enzyme activity, and fluorescence. For a better understanding of the environmental effects on nestlings' physiological condition, biomarkers can be measured in plasma and S9.
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Affiliation(s)
- Dora Bjedov
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
| | - Alma Mikuška
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
| | - Carina Lackmann
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lidija Begović
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
| | - Tibor Mikuška
- Croatian Society for Birds and Nature Protection, 31000 Osijek, Croatia;
| | - Mirna Velki
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
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16
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Atsavapranee B, Stark CD, Sunden F, Thompson S, Fordyce PM. Fundamentals to function: Quantitative and scalable approaches for measuring protein stability. Cell Syst 2021; 12:547-560. [PMID: 34139165 DOI: 10.1016/j.cels.2021.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/16/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.
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Affiliation(s)
| | - Catherine D Stark
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Samuel Thompson
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
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17
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Kitazaki A, Hasegawa T, Asami H, Kohno JY. Chemical denaturation of gas-phase albumin ions studied by photoelectron detachment yield spectroscopy and infrared laser ablation of droplet beams. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Alrosan M, Tan TC, Easa AM, Gammoh S, Alu'datt MH. Molecular forces governing protein-protein interaction: Structure-function relationship of complexes protein in the food industry. Crit Rev Food Sci Nutr 2021; 62:4036-4052. [PMID: 33455424 DOI: 10.1080/10408398.2021.1871589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The application of protein-protein interaction (PPI) has been widely used in various industries, such as food, nutraceutical, and pharmaceutical. A deeper understanding of PPI is needed, and the molecular forces governing proteins and their interaction must be explained. The design of new structures with improved functional properties, e.g., solubility, emulsion, and gelation, has been fueled by the development of structural and colloidal building blocks. In this review, the molecular forces of protein structures are discussed, followed by the relationship between molecular force and structure, ways of a bind of proteins together in solution or at the interface, and functional properties. A more detailed look is thus taken at the relationship between the various influencing factors on molecular forces involved in PPI. These factors include protein properties, such as types, concentration, and mixing ratio, and solvent conditions, such as ionic strength and pH. This review also summarizes methods tha1t are capable of identifying molecular forces in protein and PPI, as well as characterizing protein structure.
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Affiliation(s)
- Mohammad Alrosan
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia.,Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Thuan-Chew Tan
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
| | - Azhar Mat Easa
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang, Malaysia
| | - Sana Gammoh
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Muhammad H Alu'datt
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
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19
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Realtime and in-situ monitoring of membrane fouling with fiber-optic reflectance UV-vis spectrophotometry (FORUS). CHEMICAL ENGINEERING JOURNAL ADVANCES 2020. [DOI: 10.1016/j.ceja.2020.100058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Galindo-Luján R, Pont L, Sanz-Nebot V, Benavente F. Classification of quinoa varieties based on protein fingerprinting by capillary electrophoresis with ultraviolet absorption diode array detection and advanced chemometrics. Food Chem 2020; 341:128207. [PMID: 33035861 DOI: 10.1016/j.foodchem.2020.128207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/10/2020] [Accepted: 09/23/2020] [Indexed: 12/24/2022]
Abstract
Quinoa (Chenopodium quinoa Willd.) is an andean grain with exceptional nutritional properties that has been progressively introduced in western countries as a protein-rich super food with a broad amino acid spectrum. Quinoa is consumed as whole grain, but it is also milled to produce high-value flour, which is susceptible to adulteration. Therefore, there is a growing interest in developing novel analytical methods to get further information about quinoa at the chemical level. In this study, we developed a rapid and simple capillary electrophoresis-ultraviolet absorption diode array detection (CE-UV-DAD) method to obtain characteristic multiwavelength electrophoretic profiles of soluble protein extracts from different quinoa grain varieties. Then, advanced chemometric methods (i.e. multivariate curve resolution alternating least squares, MCR-ALS, followed by principal component analysis, PCA, and partial least squares discriminant analysis, PLS-DA) were applied to deconvolute the components present in the electropherograms and classify the quinoa varieties according to their differential protein composition.
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Affiliation(s)
- Rocío Galindo-Luján
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Laura Pont
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain.
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21
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Belanger E, Wolf SM, Zatt SA, Christoff J, Rojeab Y. Chemical Stability of Reconstituted Sincalide in Sterile Water Under 2 Different Storage Conditions. J Nucl Med Technol 2020; 48:174-176. [DOI: 10.2967/jnmt.119.230441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022] Open
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22
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23
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Ogunmoyole T, Fodeke AA, Adewale IO. Denaturation studies of Clarias gariepinus glutathione transferase in dilute and crowded solutions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:789-801. [DOI: 10.1007/s00249-019-01405-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/01/2019] [Accepted: 10/13/2019] [Indexed: 01/12/2023]
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24
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Yang Y, Wang R, Feng W, Zhou X, Chen Z, Wang T. Carboxymethylcellulose/pectin inhibiting structural folding of rice proteins via trinary structural interplays. Int J Biol Macromol 2019; 133:93-100. [DOI: 10.1016/j.ijbiomac.2019.04.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/31/2022]
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25
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Wang R, Xu P, Chen Z, Zhou X, Wang T. Complexation of rice proteins and whey protein isolates by structural interactions to prepare soluble protein composites. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.11.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Ganji VK, Biswal JK, Lalzampuia H, Basagoudanavar SH, Saravanan P, Tamil Selvan RP, Umapathi V, Reddy GR, Sanyal A, Dechamma HJ. Mutation in the VP2 gene of P1-2A capsid protein increases the thermostability of virus-like particles of foot-and-mouth disease virus serotype O. Appl Microbiol Biotechnol 2018; 102:8883-8893. [PMID: 30136205 DOI: 10.1007/s00253-018-9278-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/21/2018] [Accepted: 07/25/2018] [Indexed: 11/30/2022]
Abstract
Foot-and-mouth disease (FMD) is an economically important, global disease of cloven-hoofed animals. The conventional vaccine could bring down the incidence of disease in many parts of the world but has many limitations and in India, the disease is enzootic. More promisingly, the alternate vaccine candidates, virus-like particles (VLPs) are as immunogenic as a native virus but are more labile to heat than the live virus capsids. To produce stable VLPs, a single amino acid residue was mutated at 93 and 98 positions at VP2 inter-pentamer region of the P1-2A gene of FMD virus serotype O (IND/R2/75). The mutated capsid protein was expressed in insect cells and characterized for temperature and varying pH stability. Out of S93Y, S93F, S93C, S93H, and Y98F mutant, VLPs, S93Y, S93F, and Y98F showed improved stability at 37 °C for 75 days compared to wild capsid, which was evaluated by sandwich ELISA. Further, the stability analysis of purified VLPs either by differential scanning fluorescence (DSF) stability assay at different temperatures and pH conditions or by dissociation kinetics showed that the Y98F mutant VLPs were more stable than S93Y, S93F, S93C, and S93H mutant and wild-type VLPs. Immunization of guinea pigs with Y98F VLPs induced neutralizing antibodies and 60% of the animals were protected from the FMDV "O" 100 GPID50 challenge virus.
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Affiliation(s)
| | - Jitendra K Biswal
- ICAR-Project Directorate on Foot-and-Mouth Disease, Mukteswar, Nainital, 263138, India
| | - H Lalzampuia
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India
| | | | - P Saravanan
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India
| | - R P Tamil Selvan
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India
| | - V Umapathi
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India
| | - G R Reddy
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India
| | - Aniket Sanyal
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India
| | - H J Dechamma
- Indian Veterinary Research Institute, Hebbal, Bengaluru, 560024, India.
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27
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Toward water-solvation of rice proteins via backbone hybridization by casein. Food Chem 2018; 258:278-283. [DOI: 10.1016/j.foodchem.2018.03.084] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 11/24/2022]
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28
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Wang T, Xu P, Chen Z, Zhou X, Wang R. Alteration of the structure of rice proteins by their interaction with soy protein isolates to design novel protein composites. Food Funct 2018; 9:4282-4291. [DOI: 10.1039/c8fo00661j] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RPs and SPIs were fabricated into nanoscale composites through synergistic structural interactions.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Pengcheng Xu
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Zhengxing Chen
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Xing Zhou
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Ren Wang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
- National Engineering Laboratory for Cereal Fermentation Technology
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29
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Ishikawa Y, Holden P, Bächinger HP. Heat shock protein 47 and 65-kDa FK506-binding protein weakly but synergistically interact during collagen folding in the endoplasmic reticulum. J Biol Chem 2017; 292:17216-17224. [PMID: 28860186 DOI: 10.1074/jbc.m117.802298] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/18/2017] [Indexed: 12/21/2022] Open
Abstract
Collagen is the most abundant protein in the extracellular matrix in humans and is critical to the integrity and function of many musculoskeletal tissues. A molecular ensemble comprising more than 20 molecules is involved in collagen biosynthesis in the rough endoplasmic reticulum. Two proteins, heat shock protein 47 (Hsp47/SERPINH1) and 65-kDa FK506-binding protein (FKBP65/FKBP10), have been shown to play important roles in this ensemble. In humans, autosomal recessive mutations in both genes cause similar osteogenesis imperfecta phenotypes. Whereas it has been proposed that Hsp47 and FKBP65 interact in the rough endoplasmic reticulum, there is neither clear evidence for this interaction nor any data regarding their binding affinities for each other. In this study using purified endogenous proteins, we examined the interaction between Hsp47, FKBP65, and collagen and also determined their binding affinities and functions in vitro Hsp47 and FKBP65 show a direct but weak interaction, and FKBP65 prefers to interact with Hsp47 rather than type I collagen. Our results suggest that a weak interaction between Hsp47 and FKBP65 confers mutual molecular stability and also allows for a synergistic effect during collagen folding. We also propose that Hsp47 likely acts as a hub molecule during collagen folding and secretion by directing other molecules to reach their target sites on collagens. Our findings may explain why osteogenesis imperfecta-causing mutations in both genes result in similar phenotypes.
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Affiliation(s)
- Yoshihiro Ishikawa
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University and Shriners Hospital for Children, Research Department, Portland, Oregon 97239
| | - Paul Holden
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University and Shriners Hospital for Children, Research Department, Portland, Oregon 97239
| | - Hans Peter Bächinger
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University and Shriners Hospital for Children, Research Department, Portland, Oregon 97239
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30
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Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R. DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis. Biopreserv Biobank 2016; 14:264-70. [PMID: 27158753 PMCID: PMC4991598 DOI: 10.1089/bio.2015.0064] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-quality human DNA samples and associated information of individuals are necessary for biomedical research. Biobanks act as a support infrastructure for the scientific community by providing a large number of high-quality biological samples for specific downstream applications. For this purpose, biobank methods for sample preparation must ensure the usefulness and long-term functionality of the products obtained. Quality indicators are the tool to measure these parameters, the purity and integrity determination being those specifically used for DNA. This study analyzes the quality indicators in DNA samples derived from 118 frozen human tissues in optimal cutting temperature (OCT) reactive, 68 formalin-fixed paraffin-embedded (FFPE) tissues, 119 frozen blood samples, and 26 saliva samples. The results obtained for DNA quality are discussed in association with the usefulness for downstream applications and availability of the DNA source in the target study. In brief, if any material is valid, blood is the most approachable option of prospective collection of samples providing high-quality DNA. However, if diseased tissue is a requisite or samples are available, the recommended source of DNA would be frozen tissue. These conclusions will determine the best source of DNA, according to the planned downstream application. Furthermore our results support the conclusion that a complete procedure of DNA quantification and qualification is necessary to guarantee the appropriate management of the samples, avoiding low confidence results, high costs, and a waste of samples.
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Affiliation(s)
- Gema Lucena-Aguilar
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - Ana María Sánchez-López
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | | | - José Antonio Carrillo-Ávila
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - José Antonio López-Guerrero
- 3 Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología , Valencia, Spain .,4 Biobank, Fundación Instituto Valenciano de Oncología , Valencia, Spain
| | - Rocío Aguilar-Quesada
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
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NMR Structure and Dynamics of the Resuscitation Promoting Factor RpfC Catalytic Domain. PLoS One 2015; 10:e0142807. [PMID: 26576056 PMCID: PMC4648573 DOI: 10.1371/journal.pone.0142807] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/27/2015] [Indexed: 12/03/2022] Open
Abstract
Mycobacterium tuberculosis latent infection is maintained for years with no clinical symptoms and no adverse effects for the host. The mechanism through which dormant M. tuberculosis resuscitates and enters the cell cycle leading to tuberculosis is attracting much interest. The RPF family of proteins has been found to be responsible for bacteria resuscitation and normal proliferation. This family of proteins in M. tuberculosis is composed by five homologues (named RpfA-E) and understanding their conformational, structural and functional peculiarities is crucial to the design of therapeutic strategies.Therefore, we report the structural and dynamics characterization of the catalytic domain of RpfC from M. tubercolosis by combining Nuclear Magnetic Resonance, Circular Dichroism and Molecular Dynamics data. We also show how the formation of a disulfide bridge, highly conserved among the homologues, is likely to modulate the shape of the RpfC hydrophobic catalytic cleft. This might result in a protein function regulation via a “conformational editing” through a disulfide bond formation.
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Thyparambil AA, Wei Y, Latour RA. Evaluation of the Effectiveness of Surfactants and Denaturants to Elute and Denature Adsorbed Protein on Different Surface Chemistries. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11814-11824. [PMID: 26449787 DOI: 10.1021/acs.langmuir.5b02741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The elution and/or denaturation of proteins from material surfaces by chemical excipients such as surfactants and denaturants is important for numerous applications including medical implant reprocessing, bioanalyses, and biodefense. The objective of this study was to develop and apply methods to quantitatively assess how surface chemistry and adsorption conditions influence the effectiveness of three commonly used surfactants (sodium dodecyl sulfate, n-octyl-β-d-glucoside, and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate) and two denaturants (guanidium hydrochloride and urea) to elute protein (hen egg white lysozyme and bovine pancreatic ribonuclease A) from three different surface chemistries (silica glass, poly(methyl methacrylate), and high-density polyethylene). The structure and bioactivity of residual protein on the surface following elution were characterized using circular dichroism spectropolarimetry and enzyme assays to assess the extent of protein denaturation. Our results indicate that the denaturants were generally more effective than the surfactants in removing the adsorbed proteins from each type of surface. Also, the denaturing capacity of these excipients on the residual proteins on the surfaces was distinctly different from their influence on the proteins in solution and was unique for each of the adsorption conditions. Taken altogether, these results reveal that the effectiveness of surfactants and denaturants to elute and denature adsorbed protein is significantly influenced by surface chemistry and the conditions from which the protein was adsorbed. These results provide a basis for the selection, design, and further development of chemical agents for protein elution and surface decontamination.
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Affiliation(s)
- Aby A Thyparambil
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University , Clemson, South Carolina 29634, United States
| | - Yang Wei
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University , Clemson, South Carolina 29634, United States
| | - Robert A Latour
- Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University , Clemson, South Carolina 29634, United States
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33
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Imidazolium based ionic liquid type surfactant improves activity and thermal stability of lipase of Rhizopus oryzae. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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Rašković B, Popović M, Ostojić S, Anđelković B, Tešević V, Polović N. Fourier transform infrared spectroscopy provides an evidence of papain denaturation and aggregation during cold storage. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:238-246. [PMID: 26051646 DOI: 10.1016/j.saa.2015.05.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
Papain is a cysteine protease with wide substrate specificity and many applications. Despite its widespread applications, cold stability of papain has never been studied. Here, we used differential spectroscopy to monitor thermal denaturation process. Papain was the most stabile from 45 °C to 60 °C with ΔG°321 of 13.9±0.3 kJ/mol and Tm value of 84±1 °C. After cold storage, papain lost parts of its native secondary structures elements which gave an increase of 40% of intermolecular β-sheet content (band maximum detected at frequency of 1621 cm(-1) in Fourier transform infrared (FT-IR) spectrum) indicating the presence of secondary structures necessary for aggregation. The presence of protein aggregates after cold storage was also proven by analytical size exclusion chromatography. After six freeze-thaw cycles around 75% of starting enzyme activity of papain was lost due to cold denaturation and aggregation of unfolded protein. Autoproteolysis of papain did not cause significant loss of the protein activity. Upon the cold storage, papain underwent structural rearrangements and aggregation that correspond to other cold denatured proteins, rather than autoproteolysis which could have the commercial importance for the growing polypeptide based industry.
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Affiliation(s)
- Brankica Rašković
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Milica Popović
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Sanja Ostojić
- Institute of General and Physical Chemistry, Studentski trg 12, 11000 Belgrade, Serbia
| | - Boban Anđelković
- Department of Organic Chemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Vele Tešević
- Department of Organic Chemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia
| | - Natalija Polović
- Department of Biochemistry, University of Belgrade - Faculty of Chemistry, Studentski trg 12 - 16, 11000 Belgrade, Serbia.
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35
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Experimental characterization of adsorbed protein orientation, conformation, and bioactivity. Biointerphases 2015; 10:019002. [PMID: 25708632 DOI: 10.1116/1.4906485] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Protein adsorption on material surfaces is a common phenomenon that is of critical importance in many biotechnological applications. The structure and function of adsorbed proteins are tightly interrelated and play a key role in the communication and interaction of the adsorbed proteins with the surrounding environment. Because the bioactive state of a protein on a surface is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary dataset to characterize and understand the bioactive state of adsorbed protein. Over the past several years, the authors have focused on the development of such a set of complementary methods to address this need. These methods include adsorbed-state circular dichroism spectropolarimetry to determine adsorption-induced changes in protein secondary structure, amino-acid labeling/mass spectrometry to assess adsorbed protein orientation and tertiary structure by monitoring adsorption-induced changes in residue solvent accessibility, and bioactivity assays to assess adsorption-induced changes in protein bioactivity. In this paper, the authors describe the methods that they have developed and/or adapted for each of these assays. The authors then provide an example of their application to characterize how adsorption-induced changes in protein structure influence the enzymatic activity of hen egg-white lysozyme on fused silica glass, high density polyethylene, and poly(methyl-methacrylate) as a set of model systems.
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Kudr J, Nejdl L, Skalickova S, Zurek M, Milosavljevic V, Kensova R, Ruttkay-Nedecky B, Kopel P, Hynek D, Novotna M, Adam V, Kizek R. Use of nucleic acids anchor system to reveal apoferritin modification by cadmium telluride nanoparticles. J Mater Chem B 2015; 3:2109-2118. [DOI: 10.1039/c4tb01336k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aim of this study was to synthesize cadmium telluride nanoparticles (CdTe NPs) modified apoferritin, and examine if apoferritin is able to accommodate CdTe NPs.
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Affiliation(s)
- Jiri Kudr
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Sylvie Skalickova
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Michal Zurek
- Central European Institute of Technology
- Brno University of Technology
- CZ-616 00 Brno
- Czech Republic, European Union
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Renata Kensova
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Branislav Ruttkay-Nedecky
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Pavel Kopel
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - David Hynek
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Marie Novotna
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Vojtech Adam
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
| | - Rene Kizek
- Department of Chemistry and Biochemistry
- Faculty of Agronomy
- Mendel University in Brno
- CZ-613 00 Brno
- Czech Republic, European Union
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37
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Tracking Inflows in Lake Wivenhoe during a Major Flood Using Optical Spectroscopy. WATER 2014. [DOI: 10.3390/w6082339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Shpigelman A, Kyomugasho C, Christiaens S, Van Loey AM, Hendrickx ME. Thermal and high pressure high temperature processes result in distinctly different pectin non-enzymatic conversions. Food Hydrocoll 2014. [DOI: 10.1016/j.foodhyd.2014.01.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Protein nanoparticle electrostatic interaction: size dependent counterions induced conformational change of hen egg white lysozyme. Colloids Surf B Biointerfaces 2014; 118:1-6. [PMID: 24704636 DOI: 10.1016/j.colsurfb.2014.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 11/22/2022]
Abstract
In our earlier paper (Ghosh et al., 2013), we have shown that (i) the positively charged hen egg white lysozyme (HEWL), dispersed in water, binds electrostatically with the negatively functionalized iron oxide nanoparticles (IONPs), and (ii) the Na(+) counterions, associated with functionalized IONPs, diffuse into bound proteins and irreversibly unfold them. Having this information, we have extended our investigation and report here the effect of the size and the charge of alkaline metal counterions on the conformational modification of HEWL. In order to obtain a negative functional 'shell' on IONPs and the counterions of different size and charge we have functionalized IONPs with different derivatives of citrate, namely, tri-lithium citrate (TLC, Li3C6H5O7), tri-sodium citrate (TSC, Na3C6H5O7), tri-potassium citrate (TKC, K3C6H5O7) and tri-magnesium citrate (TMC, Mg3C12H10O14). The size of counterions varies as Mg(2+)<Li(+)<Na(+)<K(+). After interaction with the functionalized IONPs, the unfolding of HEWL was the maximum in presence of Li(+), and was decreasing with increasing size of counterions. The UV-vis absorption measurements indicated that the unfolding of HEWL was due to modification in the hydrophobic environment around the tryptophan regions. The unfolding of HEWL was associated with the change of folding conformation from the α-helix to the β-sheet. In absence of counterions, ligand-IONPs have no effect on the native conformation of HEWL. An effective use of counterions in order to modify protein conformation (and, the functionality) via protein-nanoparticle electrostatic interaction is a new finding, and be useful for an alternative medical therapy.
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40
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Haas S, Plivelic TS, Dicko C. Combined SAXS/UV-vis/Raman as a diagnostic and structure resolving tool in materials and life sciences applications. J Phys Chem B 2014; 118:2264-73. [PMID: 24484407 DOI: 10.1021/jp412229j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to diagnose and fully correlate structural, chemical, and functional features of macromolecules and particles in solution, we propose the integration of spectroscopy and scattering on the same measuring volume and at the same time in a dedicated sample environment with multiple probes. Combined SAXS/UV-vis and SAXS/Raman information are employed to study the radiation damage effect in proteins in solution and the scattering from single wall carbon nanotubes (SWNTs) in SDS dispersion, respectively. In the first case, a clear correlation is observed between the time dependence of the radius of gyration (Rg) of the protein determined by SAXS and the turbidity of the protein solution extracted from simultaneous UV-vis measurements. In the second case, the ratio of bundled/isolated carbon nanotubes is obtained unambiguously through proper modeling of the scattering data and cross-validated with the Raman information. The uses of convex constraint analysis (CCA) and two-dimensional correlation analyses (2DCOS and 2DHCOS) are introduced to fully explore the combination of data sets from different techniques and to extract unique insights from the sample.
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Affiliation(s)
- Sylvio Haas
- MAX IV Laboratory, Lund University , P.O. Box 118, SE-22100 Lund, Sweden
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41
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Ojopagogo YA, Adewale IO, Afolayan A. Preliminary studies on the renaturation of denatured catfish (Clarias gariepinus) glutathione transferase. FISH PHYSIOLOGY AND BIOCHEMISTRY 2013; 39:1657-1663. [PMID: 23748965 DOI: 10.1007/s10695-013-9817-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/31/2013] [Indexed: 06/02/2023]
Abstract
Purified juvenile catfish (Clarias gariepinus) glutathione transferase (cgGST) was denatured in vitro and renatured in the absence and presence of different concentrations of endogenous or xenobiotic model substrates. Protein transitions during unfolding and refolding were monitored by activity measurement as well as changes in protein conformation using UV difference spectra at 230 nm. Gdn-HCl at 0.22 M caused 50 % inactivation of the enzyme and at 1.1 M, the enzyme was completely unfolded. Refolding of cgGST main isozyme was not completely reversible at higher concentrations of Gdn-HCl and is dependent on protein concentration. An enzyme concentration of 30 μg/ml yielded 40 % percentage residual activity in the presence of glutathione (GSH), regardless of the concentration that was present as opposed to 30 % obtained in its absence. The xenobiotic model substrate, lindane, appears to have no effect on the refolding of the enzyme. In summary, our results show that GSH assists in the refolding of cgGST in a concentration-independent manner and may be involved in the same function in vivo whereas the xenobiotic model substrate does not.
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42
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Schlebach JP, Peng D, Kroncke BM, Mittendorf KF, Narayan M, Carter BD, Sanders CR. Reversible folding of human peripheral myelin protein 22, a tetraspan membrane protein. Biochemistry 2013; 52:3229-41. [PMID: 23639031 DOI: 10.1021/bi301635f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Misfolding of the α-helical membrane protein peripheral myelin protein 22 (PMP22) has been implicated in the pathogenesis of the common neurodegenerative disease known as Charcot-Marie-Tooth disease (CMTD) and also several other related peripheral neuropathies. Emerging evidence suggests that the propensity of PMP22 to misfold in the cell may be due to an intrinsic lack of conformational stability. Therefore, quantitative studies of the conformational equilibrium of PMP22 are needed to gain insight into the molecular basis of CMTD. In this work, we have investigated the folding and unfolding of wild type (WT) human PMP22 in mixed micelles. Both kinetic and thermodynamic measurements demonstrate that the denaturation of PMP22 by n-lauroyl sarcosine (LS) in dodecylphosphocholine (DPC) micelles is reversible. Assessment of the conformational equilibrium indicates that a significant fraction of unfolded PMP22 persists even in the absence of the denaturing detergent. However, we find the stability of PMP22 is increased by glycerol, which facilitates quantitation of thermodynamic parameters. To our knowledge, this work represents the first report of reversible unfolding of a eukaryotic multispan membrane protein. The results indicate that WT PMP22 possesses minimal conformational stability in micelles, which parallels its poor folding efficiency in the endoplasmic reticulum. Folding equilibrium measurements for PMP22 in micelles may provide an approach to assess the effects of cellular metabolites or potential therapeutic agents on its stability. Furthermore, these results pave the way for future investigation of the effects of pathogenic mutations on the conformational equilibrium of PMP22.
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Affiliation(s)
- Jonathan P Schlebach
- Department of Biochemistry and ‡Center for Structural Biology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States
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43
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Cheung MC, Evans JG, McKenna B, Ehrlich DJ. Deep ultraviolet mapping of intracellular protein and nucleic acid in femtograms per pixel. Cytometry A 2011; 79:920-32. [PMID: 21796773 PMCID: PMC3199293 DOI: 10.1002/cyto.a.21111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/28/2011] [Accepted: 06/30/2011] [Indexed: 11/09/2022]
Abstract
By using imaging spectrophotometry with paired images in the 200- to 280-nm wavelength range, we have directly mapped intracellular nucleic acid and protein distributions across a population of Chinese hamster ovary (CHO-K1) cells. A broadband 100× objective with a numerical aperture of 1.2 NA (glycerin immersion) and a novel laser-induced-plasma point source generated high-contrast images with short (∼100 ms) exposures and a lateral resolution nearing 200 nm that easily resolves internal organelles. In a population of 420 CHO-K1 cells and 477 nuclei, we found a G1 whole-cell nucleic acid peak at 26.6 pg, a nuclear-isolated total nucleic acid peak at 11.4 pg, and, as inferred by RNase treatment, a G1 total DNA mass of 7.4 pg. At the G1 peak, we found a whole-cell protein mass of 95.6 pg, and a nuclear-isolated protein mass of 39.3 pg. An algorithm for protein quantification that senses peptide-bond (220-nm) absorbance was found to have a higher signal-to-noise ratio and to provide more reliable nucleic acid and protein determinations when compared to more classical 280/260-nm algorithms when used for intracellular mass mapping. Using simultaneous imaging with common nuclear stains (Hoechst 33342, Syto-14, and Sytox Orange), we have compared staining patterns to deep-UV images of condensed chromatin and have confirmed bias of these common nuclear stains related to nuclear packaging. The approach allows absolute mass measurements with no special sample preparation or staining. It can be used in conjunction with normal fluorescence microscopy and with relatively modest modification of the microscope.
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Affiliation(s)
- Man C Cheung
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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44
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Dasnoy S, Le Bras V, Préat V, Lemoine D. High-throughput assessment of antigen conformational stability by ultraviolet absorption spectroscopy and its application to excipient screening. Biotechnol Bioeng 2011; 109:502-16. [DOI: 10.1002/bit.23336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/31/2011] [Accepted: 09/06/2011] [Indexed: 11/11/2022]
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45
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Mach H, Middaugh CR. Ultraviolet Spectroscopy as a Tool in Therapeutic Protein Development. J Pharm Sci 2011; 100:1214-27. [DOI: 10.1002/jps.22385] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 09/29/2010] [Accepted: 10/04/2010] [Indexed: 11/11/2022]
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46
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Pierre B, Xiong T, Hayles L, Guntaka VR, Kim JR. Stability of a guest protein depends on stability of a host protein in insertional fusion. Biotechnol Bioeng 2011; 108:1011-20. [DOI: 10.1002/bit.23039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/03/2010] [Accepted: 12/06/2010] [Indexed: 11/11/2022]
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