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Li A, You T, Pang X, Wang Y, Tian L, Li X, Liu Z. Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Nat Commun 2024; 15:5211. [PMID: 38890314 PMCID: PMC11189392 DOI: 10.1038/s41467-024-49532-2] [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: 08/25/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the QB site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b559, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species.
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Affiliation(s)
- Anjie Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Tingting You
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Xiaojie Pang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yidi Wang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Lijin Tian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, 310024, China.
| | - Zhenfeng Liu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
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Tan HC, Cheung GSP, Chang JWW, Zhang C, Lee AHC. Enterococcus faecalis Shields Porphyromonas gingivalis in Dual-Species Biofilm in Oxic Condition. Microorganisms 2022; 10:microorganisms10091729. [PMID: 36144331 PMCID: PMC9505435 DOI: 10.3390/microorganisms10091729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Aim: To develop a reproducible biofilm model consisting of Enterococcus faecalis (E. faecalis) and Porphyromonas gingivalis (P. gingivalis) and to evaluate the interaction between the two bacterial species. Methodology: E. faecalis and P. gingivalis were grown in mono-culture, sequential, and co-culture models for 96 h in a 96-well polystyrene microtiter plate under both aerobic and anaerobic conditions separately. The viability of the two bacterial species in the biofilms was quantified by polymerase chain reaction (qPCR). Biofilm thickness and protein contents were measured using confocal laser scanning microscopy (CLSM). Two-way analysis of variance (ANOVA) was performed to analyze cell viability and biofilm thickness among different culture models cultivated under either aerobic or anaerobic conditions. The level of significance was set at p < 0.05. Results: Different culture models tested did not show any significant difference between the viable cell counts of both E. faecalis and P. gingivalis cultivated under aerobic and anaerobic conditions (p > 0.05). Biofilm was significantly thicker (p < 0.05) in the co-culture models compared to the mono-culture and sequential models. Protein contents in the biofilms were more pronounced when both bacterial species were co-cultured under aerobic conditions. Conclusions: E. faecalis appeared to shield P. gingivalis and support its continued growth in oxic (aerobic) conditions. The co-culture model of E. faecalis and P. gingivalis produced a significantly thicker biofilm irrespective of the presence or absence of oxygen, while increased protein contents were only observed in the presence of oxygen.
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Anti-PDHA1 antibody is detected in a subset of patients with schizophrenia. Sci Rep 2020; 10:7906. [PMID: 32404964 PMCID: PMC7220915 DOI: 10.1038/s41598-020-63776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/06/2020] [Indexed: 11/30/2022] Open
Abstract
Autoantibodies have been implicated in schizophrenia aetiology. Here, novel autoantibodies were isolated from patients with schizophrenia. Autoantibody candidates were searched using two-dimensional gel electrophoresis and western blotting with rat brain proteins as antigens and two sera pools (25 schizophrenia patients versus 25 controls) as antibodies. Immunoreactive antigens were identified by mass spectrometry. Antibody prevalence were evaluated by western blotting using human recombinant proteins. Furthermore, brain magnetic resonance imaging data (regional brain volumes and diffusion tensor imaging measures) were compared. Two proteins of the mitochondrial respiration pathway were identified as candidate antigens. Three patients with schizophrenia, but no controls, expressed antibodies targeting one of the candidate antigens, i.e., pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (PDHA1, EC 1.2.4.1), which is related to mitochondrial energy production. Anti-PDHA1 antibody-positive patients (n = 3) had increased volumes in the left occipital fusiform gyrus compared to both controls (n = 23, p = 0.017) and antibody-negative patients (n = 16, p = 0.009), as well as in the left cuneus compared to antibody-negative patients (n = 16, p = 0.018). This is the first report of an anti-PDHA1 antibody in patients with schizophrenia. Compatible with recent findings of mitochondrial dysfunction in schizophrenia, this antibody may be involved in the pathogenesis of a specific subgroup of schizophrenia.
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Hashimoto A, Takeuchi S, Kajita R, Yamagata A, Kakui R, Tanaka T, Nakata K. Proteogenomic analysis of granulocyte macrophage colony- stimulating factor autoantibodies in the blood of a patient with autoimmune pulmonary alveolar proteinosis. Sci Rep 2020; 10:4923. [PMID: 32188922 PMCID: PMC7080758 DOI: 10.1038/s41598-020-61934-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Abstract
Recently, attempts to reveal the structures of autoantibodies comprehensively using improved proteogenomics technology, have become popular. This technology identifies peptides in highly purified antibodies by using an Orbitrap device to compare spectra from liquid chromatography-tandem mass spectrometry against a cDNA database obtained through next-generation sequencing. In this study, we first analyzed granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies in a patient with autoimmune pulmonary alveolar proteinosis, using the trapped ion mobility spectrometry coupled with quadrupole time-of-flight (TIMS-TOF) instrument. The TIMS-TOF instrument identified peptides that partially matched sequences in up to 156 out of 162 cDNA clones. Complementarity-determining region 3 (CDR3) was fully and partially detected in nine and 132 clones, respectively. Moreover, we confirmed one unique framework region 4 (FR4) and at least three unique across CDR3 to FR4 peptides via de novo peptide sequencing. This new technology may thus permit the comprehensive identification of autoantibody structure.
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Affiliation(s)
| | - Shiho Takeuchi
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | | | | | - Takahiro Tanaka
- Niigata University Medical & Dental Hospital, Niigata, Japan
| | - Koh Nakata
- Niigata University Medical & Dental Hospital, Niigata, Japan.
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Analysis of silver-associated proteins in pathogen via combination of native SDS-PAGE, fluorescent staining, and inductively coupled plasma mass spectrometry. J Chromatogr A 2019; 1607:460393. [PMID: 31376982 DOI: 10.1016/j.chroma.2019.460393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/16/2019] [Accepted: 07/21/2019] [Indexed: 11/19/2022]
Abstract
Characterization of silver-associated proteins is important to elucidate underlined mechanisms of silver-containing materials against microbes. Gel electrophoresis based methods are the most popular and basic strategy for the analysis of biomolecules, i.e., proteins and nucleic acids. It solely provides molecular weights of analytes. Extending the method from molecular weight to elemental composition is highly desired when investigating metal-containing molecules. Herein, a gel electrophoresis based method combining native sodium dodecyl sulfate-polyacrylamide gel electrophoresis (native SDS-PAGE), fluorescent staining, and inductively coupled plasma mass spectrometry (ICP-MS) strategy was developed for separation and detection of silver-associated proteins. Two home-made silver-labeled proteins, carbonic anhydrase and ovalbumin, were used for validation of the strategy performance. Silver-associated proteins in Pseudomonas aeruginosa and Staphylococcus aureus treated with silver nanoparticles were further characterized by this method. Some well-known and new proteins were identified to associate to silver in both P. aeruginosa and S. aureus, demonstrating the feasibility of the developed strategy. In conclusion, the current study provides a convenient method for readily identification of silver-associated proteins in biological samples.
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Development of high-performance two-dimensional gel electrophoresis for human hair shaft proteome. PLoS One 2019; 14:e0213947. [PMID: 30889197 PMCID: PMC6424392 DOI: 10.1371/journal.pone.0213947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/04/2019] [Indexed: 11/19/2022] Open
Abstract
The primary components of human hair shaft—keratin and keratin-associated proteins (KAPs), together with their cross-linked networks—are the underlying reason for its rigid structure. It is therefore requisite to overcome the obstacle of hair insolubility and establish a reliable protocol for the proteome analysis of this accessible specimen. The present study employed an alkaline-based method for the efficient isolation of hair proteins and subsequently examined them using gel-based proteomics. The introduction of two proteomic protocols, namely the conventional and modified protocol, have resulted in the detection of more than 400 protein spots on the two-dimensional gel electrophoresis (2DE). When compared, the modified protocol is deemed to improve overall reproducibility, whilst offering a quick overview of the total protein distribution of hair. The development of this high-performance protocol is hoped to provide a new approach for hair analysis, which could possibly lead to the discovery of biomarkers for hair in health and diseases in the future.
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Assadsangabi A, Evans CA, Corfe BM, Lobo A. Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives. Gastroenterol Res Pract 2019; 2019:1426954. [PMID: 30774653 PMCID: PMC6350533 DOI: 10.1155/2019/1426954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.
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Affiliation(s)
- Arash Assadsangabi
- Gastroenterology Unit, Salford Royal Hospital, Salford, UK
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology and Insigneo Institute, University of Sheffield, Sheffield, UK
| | - Caroline A. Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Bernard M. Corfe
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology and Insigneo Institute, University of Sheffield, Sheffield, UK
| | - Alan Lobo
- Gastroenterology Unit, Salford Royal Hospital, Salford, UK
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Gel-based proteomics in disease research: Is it still valuable? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:9-16. [PMID: 30392562 DOI: 10.1016/j.bbapap.2018.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/30/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022]
Abstract
Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.
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Ranjitha Dhanasekaran A, Gardiner KJ. RPPAware: A software suite to preprocess, analyze and visualize reverse phase protein array data. J Bioinform Comput Biol 2018; 16:1850001. [PMID: 29478376 DOI: 10.1142/s0219720018500014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reverse Phase Protein Arrays (RPPA) is a high-throughput technology used to profile levels of protein expression. Handling the large datasets generated by RPPA can be facilitated by appropriate software tools. Here, we describe RPPAware, a free and intuitive software suite that was developed specifically for analysis and visualization of RPPA data. RPPAware is a portable tool that requires no installation and was built using Java. Many modules of the tool invoke R to utilize the statistical features. To demonstrate the utility of RPPAware, data generated from screening brain regions of a mouse model of Down syndrome with 62 antibodies were used as a case study. The ease of use and efficiency of RPPAware can accelerate data analysis to facilitate biological discovery. RPPAware 1.0 is freely available under GNU General Public License from the project website at http://downsyndrome.ucdenver.edu/iddrc/rppaware/home.htm along with a full documentation of the tool.
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Affiliation(s)
- A Ranjitha Dhanasekaran
- * Rocky Mountain Alzheimer's Disease Center, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- † Department of Neurology, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- ‡ Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Katheleen J Gardiner
- ‡ Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- § Department of Pediatrics, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
- ¶ Human Medical Genetics and Genomics and Neuroscience Programs, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado 80045, USA
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Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial Strains. Methods Mol Biol 2017. [PMID: 29222758 DOI: 10.1007/978-1-4939-7528-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species. The proteomic results consist of a dynamic portray of over- and down-represented protein species that, with the integration of gene ontology resources, allow obtaining a comprehensive understanding of the complex network of molecular signaling, regulatory circuits, and biochemical reactions occurring in cellular contexts. For this reason, proteomics has been widely used for studying molecular physiology of Gram-positive bacterial strains producing bioactive metabolites and belonging to actinomycete family. This highlighted the complex relationships linking overall regulatory processes and metabolic pathways to the biosynthesis of interesting bioactive molecules. In this chapter, we provide a detailed description of the procedures adopted to perform a differential proteomic analysis of the actinomycete Microbispora ATCC-PTA-5024, producing the promising NAI-107 lantibiotic. Although each experimental proteomic procedure has to be optimized to face the specific molecular characteristics of the organism under investigation, the protocols here described have also been used with minor modifications for proteomic studies on other bacterial strains, including the actinomycetes Streptomyces coelicolor, S. ambofaciens, Amycolatopsis balhimycina, and the Gram-negative proteobacteria Klebsiella oxytoca and Pseudoalteromonas haloplanktis.
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Kashiwazaki D, Uchino H, Kuroda S. Downregulation of Apolipoprotein-E and Apolipoprotein-J in Moyamoya Disease-A Proteome Analysis of Cerebrospinal Fluid. J Stroke Cerebrovasc Dis 2017; 26:2981-2987. [PMID: 28843803 DOI: 10.1016/j.jstrokecerebrovasdis.2017.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/18/2017] [Accepted: 07/25/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND PURPOSE Genetic factors are closely involved in the etiology of moyamoya disease (MMD). However, its postgenomic mechanisms are still unknown. This study was aimed to identify specific biomarkers in the cerebrospinal fluid (CSF) of patients with MMD, using quantitative proteome technique. METHODS This study included 10 patients with MMD and 4 controls. The CSF was collected without blood contamination during surgery. A comparative 2-dimensional gel electrophoresis study (2D-PAGE) was performed. Protein spots that showed significant differences between moyamoya patients and controls were selected for further analysis by mass spectrometry. RESULTS On 2D-PAGE, 2 proteins were significantly upregulated, and 2 other proteins were downregulated in the CSF of MMD. Further mass spectrometry analysis revealed that haptoglobin and α-1-B-glycoprotein (A1BG) were upregulated. On the other hand, apolipoprotein-E (apoE), apoE precursor, and apolipoprotein-J (apoJ) were significantly downregulated in the CSF of MMD. The observed probability-based MOWSE score was 72 for haptoglobin (P <.05), 521 for A1BG (P <.05), 62 for apoE (P <.05), 72 for apoE precursor (P <.05), and 112 for apoJ (P <.05). CONCLUSION Although the role of A1BG in the central nervous system is still unknown, the overexpressed haptoglobin may indicate the inflammation and/or angiogenesis in MMD. The downregulation of apoE and apoJ strongly suggests a critical role of lipid metabolism in the development and progression of MMD. These proteins may be novel biomarkers in shedding light on the pathogenesis of MMD, although further studies would be warranted.
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Affiliation(s)
- Daina Kashiwazaki
- Department of Neurosurgery, Graduate School of Medicine and Pharmaceutical Science, University of Toyama University, Toyama, Japan.
| | - Haruto Uchino
- Department of Neurosurgery, Graduate School of Medicine and Pharmaceutical Science, University of Toyama University, Toyama, Japan
| | - Satoshi Kuroda
- Department of Neurosurgery, Graduate School of Medicine and Pharmaceutical Science, University of Toyama University, Toyama, Japan
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Yu D, Wang Y, Zhang S, Chen Z, Xue M, Wang Y, Cong W, Jin L, Zhu Z. An ultrasensitive stain for negative protein detection in SDS-PAGE via 4′,5′-Dibromofluorescein. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang Y, Yu D, Dai J, Wang X, Zhu Z, Huang Y, Sun J, Chen Z, Jin L, Wang Y. A method for rapid and sensitive negative staining of proteins in SDS-PAGE using 2′,7′-dichlorofluorescein. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Yuan Zhang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Dongdong Yu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jiangbo Dai
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Xu Wang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Zhongxin Zhu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yewei Huang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jia Sun
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Zhiwei Chen
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Litai Jin
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yang Wang
- Institute of neuroscience, Department of histology and embryology; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
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Abstract
The oral environment contains diverse communities of micro-organisms including bacteria, fungi, protozoa, and viruses. Studies of oral ecology have led to an appreciation of the complexity of the interactions that oral micro-organisms have with the host in both health and disease. Despite this, diseases such as dental caries and periodontal diseases are still worldwide human ailments, resulting in a high level of morbidity and an economic burden to society. Proteomics offers a new approach to the understanding of holistic changes occurring as oral micro-organisms adapt to environmental change within their habitats in the mouth.
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Affiliation(s)
- D J Macarthur
- Institute of Dental Research, Westmead Centre for Oral Health, PO Box 533, Wentworthville, NSW 2145, Australia
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Ferroni L, Suorsa M, Aro EM, Baldisserotto C, Pancaldi S. Light acclimation in the lycophyte Selaginella martensii depends on changes in the amount of photosystems and on the flexibility of the light-harvesting complex II antenna association with both photosystems. THE NEW PHYTOLOGIST 2016; 211:554-68. [PMID: 27058989 DOI: 10.1111/nph.13939] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/20/2016] [Indexed: 05/22/2023]
Abstract
Vascular plants have evolved a long-term light acclimation strategy primarily relying on the regulation of the relative amounts of light-harvesting complex II (LHCII) and of the two photosystems, photosystem I (PSI) and photosystem II (PSII). We investigated whether such a model is also valid in Selaginella martensii, a species belonging to the early diverging group of lycophytes. Selaginella martensii plants were acclimated to three natural light regimes (extremely low light (L), medium light (M) and full sunlight (H)) and thylakoid organization was characterized combining ultrastructural, biochemical and functional methods. From L to H plants, thylakoid architecture was rearranged from (pseudo)lamellar to predominantly granal, the PSII : PSI ratio changed in favour of PSI, and the photochemical capacity increased. However, regulation of light harvesting did not occur through variations in the amount of free LHCII, but rather resulted from the flexibility of the association of free LHCII with PSII and PSI. In lycophytes, the free interspersed LHCII serves a fixed proportion of reaction centres, either PSII or PSI, and the regulation of PSI-LHCII(-PSII) megacomplexes is an integral part of long-term acclimation. Free LHCII ensures photoprotection of PSII, allows regulated use of PSI as an energy quencher, and can also quench endangered PSI.
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Affiliation(s)
- Lorenzo Ferroni
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este 32, 44121, Ferrara, Italy
| | - Marjaana Suorsa
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Eva-Mari Aro
- Department of Biochemistry, Molecular Plant Biology, University of Turku, FI-20014, Turku, Finland
| | - Costanza Baldisserotto
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este 32, 44121, Ferrara, Italy
| | - Simonetta Pancaldi
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este 32, 44121, Ferrara, Italy
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17
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Chen YC, Chen CC, Chen ST, Hsieh JF. Proteomic profiling of the coagulation of milk proteins induced by glucono-delta-lactone. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Miyake T, Pradeep S, Wu SY, Rupaimoole R, Zand B, Wen Y, Gharpure KM, Nagaraja AS, Hu W, Cho MS, Dalton HJ, Previs RA, Taylor ML, Hisamatsu T, Kang Y, Liu T, Shacham S, McCauley D, Hawke DH, Wiktorowicz JE, Coleman RL, Sood AK. XPO1/CRM1 Inhibition Causes Antitumor Effects by Mitochondrial Accumulation of eIF5A. Clin Cancer Res 2015; 21:3286-97. [PMID: 25878333 PMCID: PMC4506247 DOI: 10.1158/1078-0432.ccr-14-1953] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 02/26/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE XPO1 inhibitors have shown promise for cancer treatment, and yet the underlying mechanisms for the antitumor effects are not well understood. In this study, we explored the usefulness of selective inhibitors of nuclear export (SINE) compounds that are specific inhibitors of XPO1. EXPERIMENTAL DESIGN We used proteomic analysis in XPO1 inhibitor-treated ovarian cancer cell lines and examined antitumor effects in ovarian and breast cancer mouse models. We also studied the effects of XPO1 inhibitor in combination with chemotherapeutic agents. RESULTS XPO1 inhibitor treatment substantially increased the percentage of apoptotic cells (60%) after 72 hours of incubation. XPO1 inhibitor promoted the accumulation of eIF5A in mitochondria, leading to cancer cell death. Topotecan showed the greatest synergistic effect with XPO1 inhibitor. XPO1 inhibitors prevented the translocation of IGF2BP1 from the nucleus to the cytoplasm, thereby permitting the localization of eIF5A in the mitochondria. This process was p53, RB, and FOXO independent. Significant antitumor effects were observed with XPO1 inhibitor monotherapy in orthotopic ovarian (P < 0.001) and breast (P < 0.001) cancer mouse models, with a further decrease in tumor burden observed in combination with topotecan or paclitaxel (P < 0.05). This mitochondrial accumulation of eIF5A was highly dependent on the cytoplasmic IGF2BP1 levels. CONCLUSIONS We have unveiled a new understanding of the role of eIF5A and IGF2BP1 in XPO1 inhibitor-mediated cell death and support their clinical development for the treatment of ovarian and other cancers. Our data also ascertain the combinations of XPO1 inhibitors with specific chemotherapy drugs for therapeutic trials.
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MESH Headings
- Active Transport, Cell Nucleus/drug effects
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Cell Line, Tumor
- Chromatography, Liquid
- Electrophoresis, Gel, Two-Dimensional
- Enzyme Inhibitors/pharmacology
- Female
- Fluorescent Antibody Technique
- Humans
- Immunohistochemistry
- Karyopherins/antagonists & inhibitors
- Mammary Neoplasms, Experimental/metabolism
- Mice
- Mice, Nude
- Mitochondria/metabolism
- Ovarian Neoplasms/metabolism
- Peptide Initiation Factors/metabolism
- Proteomics
- RNA, Small Interfering
- RNA-Binding Proteins/metabolism
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Signal Transduction/drug effects
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry
- Transfection
- Xenograft Model Antitumor Assays
- Eukaryotic Translation Initiation Factor 5A
- Exportin 1 Protein
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Affiliation(s)
- Takahito Miyake
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sunila Pradeep
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Y Wu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajesha Rupaimoole
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Behrouz Zand
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yunfei Wen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kshipra M Gharpure
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Archana S Nagaraja
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Hu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Min Soon Cho
- Department of Benign Hematology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Heather J Dalton
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rebecca A Previs
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Morgan L Taylor
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Takeshi Hisamatsu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yu Kang
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tao Liu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - David H Hawke
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John E Wiktorowicz
- Department of Biochemistry and Molecular Biology, NHLBI Proteomics Center, The University of Texas Medical Branch, Galveston, Texas
| | - Robert L Coleman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Center for RNA Interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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19
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Chatterjee S, Karuso P, Boulangé A, Franck X, Datta A. Excited State Dynamics of Brightly Fluorescent Second Generation Epicocconone Analogues. J Phys Chem B 2015; 119:6295-303. [DOI: 10.1021/acs.jpcb.5b02190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soumit Chatterjee
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Peter Karuso
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Agathe Boulangé
- Normandie Univ,
COBRA, UMR 6014 et FR 3038, CNRS, Univ Rouen, INSA Rouen, 1 rue Tesnières, 76821 Mont-Saint-Aignan, Cedex, France
| | - Xavier Franck
- Normandie Univ,
COBRA, UMR 6014 et FR 3038, CNRS, Univ Rouen, INSA Rouen, 1 rue Tesnières, 76821 Mont-Saint-Aignan, Cedex, France
| | - Anindya Datta
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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20
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Chen CC, Chen ST, Hsieh JF. Proteomic analysis of polysaccharide-milk protein interactions induced by chitosan. Molecules 2015; 20:7737-49. [PMID: 25927902 PMCID: PMC6272545 DOI: 10.3390/molecules20057737] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 11/16/2022] Open
Abstract
The chitosan-induced coacervation of milk proteins was investigated using a proteomic approach. The addition of 0.8% chitosan to milk caused the milk proteins to coacervate after a 1 h incubation period. Approximately 86% of the milk proteins were present in the milk pellet fraction (MPF), and the protein concentration of the milk supernatant fraction (MSF) decreased from 29.4±0.2 to 4.2±0.6 mg/mL. SDS-PAGE analysis showed that the total intensities of serum albumin (BSA), αS-casein (αS-CN), β-casein (β-CN), κ-casein (κ-CN) and β-lactoglobulin (β-LG) in the MSF decreased to 8.5%±0.2%, 0.9%±0.3%, 0.7%±0.3%, 0.5%±0.2% and 15.0%±0.5%, respectively. Two-dimensional electrophoresis analysis indicated that αS1-, αS2-, β- and κ-CN and a fraction of the β-LG and BSA were found in the MSF following incubation with 0.8% chitosan. Isothermal titration calorimetry analysis indicated that binding of chitosan to milk proteins is an exothermic reaction based on binding titration curves of milk proteins dispersions with chitosan, and the enthalpy of binding (ΔH) and binding constant (Ka) were -7.85×10(4) cal/mol and 1.06×10(5)/mol, respectively. These results suggested that the addition of 0.8% chitosan causes milk proteins to coacervate due to polysaccharide-protein interactions.
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Affiliation(s)
- Chun-Chi Chen
- Ph.D. Program in Nutrition & Food Science, Fu Jen Catholic University, Taipei 242, Taiwan.
- Department of Food Science, Fu Jen Catholic University, Taipei 242, Taiwan.
| | - Shui-Tein Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Jung-Feng Hsieh
- Ph.D. Program in Nutrition & Food Science, Fu Jen Catholic University, Taipei 242, Taiwan.
- Department of Food Science, Fu Jen Catholic University, Taipei 242, Taiwan.
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21
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Puumalainen TJ, Puustinen A, Poikonen S, Turjanmaa K, Palosuo T, Vaali K. Proteomic identification of allergenic seed proteins, napin and cruciferin, from cold-pressed rapeseed oils. Food Chem 2014; 175:381-5. [PMID: 25577095 DOI: 10.1016/j.foodchem.2014.11.084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/08/2014] [Accepted: 11/15/2014] [Indexed: 11/16/2022]
Abstract
In Finland and France atopic children commonly react to seeds of oilseed rape and turnip rape in skin prick tests (SPT) and open food challenges. These seeds are not as such in dietary use and therefore the routes of sensitization are unknown. Possible allergens were extracted from commercial cold-pressed and refined rapeseed oils and identified by gel-based tandem nanoflow liquid chromatography mass spectrometry (LC-MS/MS). Napin (a 2S albumin), earlier identified as a major allergen in the seeds of oilseed rape and turnip rape, and cruciferin (an 11S globulin), a new potential seed allergen, were detected in cold-pressed oils, but not in refined oils. Pooled sera from five children sensitized or allergic to oilseed rape and turnip rape seeds reacted to these proteins from cold-pressed oil preparations and individual sera from five children reacted to these proteins extracted from the seeds when examined with IgE immunoblotting. Hence cold-pressed rapeseed oil might be one possible route of sensitization for these allergens.
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Affiliation(s)
- T J Puumalainen
- Haartman Institute, Department of Bacteriology and Immunology, University of Helsinki, Finland; Immune Response Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - A Puustinen
- Unit of Immunotoxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - S Poikonen
- Department of Dermatology, Central Finland Health Care District, Jyväskylä, Finland
| | - K Turjanmaa
- Department of Dermatology, Tampere University and University Hospital, Tampere, Finland
| | - T Palosuo
- Immune Response Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - K Vaali
- Haartman Institute, Department of Bacteriology and Immunology, University of Helsinki, Finland; Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway.
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22
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Xiao S, Caglar E, Maldonado P, Das D, Nadeem Z, Chi A, Trinité B, Li X, Saxena A. Induced expression of nucleolin phosphorylation-deficient mutant confers dominant-negative effect on cell proliferation. PLoS One 2014; 9:e109858. [PMID: 25313645 PMCID: PMC4196967 DOI: 10.1371/journal.pone.0109858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/08/2014] [Indexed: 11/25/2022] Open
Abstract
Nucleolin (NCL) is a major nucleolar phosphoprotein that has pleiotropic effects on cell proliferation and is elevated in a variety of tumors. NCL is highly phosphorylated at the N-terminus by two major kinases: interphase casein kinase 2 (CK2) and mitotic cyclin-dependent kinase 1 (CDK1). Earlier we demonstrated that a NCL-mutant that is partly defective in undergoing phosphorylation by CK2 inhibits chromosomal replication through its interactions with Replication Protein A, mimicking the cellular response to DNA damage. We further delineated that the N-terminus of NCL associates with Hdm2, the most common E3 ubiquitin ligase of p53. We reported that NCL antagonizes Hdm2 to stabilize p53 and stimulates p53 transcriptional activity. Although NCL-phosphorylation by CK2 and ribosomal DNA transcription are closely coordinated during interphase, the role of NCL phosphorylation in regulating cell proliferation remains unexplored. We have therefore engineered unique human cells that specifically induce expression of NCL-wild type (WT) or a phosphorylation-deficient NCL-mutant, 6/S*A where all the six CK2 consensus serine sites residing in the N-terminus NCL were mutated to alanine. Here we show that this NCL-mutant is defective in undergoing phosphorylation by CK2. We also demonstrate that NCL-phosphorylation by CK2 is required through the S-phase progression in cell cycle and hence proliferation. Induced expression of NCL with mutated CK2 phosphorylation sites stabilizes p53, results in higher expression of Bcl2 (B-cell lymphoma 2) homology 3 (BH3)-only apoptotic markers and causes a dominant-negative effect on cell viability. Our unique cellular system thus provides the first evidential support to delineate phospho-specific functions of NCL on cell proliferation.
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Affiliation(s)
- Shu Xiao
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
| | - Elif Caglar
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
| | - Priscilla Maldonado
- New York University School of Medicine, New York, New York, United States of America
| | - Dibash Das
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
| | - Zaineb Nadeem
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
| | - Angela Chi
- Great Neck South High School, Great Neck, New York, United States of America
| | - Benjamin Trinité
- New York University College of Dentistry, New York, New York, United States of America
| | - Xin Li
- New York University College of Dentistry, New York, New York, United States of America
| | - Anjana Saxena
- Biology Department, Brooklyn College, Brooklyn, New York, United States of America
- City University of New York, Graduate Center, New York, New York, United States of America
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23
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Zhu-Shimoni J, Yu C, Nishihara J, Wong RM, Gunawan F, Lin M, Krawitz D, Liu P, Sandoval W, Vanderlaan M. Host cell protein testing by ELISAs and the use of orthogonal methods. Biotechnol Bioeng 2014; 111:2367-79. [PMID: 24995961 DOI: 10.1002/bit.25327] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 02/05/2023]
Abstract
Host cell proteins (HCPs) are among the process-related impurities monitored during recombinant protein pharmaceutical process development. The challenges of HCP detection include (1) low levels of residual HCPs present in large excess of product protein, (2) the assay must measure a large number of different protein analytes, and (3) the population of HCP species may change during process development. Suitable methods for measuring process-related impurities are needed to support process development, process validation, and control system testing. A multi-analyte enzyme-linked immunosorbent assay (ELISA) is the workhorse method for HCP testing due to its high throughput, sensitivity and selectivity. However, as the anti-HCP antibodies, the critical reagents for HCP ELISA, do not comprehensively recognize all the HCP species, it is especially important to ensure that weak and non-immunoreactive HCPs are not overlooked by the ELISA. In some cases limited amount of antibodies to HCP species or antigen excess causes dilution-dependent non-linearity with multi-product HCP ELISA. In our experience, correct interpretation of assay data can lead to isolation and identification of co-purifying HCP with the product in some cases. Moreover, even if the antibodies for a particular HCP are present in the reagent, the corresponding HCP may not be readily detected in the ELISA due to antibody/antigen binding conditions and availability of HCP epitopes. This report reviews the use of the HCP ELISA, discusses its limitations, and demonstrates the importance of orthogonal methods, including mass spectrometry, to complement the platform HCP ELISA for support of process development. In addition, risk and impact assessment for low-level HCPs is also outlined, with consideration of clinical information.
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Affiliation(s)
- Judith Zhu-Shimoni
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080.
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24
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Ardila HD, Fernández RG, Higuera BL, Redondo I, Martínez ST. Protein extraction and gel-based separation methods to analyze responses to pathogens in carnation (Dianthus caryophyllus L). Methods Mol Biol 2014; 1072:573-591. [PMID: 24136548 DOI: 10.1007/978-1-62703-631-3_39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We are currently using a 2-DE-based proteomics approach to study plant responses to pathogenic fungi by using the carnation (Dianthus caryophyllus L)-Fusarium oxysporum f. sp. dianthi pathosystem. It is clear that the protocols for the first stages of a standard proteomics workflow must be optimized to each biological system and objectives of the research. The optimization procedure for the extraction and separation of proteins by 1-DE and 2-DE in the indicated system is reported. This strategy can be extrapolated to other plant-pathogen interaction systems in order to perform an evaluation of the changes in the host protein profile caused by the pathogen and to identify proteins which, at early stages, are involved or implicated in the plant defense response.
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Affiliation(s)
- Harold Duban Ardila
- Laboratory Research in Plant Metabolic Activities, Department of Chemistry, National University of Colombia, Bogotá, Colombia
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25
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Singh AB, Mukherjee KJ. Supplementation of substrate uptake gene enhances the expression of rhIFN-β in high cell density fed-batch cultures of Escherichia coli. Mol Biotechnol 2013. [PMID: 23180218 DOI: 10.1007/s12033-012-9611-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Over-expression of recombinant proteins in Escherichia coli triggers a metabolic stress response which causes a sharp decline in both growth and product formation rates post induction. We identified a key down-regulated substrate utilization gene, glycerol kinase (glpK), whose up-regulation could help alleviate this stress response. In a proof of principal study conducted in shake flask cultures, the glpK gene under the "ara" promoter in a pPROLar.A122 vector was co-transformed along with the recombinant interferon-β (rhIFN-β) gene in a pET22b vector into E. coli BL-21(DE3) cells. Co-expression of glpK improved the expression levels of rhIFN-β in glycerol containing medium, while no such gain was observed in medium without glycerol. This study was extended to high cell density fed-batch cultures where exponential feeding of complex substrates was done to increase biomass and hence product titers. For this we first constructed a modified E. coli strain BL-21(glpK (+)) where the glpK gene was inserted downstream of the ibpA promoter in the host chromosome. There was a significant improvement in growth as well as expression levels of rhIFN-β in this modified strain when the feed medium contained high glycerol. A final product concentration of 4.8 g/l of rhIFN-β was obtained with the modified strain which was 35 % higher than the control.
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Affiliation(s)
- Anuradha B Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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26
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Wöhlbrand L, Trautwein K, Rabus R. Proteomic tools for environmental microbiology-A roadmap from sample preparation to protein identification and quantification. Proteomics 2013; 13:2700-30. [DOI: 10.1002/pmic.201300175] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/07/2013] [Accepted: 06/28/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Kathleen Trautwein
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM); Carl von Ossietzky University Oldenburg; Oldenburg Germany
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27
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Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
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28
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Schowalter RM, Buck CB. The Merkel cell polyomavirus minor capsid protein. PLoS Pathog 2013; 9:e1003558. [PMID: 23990782 PMCID: PMC3749969 DOI: 10.1371/journal.ppat.1003558] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/02/2013] [Indexed: 01/02/2023] Open
Abstract
The surface of polyomavirus virions is composed of pentameric knobs of the major capsid protein, VP1. In previously studied polyomavirus species, such as SV40, two interior capsid proteins, VP2 and VP3, emerge from the virion to play important roles during the infectious entry process. Translation of the VP3 protein initiates at a highly conserved Met-Ala-Leu motif within the VP2 open reading frame. Phylogenetic analyses indicate that Merkel cell polyomavirus (MCV or MCPyV) is a member of a divergent clade of polyomaviruses that lack the conserved VP3 N-terminal motif. Consistent with this observation, we show that VP3 is not detectable in MCV-infected cells, VP3 is not found in native MCV virions, and mutation of possible alternative VP3-initiating methionine codons did not significantly affect MCV infectivity in culture. In contrast, VP2 knockout resulted in a >100-fold decrease in native MCV infectivity, despite normal virion assembly, viral DNA packaging, and cell attachment. Although pseudovirus-based experiments confirmed that VP2 plays an essential role for infection of some cell lines, other cell lines were readily transduced by pseudovirions lacking VP2. In cell lines where VP2 was needed for efficient infectious entry, the presence of a conserved myristoyl modification on the N-terminus of VP2 was important for its function. The results show that a single minor capsid protein, VP2, facilitates a post-attachment stage of MCV infectious entry into some, but not all, cell types. Merkel cell polyomavirus (MCV or MCPyV) is a recently discovered member of the viral family Polyomaviridae. The virus plays a causal role in Merkel cell carcinoma, a highly lethal form of skin cancer. MCV encodes a major capsid protein, VP1, which forms the non-enveloped surface of the virion. Other polyomavirus species encode two minor capsid proteins, VP2 and VP3, which associate with the inner surface of the capsid and facilitate infectious entry. In this report we show that MCV does not have a VP3 minor capsid protein. Sequence analyses suggest that more than a quarter of known polyomavirus species share MCV's lack of a VP3 protein. In contrast to VP3, VP2-knockout MCV mutants displayed dramatically reduced infectivity. Consistent with native virion findings, MCV pseudovirions lacking VP2 or carrying mutations in the VP2 myristoylation motif displayed reduced infectivity on several cell lines. Puzzlingly, MCV pseudoviruses lacking VP2 successfully transduced other cell lines with high efficiency. Taken together, the data show that the lone MCV minor capsid protein, VP2, plays an important role during infectious entry into some cell types, but is dispensable for entry into other cell types.
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Affiliation(s)
- Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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29
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Duncombe TA, Herr AE. Photopatterned free-standing polyacrylamide gels for microfluidic protein electrophoresis. LAB ON A CHIP 2013; 13:2115-2123. [PMID: 23609800 DOI: 10.1039/c3lc50269d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Designed for compatibility with slab-gel polyacrylamide gel electrophoresis (PAGE) reagents and instruments, we detail development of free-standing polyacrylamide gel (fsPAG) microstructures supporting electrophoretic performance rivalling that of microfluidic platforms. For the protein electrophoresis study described here, fsPAGE lanes are comprised of a sample reservoir and contiguous separation gel. No enclosed microfluidic channels are employed. The fsPAG devices (120 μm tall) are directly photopatterned atop of and covalently attached to planar polymer or glass surfaces. Leveraging the fast <1 h design-prototype-test cycle - significantly faster than mold based fabrication techniques - we optimize the fsPAG architecture to minimize injection dispersion for rapid (<1 min) and short (1 mm) protein separations. The facile fabrication and prototyping of the fsPAGE provides researchers a powerful tool for developing custom analytical assays. We highlight the utility of assay customization by fabricating a polyacrylamide gel with a spatial pore-size distribution and demonstrate the resulting enhancement in separation performance over a uniform gel. Further, we up-scale from a unit separation to an array of 96 concurrent fsPAGE assays in 10 min run time driven by one electrode pair. The fsPAG array layout matches that of a 96-well plate to facilitate integration of the planar free standing gel array with multi-channel pipettes while remaining compatible with conventional slab-gel PAGE reagents, such as staining for label-free protein detection. Notably, the entire fsPAGE workflow from fabrication, to operation, and readout uses readily available materials and instruments - making this technique highly accessible.
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Affiliation(s)
- Todd A Duncombe
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, 342 Stanley Hall, Berkeley, California 94720, USA
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Zhan X, Wang X, Desiderio DM. Pituitary adenoma nitroproteomics: current status and perspectives. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:580710. [PMID: 23533694 PMCID: PMC3606787 DOI: 10.1155/2013/580710] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 01/14/2013] [Indexed: 11/30/2022]
Abstract
Oxidative stress is extensively associated with tumorigenesis. A series of studies on stable tyrosine nitration as a marker of oxidative damage were performed in human pituitary and adenoma. This paper reviews published research on the mass spectrometry characteristics of nitropeptides and nitroproteomics of pituitary controls and adenomas. The methodology used for nitroproteomics, the current status of human pituitary nitroproteomics studies, and the future perspectives are reviewed. Enrichment of those low-abundance endogenous nitroproteins from human tissues or body fluid samples is the first important step for nitroproteomics studies. Mass spectrometry is the essential approach to determine the amino acid sequence and locate the nitrotyrosine sites. Bioinformatics analyses, including protein domain and motif analyses, are needed to locate the nitrotyrosine site within the corresponding protein domains/motifs. Systems biology techniques, including pathway analysis, are necessary to discover signaling pathway networks involving nitroproteins from the systematically global point of view. Future quantitative nitroproteomics will discover pituitary adenoma-specific nitroprotein(s). Structural biology techniques such as X-ray crystallography analysis will solidly clarify the effects of tyrosine nitration on structure and functions of a protein. Those studies will eventually address the mechanisms and biological functions of tyrosine nitration in pituitary tumorigenesis and will discover nitroprotein biomarkers for pituitary adenomas and targets for drug design for pituitary adenoma therapy.
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Affiliation(s)
- Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China.
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Abstract
Understanding changes in the expression of specific proteins and/or alterations in their posttranslational modifications is crucial to elucidating the molecular mechanisms underlying disease states such as alcoholic liver disease. Protein separation and analysis techniques such as two-dimensional electrophoresis and mass spectrometry can be used for identifying biomarker proteins that are altered during progression of alcoholic liver disease. In this chapter, we outline methods for resolving liver tissue proteins from a rodent model of alcoholic liver disease using two-dimensional electrophoresis and identifying differentially expressed proteins using mass spectrometry. In addition, since oxidative stress strongly correlates with alcoholic liver disease, we also describe methods for identifying oxidatively modified proteins from liver tissue. We specifically focus on identifying proteins that are carbonylated as protein carbonylation is a permanent modification and considered deleterious to cells. The combination of two-dimensional electrophoresis for protein resolution, mass spectrometry for protein identification, and affinity-based methods for enriching and identifying carbonylated proteins is a powerful methodology for protein biomarker identification.
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Ilyas A, Asghar W, Allen PB, Duhon H, Ellington AD, Iqbal SM. Electrical detection of cancer biomarker using aptamers with nanogap break-junctions. NANOTECHNOLOGY 2012; 23:275502. [PMID: 22706642 PMCID: PMC3404891 DOI: 10.1088/0957-4484/23/27/275502] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Epidermal growth factor receptor (EGFR) is a cell surface protein overexpressed in cancerous cells. It is known to be the most common oncogene. EGFR concentration also increases in the serum of cancer patients. The detection of small changes in the concentration of EGFR can be critical for early diagnosis, resulting in better treatment and improved survival rate of cancer patients. This article reports an RNA aptamer based approach to selectively capture EGFR protein and an electrical scheme for its detection. Pairs of gold electrodes with nanometer separation were made through confluence of focused ion beam scratching and electromigration. The aptamer was hybridized to a single stranded DNA molecule, which in turn was immobilized on the SiO(2) surface between the gold nanoelectrodes. The selectivity of the aptamer was demonstrated by using control chips with mutated non-selective aptamer and with no aptamer. Surface functionalization was characterized by optical detection and two orders of magnitude increase in direct current (DC) was measured when selective capture of EGFR occurred. This represents an electronic biosensor for the detection of proteins of interest for medical applications.
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Affiliation(s)
- Azhar Ilyas
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, Texas 76011, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, Texas 76019, USA
- Nano-Bio Lab, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Waseem Asghar
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, Texas 76011, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, Texas 76019, USA
- Nano-Bio Lab, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Peter B. Allen
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Holli Duhon
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D. Ellington
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Samir M. Iqbal
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, Texas 76011, USA
- Nanotechnology Research and Teaching Facility, University of Texas at Arlington, Arlington, Texas 76019, USA
- Nano-Bio Lab, University of Texas at Arlington, Arlington, Texas 76019, USA
- Joint Graduate Committee of Bioengineering Program, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, Arlington, Texas 76010, USA
- Department of Bioengineering, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, Arlington, Texas 76010, USA
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Kuwana R, Yamamoto N. Increases in GroES and GroEL from Lactobacillus acidophilus L-92 in response to a decrease in medium pH, and changes in cytokine release from splenocytes: Transcriptome and proteome analyses. J Biosci Bioeng 2012; 114:9-16. [DOI: 10.1016/j.jbiosc.2012.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/06/2012] [Accepted: 02/13/2012] [Indexed: 11/24/2022]
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Klinbunga S, Petkorn S, Kittisenachai S, Phaonakrop N, Roytrakul S, Khamnamtong B, Menasveta P. Identification of reproduction-related proteins and characterization of proteasome alpha 3 and proteasome beta 6 cDNAs in testes of the giant tiger shrimp Penaeus monodon. Mol Cell Endocrinol 2012; 355:143-52. [PMID: 22361323 DOI: 10.1016/j.mce.2012.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 01/11/2012] [Accepted: 02/07/2012] [Indexed: 11/18/2022]
Abstract
Cellular proteomic analysis was carried out to identify reproduction-related proteins in testes of wild and domesticated broodstock of Penaeus monodon. In total, 642 protein spots were characterized and 287 spots (44.70%) significantly matched protein sequences in the databases (P<0.05). To examine a role of the proteasome system in testicular development of P. monodon, the expression profiles of proteasome alpha 3 subunit (PmPsma3) and proteasome beta 6 (PmPsmb6) mRNA in different groups of domesticated shrimp and in wild broodstock were examined. The expression levels of these transcripts in testes of 18-month-old domesticated shrimp were significantly lower than those of wild broodstock (P<0.05). Interestingly, the expression levels of testicular PmPsma3 and PmPsmb6 in 18-month-old shrimp were significantly increased at 24 h following serotonin injection (50 μg/g body weight). Results suggested that reduced degrees of maturation in captive P. monodon males may be partially resolved by exogenous 5-HT administration.
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Affiliation(s)
- Sirawut Klinbunga
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong 1, Klong Luang, Pathumthani 12120, Thailand.
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Skillman KM, Daher W, Ma CI, Soldati-Favre D, Sibley LD. Toxoplasma gondii profilin acts primarily to sequester G-actin while formins efficiently nucleate actin filament formation in vitro. Biochemistry 2012; 51:2486-95. [PMID: 22397711 DOI: 10.1021/bi201704y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Apicomplexan parasites employ gliding motility that depends on the polymerization of parasite actin filaments for host cell entry. Despite this requirement, parasite actin remains almost entirely unpolymerized at steady state; formation of filaments required for motility relies on a small repertoire of actin-binding proteins. Previous studies have shown that apicomplexan formins and profilin exhibit canonical functions on heterologous actins from higher eukaryotes; however, their biochemical properties on parasite actins are unknown. We therefore analyzed the impact of T. gondii profilin (TgPRF) and FH1-FH2 domains of two formin isoforms in T. gondii (TgFRM1 and TgFRM2) on the polymerization of T. gondii actin (TgACTI). Our findings based on in vitro assays demonstrate that TgFRM1-FH1-FH2 and TgFRM2-FH1-FH2 dramatically enhanced TgACTI polymerization in the absence of profilin, making them the sole protein factors known to initiate polymerization of this normally unstable actin. In addition, T. gondii formin domains were shown to both initiate polymerization and induce bundling of TgACTI filaments; however, they did not rely on TgPRF for these activities. In contrast, TgPRF sequestered TgACTI monomers, thus inhibiting polymerization even in the presence of formins. Collectively, these findings provide insight into the unusual control mechanisms of actin dynamics within the parasite.
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Affiliation(s)
- Kristen M Skillman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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Chao TC, Hansmeier N. The current state of microbial proteomics: Where we are and where we want to go. Proteomics 2012; 12:638-50. [DOI: 10.1002/pmic.201100381] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 08/15/2011] [Accepted: 08/22/2011] [Indexed: 11/11/2022]
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Wang X, Wang D, Wang D, Wang H, Chang L, Yi X, Peng M, Guo A. Systematic comparison of technical details in CBB methods and development of a sensitive GAP stain for comparative proteomic analysis. Electrophoresis 2012; 33:296-306. [DOI: 10.1002/elps.201100300] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xuchu Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Dongyang Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Dan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Haiyan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Lili Chang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Xiaoping Yi
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Ming Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Anping Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
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Buyel JF, Bautista JA, Fischer R, Yusibov VM. Extraction, purification and characterization of the plant-produced HPV16 subunit vaccine candidate E7 GGG. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 880:19-26. [PMID: 22134037 DOI: 10.1016/j.jchromb.2011.11.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 11/03/2011] [Accepted: 11/06/2011] [Indexed: 11/22/2022]
Abstract
Several studies indicated that biopharmaceuticals based on the recombinant protein E7 of human papillomavirus (HPV) can serve as therapeutic vaccines preventing the development of cancer in women infected with high-risk types of HPV such as HPV16. Here, we report effective extraction and purification of a plant-produced E7GGG-lichenase fusion protein, an HPV16 subunit vaccine candidate, from Nicotiana benthamiana plants, to a high yield. The target contains the modified HPV16 E7 protein internally fused to the surface loop of a truncated, hexa-His- and KDEL-tagged variant of bacterial lichenase, and has been previously shown to possess anti-cancer activity in an animal model. We purified the protein using a combination of immobilized metal-ion affinity chromatography and gel filtration. The achieved purity of the final product was 99% as confirmed by Coomassie or SYPRO Ruby staining after sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by analytical size exclusion chromatography coupled with multi-angle laser light scattering. The overall yield was 50% corresponding to 0.1g of protein per 1 kg plant biomass. Only slight changes in these parameters were observed during the process scale-up from 50 g to 1 kg of processed leaf biomass.
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Affiliation(s)
- J F Buyel
- Fraunhofer USA Center for Molecular Biotechnology, Newark, DE 19711, USA.
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Singh AB, Sharma AK, Mukherjee KJ. Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon-beta in high cell density fed batch cultures using time course transcriptomic data. MOLECULAR BIOSYSTEMS 2011; 8:615-28. [PMID: 22134216 DOI: 10.1039/c1mb05414g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fed batch cultures expressing recombinant interferon beta under the T7 promoter were run with different exponential feeding rates of a complex substrate and induced at varying cell densities. Post-induction profiles of the specific product formation rates showed a strong dependence on the specific growth rate with the maximum product yield obtained at 0.2 h(-1). A study of the relative transcriptomic profiles as a function of pre-induction μ was therefore done to provide insight into the role of cellular physiology in enhancing recombinant protein expression. Hierarchical clustering analysis of the significantly regulated genes allowed us to identify biologically important groups of genes which fall under specific master regulators. The groups were: rpoH, ArcB, CreB, Lrp, RelA, Fis and Hfq. The response of these regulators, which exert a feedback control on the growth and product formation rates correlated well with the expression levels obtained. Thus at the optimum pre-induction μ, the alternative sigma factors and ribosomal machinery genes did not get depressed till the 6th hour post-induction unlike at other specific growth rates, demonstrating a critical role for the genes in sustaining recombinant protein expression.
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Affiliation(s)
- Anuradha B Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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40
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Characterization of adhesive molecule with affinity to Caco-2 cells in Lactobacillus acidophilus by proteome analysis. J Biosci Bioeng 2011; 112:333-7. [DOI: 10.1016/j.jbiosc.2011.06.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/23/2011] [Accepted: 06/07/2011] [Indexed: 01/26/2023]
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Yasui Y, Tanaka T. Protein expression analysis of inflammation-related colon carcinogenesis. J Carcinog 2011; 8:10. [PMID: 19491504 PMCID: PMC2699605 DOI: 10.4103/1477-3163.51851] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background: Chronic inflammation is a risk factor for colorectal cancer (CRC) development. The aim of this study was to determine the differences in protein expression between CRC and the surrounding nontumorous colonic tissues in the mice that received azoxymethane (AOM) and dextran sodium sulfate (DSS) using a proteomic analysis. Materials and Methods: Male ICR mice were given a single intraperitoneal injection of AOM (10 mg/kg body weight), followed by 2% (w/v) DSS in their drinking water for seven days, starting one week after the AOM injection. Colonic adenocarcinoma developed after 20 weeks and a proteomics analysis based on two-dimensional gel electrophoresis and ultraflex TOF/TOF mass spectrometry was conducted in the cancerous and nontumorous tissue specimens. Results: The proteomic analysis revealed 21 differentially expressed proteins in the cancerous tissues in comparison to the nontumorous tissues. There were five markedly increased proteins (beta-tropomyosin, tropomyosin 1 alpha isoform b, S100 calcium binding protein A9, and an unknown protein) and 16 markedly decreased proteins (Car1 proteins, selenium-binding protein 1, HMG-CoA synthase, thioredoxin 1, 1 Cys peroxiredoxin protein 2, Fcgbp protein, Cytochrome c oxidase, subunit Va, ETHE1 protein, and 7 unknown proteins). Conclusions: There were 21 differentially expressed proteins in the cancerous tissues of the mice that received AOM and DSS. Their functions include metabolism, the antioxidant system, oxidative stress, mucin production, and inflammation. These findings may provide new insights into the mechanisms of inflammation-related colon carcinogenesis and the establishment of novel therapies and preventative strategies to treat carcinogenesis in the inflamed colon.
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Affiliation(s)
- Yumiko Yasui
- Department of Oncologic Pathology, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Ishikawa 920-0293, Japan.
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Identification and characterization of a heme periplasmic-binding protein in Haemophilus ducreyi. Biometals 2011; 24:709-22. [PMID: 21347851 DOI: 10.1007/s10534-011-9427-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
Abstract
Haemophilus ducreyi, a gram-negative and heme-dependent bacterium, is the causative agent of chancroid, a genital ulcer sexually transmitted infection. Heme acquisition in H. ducreyi proceeds via a receptor mediated process in which the initial event involves binding of hemoglobin and heme to their cognate outer membrane proteins, HgbA and TdhA, respectively. Following this specific interaction, the fate of the periplasmic deposited heme is unclear. Using protein expression profiling of the H. ducreyi periplasmic proteome, a periplasmic-binding protein, termed hHbp, was identified whose expression was enhanced under heme-limited conditions. The gene encoding this protein was situated in a locus displaying genetic characteristics of an ABC transporter. The purified protein bound heme in a dose-dependent and saturable manner and this binding was specifically competitively inhibited by heme. The hhbp gene functionally complemented an Escherichia coli heme uptake mutant. Expression of the heme periplasmic-binding protein was detected in a limited survey of H. ducreyi and H. influenzae clinical strains. These results indicate that the passage of heme into the cytoplasm of H. ducreyi involves a heme dedicated ABC transporter.
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Arnold GJ, Frohlich T. Dynamic proteome signatures in gametes, embryos and their maternal environment. Reprod Fertil Dev 2011; 23:81-93. [DOI: 10.1071/rd10223] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Comprehensive molecular analysis at the level of proteins represents a technically demanding, but indispensable, task since several post-transcriptional regulation mechanisms disable a valid prediction of quantitative protein expression profiles from transcriptome analysis. In crucial steps of gamete and early embryo development, de novo transcription is silenced, meaning that almost all macromolecular events take place at the level of proteins. In this review, we describe selected examples of dynamic proteome signatures addressing capacitation of spermatozoa, in vitro maturation of oocytes, effect of oestrous cycle on oviduct epithelial cells and embryo-induced alterations to the maternal environment. We also present details of the experimental strategies applied and the experiments performed to verify quantitative proteomic data. Far from being comprehensive, examples were selected to cover several mammalian species as well as the most powerful proteomic techniques currently applied. To enable non-experts in the field of proteomics to appraise published proteomic data, our examples are preceded by a customised description of quantitative proteomic methods, covering 2D difference gel electrophoresis (2D-DIGE), nano-liquid chromatography combined with tandem mass spectrometry, and label-free as well as stable-isotope labelling strategies for mass spectrometry-based quantifications.
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Serda RE, Blanco E, Mack A, Stafford SJ, Amra S, Li Q, van de Ven A, Tanaka T, Torchilin VP, Wiktorowicz JE, Ferrari M. Proteomic Analysis of Serum Opsonins Impacting Biodistribution and Cellular Association of Porous Silicon Microparticles. Mol Imaging 2011. [DOI: 10.2310/7290.2011.00008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rita E. Serda
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Elvin Blanco
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Aaron Mack
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Susan J. Stafford
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Sarah Amra
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Qingpo Li
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Anne van de Ven
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Takemi Tanaka
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Vladimir P. Torchilin
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - John E. Wiktorowicz
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
| | - Mauro Ferrari
- From the Department of Nanomedicine and Biomedical Engineering, University of Texas Health Science Center, Houston, TX; Biomolecular Resource Facility and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA; Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX; and Department of Bioengineering, Rice University, Houston, TX
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Yarmoluk SM, Kovalska VB, Volkova KD. Optimized Dyes for Protein and Nucleic Acid Detection. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Suh MS, Seo J, Thangadurai TD, Rhee YH, Shin SK, Yoon HJ. Aliphatic dipeptide tags for multi-2-plex protein quantification. Analyst 2011; 136:1614-9. [DOI: 10.1039/c0an00710b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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48
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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Hong Y, Feng C, Yu Y, Liu J, Lam JWY, Luo KQ, Tang BZ. Quantitation, visualization, and monitoring of conformational transitions of human serum albumin by a tetraphenylethene derivative with aggregation-induced emission characteristics. Anal Chem 2010; 82:7035-43. [PMID: 20704392 DOI: 10.1021/ac1018028] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human serum albumin (HSA) is a major protein component of blood plasma, and its assay is of obvious value to biological research. We, herein, present a readily accessible fluorescent bioprobe for HSA detection and quantitation. A nonemissive tetraphenylethene derivative named sodium 1,2-bis[4-(3-sulfonatopropoxyl)phenyl]-1,2-diphenylethene (BSPOTPE) is induced to emit by HSA, showing a novel phenomenon of aggregation-induced emission (AIE). The AIE bioprobe enjoys a broad working range (0-100 nM), a low detection limit (down to 1 nM), and a superior selectivity to albumins. The fluorescent bioassay is unperturbed by the miscellaneous bioelectrolytes in the artificial urine. The AIE luminogen can also be used as a rapid and sensitive protein stain in gel electrophoresis for HSA visualization. Utilizing the AIE feature of BSPOTPE and the Forster resonance energy transfer from HSA to BSPOTPE, the unfolding process of HSA induced by guanidine hydrochloride is monitored, which reveals a multistep transition with the involvement of molten globule intermediates. Computational modeling suggests that the AIE luminogens dock in the hydrophobic cleft between subdomains IIA and IIIA of HSA with the aid of hydrophobic effect, charge neutralization, and hydrogen bonding interactions, offering mechanistic insight into the microenvironment inside the hydrophobic cavity.
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Affiliation(s)
- Yuning Hong
- Nano Science and Technology Program, Department of Chemistry, Institute of Molecular Functional Materials, The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
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Wang X, Hwang SY, Cong WT, Jin LT, Choi JK. Promoted negative staining of proteins in SDS-PAGE using Eosin B compounded with magnesium chloride. Electrophoresis 2010; 31:3808-15. [DOI: 10.1002/elps.201000343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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