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Lomeli G, Herr AE. Reducing Cathodic Drift during Isoelectric Focusing Using Microscale Immobilized pH Gradient Gels. Anal Chem 2024; 96:8648-8656. [PMID: 38716690 PMCID: PMC11140684 DOI: 10.1021/acs.analchem.4c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Microfluidic analytical tools play an important role in miniaturizing targeted proteomic assays for improved detection sensitivity, throughput, and automation. Microfluidic isoelectric focusing (IEF) can resolve proteoforms in lysate from low-to-single cell numbers. However, IEF assays often use carrier ampholytes (CAs) to establish a pH gradient for protein separation, presenting limitations like pH instability in the form of cathodic drift (migration of focused proteins toward the cathode). Immobilized pH gradient (IPG) gels reduce cathodic drift by covalently immobilizing the pH buffering components to a matrix. To our knowledge, efforts to implement IPG gels at the microscale have been limited to glass microdevices. To adapt IEF using IPGs to widely used microfluidic device materials, we introduce a polydimethylsiloxane (PDMS)-based microfluidic device and compare the microscale pH gradient stability of IEF established with IPGs, CAs, and a hybrid formulation of IPG gels and CAs (mixed-bed IEF). The PDMS-based IPG microfluidic device (μIPG) resolved analytes differing by 0.1 isoelectric point within a 3.5 mm separation lane over a 20 min focusing duration. During the 20 min duration, we observed markedly different cathodic drift velocities among the three formulations: 60.1 μm/min in CA-IEF, 2.5 μm/min in IPG-IEF (∼24-fold reduction versus CA-IEF), and 1.4 μm/min in mixed-bed IEF (∼43-fold reduction versus CA-IEF). Lastly, mixed-bed IEF in a PDMS device resolved green fluorescent protein (GFP) proteoforms from GFP-expressing human breast cancer cell lysate, thus establishing stability in lysate from complex biospecimens. μIPG is a promising and stable technique for studying proteoforms from small volumes.
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Affiliation(s)
- Gabriela Lomeli
- The
UC Berkeley−UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Amy E. Herr
- The
UC Berkeley−UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
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2
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Stutz H. Advances and applications of electromigration methods in the analysis of therapeutic and diagnostic recombinant proteins – A Review. J Pharm Biomed Anal 2022; 222:115089. [DOI: 10.1016/j.jpba.2022.115089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/29/2022]
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3
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Salim APAA, Wang Y, Li S, Conte-Junior CA, Chen J, Zhu H, Rentfrow G, Suman SP. Sarcoplasmic Proteome Profile and Internal Color of Beef Longissimus Lumborum Steaks Cooked to Different Endpoint Temperatures. MEAT AND MUSCLE BIOLOGY 2020. [DOI: 10.22175/mmb.9470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The complex relationship between endpoint temperature, sarcoplasmic proteome, and internal color in cooked steaks is yet to be examined. The objective of the present study was to characterize the changes in sarcoplasmic proteome and their influence on the internal color of beef longissimus lumborum (LL) steaks cooked to different endpoint temperatures. Two 2.5-cm-thick LL steaks were fabricated from 9 beef strip loins and were cooked to an internal endpoint temperature of either 60°C (C-60) or 71°C (C-71). Cooked steaks were cooled and sliced parallel to the grilled surface, and internal color was evaluated instrumentally. Sarcoplasmic proteome from the interiors of the cooked steaks was analyzed using two-dimensional electrophoresis, and the gel images were digitally analyzed. The protein spots exhibiting more than 2-fold intensity differences (P < 0.05) were subjected to in-gel tryptic digestion and were identified by tandem mass spectrometry. The C-60 steaks demonstrated greater (P < 0.05) redness and color stability than the C-71 ones. Eleven differentially abundant protein spots were identified, and they belonged to 6 functional groups (transport proteins, enzymes in energy metabolism, chaperones, antioxidant proteins, enzymes in amino acid metabolism, and glycolytic enzymes). While 10 spots were overabundant (P < 0.05) in C-60 steaks, 1 spot was overabundant (P < 0.05) in C-71 steaks. The spot overabundant in C-71 samples was identified as myoglobin, suggesting the possible role of post-translational modifications in the heme protein’s thermal stability. The results indicated that the endpoint cooking temperature influenced sarcoplasmic proteome profile and internal color of cooked beef LL steaks. The overabundant proteins in steaks cooked to 60°C may be exploited as potential biomarkers for undercooked beef, which is a source for foodborne infections.
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Affiliation(s)
| | - Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | | | | | | | | | - Gregg Rentfrow
- University of Kentucky Department of Animal and Food Sciences
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4
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Hristova SH, Zhivkov AM. Isoelectric point of free and adsorbed cytochrome c determined by various methods. Colloids Surf B Biointerfaces 2019; 174:87-94. [DOI: 10.1016/j.colsurfb.2018.10.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/18/2018] [Accepted: 10/31/2018] [Indexed: 01/09/2023]
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Qian S, Yang Y, Li N, Cheng T, Wang X, Liu J, Li X, Desiderio DM, Zhan X. Prolactin Variants in Human Pituitaries and Pituitary Adenomas Identified With Two-Dimensional Gel Electrophoresis and Mass Spectrometry. Front Endocrinol (Lausanne) 2018; 9:468. [PMID: 30210449 PMCID: PMC6121189 DOI: 10.3389/fendo.2018.00468] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
Human prolactin (hPRL) plays multiple roles in growth, metabolism, development, reproduction, and immunoregulation, which is an important protein synthesized in a pituitary. Two-dimensional gel electrophoresis (2DE) is an effective method in identity of protein variants for in-depth insight into functions of that protein. 2DE, 2DE-based PRL-immunoblot, mass spectrometry, and bioinformatics were used to analyze hPRL variants in human normal (control; n = 8) pituitaries and in five subtypes of pituitary adenomas [NF- (n = 3)-, FSH+ (n = 3)-, LH+ (n = 3)-, FSH+/LH+ (n = 3)-, and PRL+ (n = 3)-adenomas]. Six hPRL variants were identified with different isoelectric point (pI)-relative molecular mass (Mr ) distribution on a 2DE pattern, including variants V1 (pI 6.1; 26.0 kDa), V2 (pI 6.3; 26.4 kDa), V3 (pI 6.3; 27.9 kDa), V4 (pI 6.5; 26.1 kDa), V5 (pI 6.8; 25.9 kDa), and V6 (pI 6.7; 25.9 kDa). Compared to controls, except for variants V2-V6 in PRL-adenomas, V2 in FSH+-adenomas, and V3 in NF--adenomas, the other PRL variants were significantly downregulated in each subtype of pituitary adenomas. Moreover, the pattern of those six PRL variants was significantly different among five subtypes of pituitary adenomas relative to control pituitaries. Different hPRL variants might be involved in different types of PRL receptor-signaling pathways in a given condition. Those findings clearly revealed the existence of six hPRL variants in human pituitaries, and the pattern changes of six hPRL variants among different subtypes of pituitary adenomas, which provide novel clues to further study the functions, and mechanisms of action, of hPRL in human pituitary and in PRL-related diseases, and the potential clinical value in pituitary adenomas.
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Affiliation(s)
- Shehua Qian
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Yongmei Yang
- Geriatric Department of Cadre's Ward, Baoji Traditional Chinese Medicine Hospital, Baoji, China
| | - Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
| | - Tingting Cheng
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaowei Wang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
| | - Jianping Liu
- Bio-Analytical Chemistry Research Laboratory, Modern Analytical Testing Center, Central South University, Changsha, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Dominic M. Desiderio
- The Charles B. Stout Neuroscience Mass Spectrometry Laboratory, Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, Changsha, China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, China
- The Laboratory of Medical Genetics, Central South University, Changsha, China
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6
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Vidanapathirana P, Hasan F, Mussio K, Pande A, Brands M, Siraj N, Grove A, Warner IM. Cationic ionic liquid surfactant-polyacrylamide gel electrophoresis for enhanced separation of acidic and basic proteins with single-step ribonuclease b glycoforms separation. J Chromatogr A 2017; 1515:245-251. [DOI: 10.1016/j.chroma.2017.07.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/26/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
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7
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Lai W, Wang Q, Li L, Hu Z, Chen J, Fang Q. Interaction of gold and silver nanoparticles with human plasma: Analysis of protein corona reveals specific binding patterns. Colloids Surf B Biointerfaces 2017; 152:317-325. [DOI: 10.1016/j.colsurfb.2017.01.037] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 01/03/2023]
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8
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Kristl T, Stutz H. Comparison of different mobilization strategies for capillary isoelectric focusing of ovalbumin variants†. J Sep Sci 2014; 38:148-56. [DOI: 10.1002/jssc.201400890] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Theresa Kristl
- Division of Chemistry and Bioanalytics; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - Hanno Stutz
- Division of Chemistry and Bioanalytics; Department of Molecular Biology; University of Salzburg; Salzburg Austria
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9
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Pitcher DS, de Mattos-Shipley K, Wang Z, Tzortzis K, Goudevenou K, Flynn H, Bohn G, Rahemtulla A, Roberts I, Snijders AP, Karadimitris A, Kleijnen MF. Nuclear proteasomes carry a constitutive posttranslational modification which derails SDS-PAGE (but not CTAB-PAGE). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2222-8. [PMID: 25192768 DOI: 10.1016/j.bbapap.2014.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/22/2014] [Accepted: 08/24/2014] [Indexed: 12/23/2022]
Abstract
We report that subunits of human nuclear proteasomes carry a previously unrecognised, constitutive posttranslational modification. Subunits with this modification are not visualised by SDS-PAGE, which is used in almost all denaturing protein gel electrophoresis. In contrast, CTAB-PAGE readily visualises such modified subunits. Thus, under most experimental conditions, with identical samples, SDS-PAGE yielded gel electrophoresis patterns for subunits of nuclear proteasomes which were misleading and strikingly different from those obtained with CTAB-PAGE. Initial analysis indicates a novel modification of a high negative charge with some similarity to polyADP-ribose, possibly explaining compatibility with (positively-charged) CTAB-PAGE but not (negatively-charged) SDS-PAGE and providing a mechanism for how nuclear proteasomes may interact with chromatin, DNA and other nuclear components.
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Affiliation(s)
- David S Pitcher
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Kate de Mattos-Shipley
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Ziming Wang
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Konstantinos Tzortzis
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Katerina Goudevenou
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Helen Flynn
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Potters Bar EN6 3LD, United Kingdom
| | - Georg Bohn
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Amin Rahemtulla
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Irene Roberts
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Ambrosius P Snijders
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Potters Bar EN6 3LD, United Kingdom
| | - Anastasios Karadimitris
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom
| | - Maurits F Kleijnen
- Centre for Haematology, Division of Experimental Medicine, Faculty of Medicine, Imperial College London, Hammersmith Campus, Commonwealth Building 4th Floor, Du Cane Road, London W12 0NN, United Kingdom.
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10
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Fíla J, Čapková V, Honys D. Phosphoproteomic studies in Arabidopsis and tobacco male gametophytes. Biochem Soc Trans 2014; 42:383-7. [PMID: 24646248 DOI: 10.1042/bst20130249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Mature pollen represents an extremely resistant quiescent structure surrounded by a tough cell wall. After its hydration on stigma papillary cells, pollen tube growth starts rapidly. Massive metabolic changes are likely to be accompanied by changes in protein phosphorylation. Protein phosphorylation belongs among the most rapid post-translational modifications. To date, only Arabidopsis thaliana and tobacco (Nicotiana tabacum) mature pollen have been subjected to phosphoproteomic studies in order to identify the phosphoproteins present. In the present mini-review, Arabidopsis and tobacco datasets were compared with each other. The representation of the O-phosphorylated amino acids was compared between these two datasets, and the putative pollen-specific or pollen-abundant phosphopeptides were highlighted. Finally, the phosphorylation sites common for both Arabidopsis and tobacco phosphoproteins are listed as well as the phosphorylation motifs identified.
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Affiliation(s)
| | - Věra Čapková
- *Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Praha 6, Czech Republic
| | - David Honys
- *Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, Praha 6, Czech Republic
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11
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Cavanagh AP, Kubien DS. Can phenotypic plasticity in Rubisco performance contribute to photosynthetic acclimation? PHOTOSYNTHESIS RESEARCH 2014; 119:203-214. [PMID: 23543330 DOI: 10.1007/s11120-013-9816-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 03/19/2013] [Indexed: 06/02/2023]
Abstract
Photosynthetic acclimation varies among species, which likely reveals variations at the biochemical level in the pathways that constitute carbon assimilation and energy transfer. Local adaptation and phenotypic plasticity affect the environmental response of photosynthesis. Phenotypic plasticity allows for a wide array of responses from a single individual, encouraging fitness in a broad variety of environments. Rubisco catalyses the first enzymatic step of photosynthesis, and is thus central to life on Earth. The enzyme is well conserved, but there is habitat-dependent variation in kinetic parameters, indicating that local adaptation may occur. Here, we review evidence suggesting that land plants can adjust Rubisco's intrinsic biochemical characteristics during acclimation. We show that this plasticity can theoretically improve CO2 assimilation; the effect is non-trivial, but small relative to other acclimation responses. We conclude by discussing possible mechanisms that could account for biochemical plasticity in land plant Rubisco.
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Affiliation(s)
- Amanda P Cavanagh
- Department of Biology, University of New Brunswick, 10 Bailey Dr., Fredericton, NB, Canada
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12
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Cong W, Zhao T, Zhu Z, Huang B, Ma W, Wang Y, Tan Y, Chakrabarti S, Li X, Jin L, Cai L. Metallothionein prevents cardiac pathological changes in diabetes by modulating nitration and inactivation of cardiac ATP synthase. J Nutr Biochem 2014; 25:463-74. [PMID: 24629910 DOI: 10.1016/j.jnutbio.2013.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/14/2013] [Accepted: 12/23/2013] [Indexed: 02/07/2023]
Abstract
Mitochondrial ATP production is the main energy source for the cell. Diabetes reduces the efficient generation of ATP, possibly due to the inactivation of ATP synthase. However, the exact mechanism by which diabetes induces inactivation of ATP synthase remains unknown, as well as whether such inactivation has a role in the development of pathological abnormalities of the diabetic heart. To address these issues, we used cardiac metallothionein-transgenic (MT-TG) and wild-type (WT) mice with streptozotocin-induced diabetes, since we have demonstrated previously that diabetes-induced cardiac damage and remodeling were found in WT diabetic mice, but not in MT-TG diabetic mice. Immunohistochemical and biochemical assays were used to compare pathological and biochemical changes of the heart between MT-TG and WT diabetic mice, and a proteomic assay to evaluate ATP synthase expression and tyrosine nitration, with its activity. LC/MS analysis revealed that diabetes increased tyrosine nitration of the ATP synthase α subunit at Tyr(271), Tyr(311), and Tyr(476), and the β subunit at Tyr(269) and Tyr(508), and also significantly reduced ATP synthase activity by ~32%. These changes were not observed in MT-TG diabetic mice. Furthermore, parallel experiments with induced expression of cardiac MT by zinc supplementation in diabetic mice produced similar effects. These results suggest that MT can preserve ATP synthase activity in streptozotocin-induced diabetes, probably through the inhibition of ATP synthase nitration.
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Affiliation(s)
- Weitao Cong
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Ting Zhao
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Zhongxin Zhu
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Binbin Huang
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Weide Ma
- Laboratory of Gynecology and Obstetrics, People's Hospital of Wenzhou, Zhejiang, P.R. China
| | - Yuehui Wang
- Department of Geriatric Medicine, The First Hospital of Jilin University, Changchun, P.R. China
| | - Yi Tan
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; Kosair Children's Hospital Research Institute (KCHRI), Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Subrata Chakrabarti
- Department of Pathology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Xiaokun Li
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Litai Jin
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China.
| | - Lu Cai
- Chinese-American Research Institute for Diabetic Complications, Wenzhou Medical University, Zhejiang, P.R. China; Kosair Children's Hospital Research Institute (KCHRI), Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY, USA.
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13
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Carabajal M, Kellner H, Levin L, Jehmlich N, Hofrichter M, Ullrich R. The secretome of Trametes versicolor grown on tomato juice medium and purification of the secreted oxidoreductases including a versatile peroxidase. J Biotechnol 2013; 168:15-23. [DOI: 10.1016/j.jbiotec.2013.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
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Abstract
During apoptosis, Bak and Bax permeabilize the mitochondrial outer membrane by undergoing major conformational change and oligomerization. This activation process in Bak is reported to require dephosphorylation of tyrosine-108 close to an activation trigger site. To investigate how dephosphorylation of Bak contributes to its activation and conformational change, one-dimensional isoelectric focusing (1D-IEF) and mutagenesis was used to monitor Bak phosphorylation. On 1D-IEF, Bak extracted from a range of cell types migrated as a single band near the predicted isoelectric point of 5.6 both before and after phosphatase treatment, indicating that Bak is not significantly phosphorylated at any residue. In contrast, three engineered ‘phosphotagged' Bak variants showed a second band at lower pI, indicating phosphorylation. Apoptosis induced by several stimuli failed to alter Bak pI, indicating little change in phosphorylation status. In addition, alanine substitution of tyrosine-108 and other putative phosphorylation sites failed to enhance Bak activation or pro-apoptotic function. In summary, Bak is not significantly phosphorylated at any residue, and Bak activation during apoptosis does not require dephosphorylation.
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15
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Wagner M, Reiche K, Blume A, Garidel P. The electrokinetic potential of therapeutic proteins and its modulation: Impact on protein stability. Colloids Surf A Physicochem Eng Asp 2012. [DOI: 10.1016/j.colsurfa.2012.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Heukeshoven J, März A, Warnecke G, Deppert W, Tolstonog GV. Recombinant p53 displays heterogeneity during isoelectric focusing. Electrophoresis 2012; 33:2818-27. [DOI: 10.1002/elps.201200205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jochen Heukeshoven
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Annette März
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Gabriele Warnecke
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Wolfgang Deppert
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Genrich V. Tolstonog
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
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17
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Eberini I, Sensi C, Bovi M, Molinari H, Galliano M, Bonomi F, Iametti S, Gianazza E. Wards in the keyway: amino acids with anomalous pK(a)s in calycins. Amino Acids 2012; 43:2457-68. [PMID: 22643844 DOI: 10.1007/s00726-012-1324-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/15/2012] [Indexed: 11/24/2022]
Abstract
As a follow-up to our recent analysis of the electrostatics of bovine β-lactoglobulin (Eberini et al. in Amino Acids 42:2019-2030, 2011), we investigated whether the occurrence in the native structure of calycins-the superfamily to which β-lactoglobulin belongs-of amino acids with anomalous pK (a)s is an infrequent or, on the contrary, a common occurrence, and whether or not a general pattern may be recognized. To this aim, we randomly selected four calycins we had either purified from natural sources or prepared with recombinant DNA technologies during our previous and current structural and functional studies on this family. Their pIs vary over several pH units and their known functions are as diverse as carriers, enzymes, immunomodulators and/or extracellular chaperones. In our survey, we used both in silico prediction methods and in vitro procedures, such as isoelectric focusing, electrophoretic titration curves and spectroscopic techniques. By comparing the results under native conditions (no exposure of the proteins to chaotropic agents) to those after protein unfolding (in the presence of 8 M urea), a shift is observed in the pK (a) of at least one amino acid per protein, which results in a measurable change in pI. Three types of amino acids are involved: Cys, Glu, and His, their position varies along the calycin sequence. Although no common mechanism may thus be recognized, we hypothesize that the 'normalization' of anomalous pK (a)s may be the phenomenon that accompanies, and favors, structural rearrangements such as those involved in ligand binding by these proteins. An interesting, if anecdotal, validation to this view comes from the behavior of human retinol binding protein, for which the pI of the folded and liganded protein is intermediate between those of the folded and unliganded and of the unfolded protein forms. Likewise, both solid (from crystallography) and solution state (from CD spectroscopy) data confirm that the protein undergoes structural rearrangement upon retinol binding.
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Affiliation(s)
- Ivano Eberini
- Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, via Giuseppe Balzaretti 9, 20133, Milan, Italy
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18
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Coulonval K, Kooken H, Roger PP. Coupling of T161 and T14 phosphorylations protects cyclin B-CDK1 from premature activation. Mol Biol Cell 2011; 22:3971-85. [PMID: 21900495 PMCID: PMC3204060 DOI: 10.1091/mbc.e11-02-0136] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 08/19/2011] [Accepted: 09/01/2011] [Indexed: 01/26/2023] Open
Abstract
Mitosis is triggered by the abrupt dephosphorylation of inhibitory Y15 and T14 residues of cyclin B1-bound cyclin-dependent kinase (CDK)1 that is also phosphorylated at T161 in its activation loop. The sequence of events leading to the accumulation of fully phosphorylated cyclin B1-CDK1 complexes remains unclear. Two-dimensional gel electrophoresis allowed us to determine whether T14, Y15, and T161 phosphorylations occur on same CDK1 molecules and to characterize the physiological occurrence of their seven phosphorylation combinations. Intriguingly, in cyclin B1-CDK1, the activating T161 phosphorylation never occurred without the T14 phosphorylation. This strict association could not be uncoupled by a substantial reduction of T14 phosphorylation in response to Myt1 knockdown, suggesting some causal relationship. However, T14 phosphorylation was not directly required for T161 phosphorylation, because Myt1 knockdown did uncouple these phosphorylations when leptomycin B prevented cyclin B1-CDK1 complexes from accumulating in cytoplasm. The coupling mechanism therefore depended on unperturbed cyclin B1-CDK1 traffic. The unexpected observation that the activating phosphorylation of cyclin B1-CDK1 was tightly coupled to its T14 phosphorylation, but not Y15 phosphorylation, suggests a mechanism that prevents premature activation by constitutively active CDK-activating kinase. This explained the opposite effects of reduced expression of Myt1 and Wee1, with only the latter inducing catastrophic mitoses.
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Affiliation(s)
- Katia Coulonval
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Campus Erasme, B-1070 Brussels, Belgium
| | - Hugues Kooken
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Campus Erasme, B-1070 Brussels, Belgium
| | - Pierre P. Roger
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Campus Erasme, B-1070 Brussels, Belgium
- WELBIO
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Krishnan HB, Natarajan SS, Kim WS. Distinct cell surface appendages produced by Sinorhizobium fredii USDA257 and S. fredii USDA191, cultivar-specific and nonspecific symbionts of soybean. Appl Environ Microbiol 2011; 77:6240-8. [PMID: 21764962 PMCID: PMC3165413 DOI: 10.1128/aem.05366-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/05/2011] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium fredii USDA257 and S. fredii USDA191 are fast-growing rhizobia that form nitrogen-fixing nodules on soybean roots. In contrast to USDA191, USDA257 exhibits cultivar specificity and can form nodules only on primitive soybean cultivars. In response to flavonoids released from soybean roots, these two rhizobia secrete nodulation outer proteins (Nop) to the extracellular milieu through a type III secretion system. In spite of the fact that Nops are known to regulate legume nodulation in a host-specific manner, very little is known about the differences in the compositions of Nops and surface appendages elaborated by USDA191 and USDA257. In this study we compared the Nop profiles of USDA191 and USDA257 by one-dimensional (1D) and 2D gel electrophoresis and identified several of these proteins by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem MS (LC-MS/MS). Examination of the surface appendages elaborated by these two strains of soybean symbionts by transmission electron microscopy revealed distinct differences in their morphologies. Even though the flagella produced by USDA191 and USDA257 were similar in their morphologies, they differed in their flagellin composition. USDA257 pili resembled long thin filaments, while USDA191 pili were short, rod shaped, and much thinner than the flagella. 2D gel electrophoresis of pilus-like appendages of USDA191 and USDA257 followed by mass spectrometry resulted in the identification of several of the Nops along with some proteins previously undetected in these strains. Some of the newly identified proteins show homology to putative zinc protease and a LabA-like protein from Bradyrhizobium sp. ORS278, fimbrial type 4 assembly proteins from Ralstonia solanacearum, and the type III effector Hrp-dependent protein from Rhizobium leguminosarum bv. trifolii.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, USDA ARS, 108 Curtis Hall, University of Missouri, Columbia, MO 65211, USA.
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20
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Zeng Z, Hincapie M, Pitteri SJ, Hanash S, Schalkwijk J, Hogan JM, Wang H, Hancock WS. A proteomics platform combining depletion, multi-lectin affinity chromatography (M-LAC), and isoelectric focusing to study the breast cancer proteome. Anal Chem 2011; 83:4845-54. [PMID: 21513341 PMCID: PMC3148019 DOI: 10.1021/ac2002802] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The discovery of breast cancer associated plasma/serum biomarkers is important for early diagnosis, disease mechanism elucidation, and determination of treatment strategy for the disease. In this study of serum samples, a multidimensional fractionation platform combined with mass spectrometric analysis were used to achieve the identification of medium to lower abundance proteins, as well as to simultaneously detect glycan and abundance changes. Immuno-affinity depletion and multi-lectin chromatography (M-LAC) were integrated into an automated HPLC platform to remove high abundance protein and fractionate glycoproteins. The collected glycoproteomes were then subjected to isoelectric focusing (IEF) separation by a digital ProteomeChip (dPC), followed by in-gel digestion and LC-MS analysis using an Orbitrap mass spectrometer. As a result, the total number of identified proteins increased significantly when the IEF fractionation step was included as part of the platform. Relevant proteins with biological and disease significance were observed and the dynamic range of the serum proteome measurement was extended. In addition, potential glycan changes were indicated by comparing proteins in control and cancer samples in terms of their affinity to the multi-lectin column (M-LAC) and the pI profiles in IEF separation. In conclusion, a proteomics platform including high abundance protein depletion, lectin affinity fractionation, IEF separation, and LC-MS analysis has been applied to discover breast cancer-associated proteins. The following candidates, thrombospondin-1 and 5, alpha-1B-glycoprotein, serum amyloid P-component, and tenascin-X, were selected as promising examples of the use of this platform. They show potential abundance and glycan changes and will be further investigated in future studies.
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Affiliation(s)
- Zhi Zeng
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, Massachusetts, USA
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21
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Zigo M, Jonáková V, Maňásková-Postlerová P. Electrophoretic and zymographic characterization of proteins isolated by various extraction methods from ejaculated and capacitated boar sperms. Electrophoresis 2011; 32:1309-18. [DOI: 10.1002/elps.201000558] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 01/10/2011] [Accepted: 01/10/2011] [Indexed: 11/06/2022]
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22
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23
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Barrabés S, Sarrats A, Fort E, De Llorens R, Rudd PM, Peracaula R. Effect of sialic acid content on glycoprotein pI analyzed by two-dimensional electrophoresis. Electrophoresis 2010; 31:2903-12. [DOI: 10.1002/elps.200900764] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Witzmann FA, Richardson MR. Two-dimensional gels for toxicological drug discovery applications. Expert Opin Drug Metab Toxicol 2009; 2:103-11. [PMID: 16863472 DOI: 10.1517/17425255.2.1.103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Two-dimensional gel electrophoresis (2DGE) continues to be a useful approach to study protein expression. Although liquid chromatographic and mass spectrometric approaches that overcome some of the limitations and labour intensity of 2DGE are increasingly popular, this electrophoretic approach still has exceptional relevance in toxicology. Despite the technical challenges, pharmacologists/toxicologists continue to use gel-based proteomics to assess the biological and health effects of chemical treatment and exposure. This brief review addresses the use of 2DGE-based proteomics in drug development and toxicology, emphasising its unique strengths and weaknesses, and considers recent developments in this strategy that have evolved to directly confront the issues of dynamic range and reproducibility that have previously limited the overall use of 2D electrophoresis.
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Affiliation(s)
- Frank A Witzmann
- Indiana University School of Medicine, Department of Cellular & Integrative Physiology, Biotechnology & Research Training Center, Indianapolis, IN 46202, USA.
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25
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Rithidech KN, Honikel L, Rieger R, Xie W, Rithidech KN, Honikel L, Rieger R, Xie W, Fischer T, Simon SR. Protein-expression profiles in mouse blood-plasma following acute whole-body exposure to137Cs γ rays. Int J Radiat Biol 2009; 85:432-47. [DOI: 10.1080/09553000902820390] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Nadai M, Bally J, Vitel M, Job C, Tissot G, Botterman J, Dubald M. High-level expression of active human alpha1-antitrypsin in transgenic tobacco chloroplasts. Transgenic Res 2009; 18:173-83. [PMID: 18686007 DOI: 10.1007/s11248-008-9209-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 07/04/2008] [Indexed: 11/26/2022]
Abstract
We have produced human alpha1-antitrypsin (A1AT), a major therapeutic protein, in genetically engineered tobacco plastids. Four different expression vectors have been evaluated which encode A1AT under the control of various 5' and 3' plastid expression elements. The use of heterologous promoter and terminator sequences derived from the corn and soybean plastid genomes leads to simpler and predictable recombinant genome patterns, avoiding unwanted recombination products between introduced and resident tobacco sequences. High level expression of unglycosylated A1AT, representing up to 2% of total soluble proteins, has been measured in leaves of transgenic tobacco lines. Some heterogeneity in the recombinant A1AT is detected after 2D protein separation, but the chloroplast-made protease inhibitors are fully active and bind to porcine pancreatic elastase.
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Affiliation(s)
- M Nadai
- Bayer BioScience, 14-20 Rue Pierre Baizet, BP 9163, 69263, Lyon cedex 09, France
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28
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Bally J, Paget E, Droux M, Job C, Job D, Dubald M. Both the stroma and thylakoid lumen of tobacco chloroplasts are competent for the formation of disulphide bonds in recombinant proteins. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:46-61. [PMID: 17944820 DOI: 10.1111/j.1467-7652.2007.00298.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Plant chloroplasts are promising vehicles for recombinant protein production, but the process of protein folding in these organelles is not well understood in comparison with that in prokaryotic systems, such as Escherichia coli. This is particularly true for disulphide bond formation which is crucial for the biological activity of many therapeutic proteins. We have investigated the capacity of tobacco (Nicotiana tabacum) chloroplasts to efficiently form disulphide bonds in proteins by expressing in this plant cell organelle a well-known bacterial enzyme, alkaline phosphatase, whose activity and stability strictly depend on the correct formation of two intramolecular disulphide bonds. Plastid transformants have been generated that express either the mature enzyme, localized in the stroma, or the full-length coding region, including its signal peptide. The latter has the potential to direct the recombinant alkaline phosphatase into the lumen of thylakoids, giving access to this even less well-characterized organellar compartment. We show that the chloroplast stroma supports the formation of an active enzyme, unlike a normal bacterial cytosol. Sorting of alkaline phosphatase to the thylakoid lumen occurs in the plastid transformants translating the full-length coding region, and leads to larger amounts and more active enzyme. These results are compared with those obtained in bacteria. The implications of these findings on protein folding properties and competency of chloroplasts for disulphide bond formation are discussed.
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Affiliation(s)
- Julia Bally
- Bayer BioScience, F-69263 Lyon cedex 09, France
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30
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Kronsteiner B, Malissa H, Stutz H. Profiling recombinant major birch pollen allergen Bet v 1a and carbamylated variants with CZE and CIEF. Electrophoresis 2007; 28:2241-51. [PMID: 17538926 DOI: 10.1002/elps.200600764] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A preparation of recombinant birch pollen allergen of Betula verrucosa isoform 1a (Bet v 1a) containing chemically modified (carbamylated) variants has been analyzed by CZE and CIEF. In CZE, employing a 100 mmol/L MES buffer at pH 6.50, with 0.4 mmol/L tetraethylenepentamine (TEPA) added, allowed for the resolution of 17 protein fractions. The CIEF profiling of the allergen preparation required a combination of a wide-pH-range carrier ampholyte (CA) of pH 3-10 with two narrow-range CAs of pH 5-6 and 5-7. For CIEF, 91 mmol/L of glycine at pH 2.12 and 20 mmol/L of CHES at pH 10.00 were applied as anolyte and catholyte, respectively. The generated pH gradient was nonlinear with a flat slope for pH 4-6, thus providing an improved resolution. In CIEF, up to 18 protein fractions were distinguished as well. The pI of the target allergen Bet v 1a was 4.9 as determined by means of two pI marker compounds flanking the allergen. Relative purity of the target allergen within the preparation containing carbamylated variants was in accordance for both separation systems and varied between 40.7 and 42.8%.
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Affiliation(s)
- Barbara Kronsteiner
- Division of Chemistry, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
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31
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John JPP, Chen WQ, Pollak A, Lubec G. Mass Spectrometric Studies on Mouse Hippocampal Synapsins Ia, IIa, and IIb and Identification of a Novel Phosphorylation Site at Serine-546. J Proteome Res 2007; 6:2695-710. [PMID: 17579389 DOI: 10.1021/pr070157r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synapsins are key phosphoproteins in the mammalian brain, and structural research on synapsins is still holding center stage. Proteins were extracted from hippocampal tissue and separated on two-dimensional gel electrophoresis (2-DE), and the spots were analyzed by MALDI-TOF-TOF and nano-LC-ESI-MS/MS. Synapsins Ia, IIa, and IIb were unambiguously identified and represented by 15 individual spots on 2-DE. Several serine phosphorylation sites were confirmed, and a novel phosphorylation site was observed at Ser-546 in synapsin IIa in all gels analyzed.
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Affiliation(s)
- Julius Paul Pradeep John
- Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18, 1090 Vienna, Austria
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32
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Hung CW, Kübler D, Lehmann WD. pI-based phosphopeptide enrichment combined with nanoESI-MS. Electrophoresis 2007; 28:2044-52. [PMID: 17523138 DOI: 10.1002/elps.200600678] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
IEF is introduced as a new principle for enrichment and separation of phosphopeptides as obtained after digestion of phosphoproteins by trypsin. Tryptic peptides and phosphopeptides exhibit pI values, which overlap in the range of about 4-6. However, after methyl esterification of all carboxyl functions, the pI values of tryptic peptides and phosphopeptides regroup in discrete clusters. In addition, mono- and diphosphorylated peptides show different but very homogeneous pI values, with variations when internal Arg, Lys, or His residues are present. Experimentally, this new concept was applied for separation of model peptides on IPG strips pH 3-10 as used in the first dimension of 2-DE. After IEF of methyl-esterified peptides, the IPG strip was cut into pieces followed by peptide extraction, desalting and MS analysis by nanoESI-MS. Phosphopeptides were found to focus in good agreement with their calculated pI values. This analytical strategy showed a resolution of about 0.2 pI units, and thus turned out to be capable of detecting minor differences in pI values, such as those occurring between pSer, pThr and pTyr residues. Using IPG strips with a pI range of 3-10, methyl esterified nonphosphorylated tryptic peptides are concentrated in the basic part of the IPG strip or even leave the strip. Thus, efficient enrichment of phosphopeptides and their subfractionation according to pI is obtained in one step. Minor hydrolytic side reactions including deamidation of Asn and partial hydrolysis of methyl esters are observed. The results show that IEF opens attractive avenues for the further advancement of analytical phosphoproteomics.
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Affiliation(s)
- Chien-Wen Hung
- Central Spectroscopy, German Cancer Research Center, Heidelberg, Germany
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Süss C, Hempel J, Zehner S, Krause A, Patschkowski T, Göttfert M. Identification of genistein-inducible and type III-secreted proteins of Bradyrhizobium japonicum. J Biotechnol 2006; 126:69-77. [PMID: 16707185 DOI: 10.1016/j.jbiotec.2006.03.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 02/07/2006] [Accepted: 03/29/2006] [Indexed: 10/24/2022]
Abstract
Flagellin is the bulk protein secreted by Bradyrhizobium japonicum. For easier identification of minor protein fractions, the flagellin genes bll6865 and bll6866 were deleted. Extracellular proteins of the corresponding mutant were purified and separated by 2D gel electrophoresis. Several of the protein spots were detectable only after addition of genistein to the growth medium-genistein is an isoflavone secreted by soybean that activates the expression of genes encoding a type III secretion system. These secreted proteins were not present in supernatants of mutants in which conserved genes of the type III secretion system or the regulatory gene ttsI, which is essential for activation of the type III secretion system, are deleted. Out of 22 genistein-inducible protein spots 8 different proteins could be identified by mass spectrometry. One of the proteins, Blr1752, has similarity to NopP of Rhizobium sp. strain NGR234 that is known to be secreted. Another protein is Blr1656 (GunA2) that was shown previously to have endoglucanase activity. Three proteins have similarity to subunits of the flagellar apparatus. Some proteins appeared in several separate spots indicating posttranslational modification. A conserved tts box motif was found in the putative promoter region of six genes encoding secreted proteins.
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Affiliation(s)
- Christin Süss
- Institut für Genetik, Technische Universität Dresden, Helmholtzstrasse 10, 01069 Dresden, Germany
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34
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Moreira PR, Duez C, Dehareng D, Antunes A, Almeida-Vara E, Frère JM, Malcata FX, Duarte JC. Molecular characterisation of a versatile peroxidase from a Bjerkandera strain. J Biotechnol 2005; 118:339-52. [PMID: 16026883 DOI: 10.1016/j.jbiotec.2005.05.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 05/02/2005] [Accepted: 05/12/2005] [Indexed: 11/25/2022]
Abstract
The cloning and sequencing of the rbpa gene coding for a versatile peroxidase from a novel Bjerkandera strain is hereby reported. The 1777 bp isolated fragment contained a 1698 bp peroxidase-encoding gene, interrupted by 11 introns. The 367 amino acid-deduced sequence includes a 27 amino acid-signal peptide. The molecular model, built via homology modelling with crystal structures of four fungal peroxidases, highlighted the amino acid residues putatively involved in manganese binding and aromatic substrate oxidation. The potential heme pocket residues (R44, F47, H48, E79, N85, H177, F194 and D239) include both distal and proximal histidines (H48 and H177). RBP possesses potential calcium-binding residues (D49, G67, D69, S71, S178, D195, T197, I200 and D202) and eight cysteine residues (C3, C15, C16, C35, C121, C250, C286, C316). In addition, RBP includes residues involved in substrate oxidation: three acidic residues (E37, E41 and D183)--putatively involved in manganese binding and H83 and W172--potentially involved in oxidation of aromatic substrates. Characterisation of nucleotide and amino acid sequences include RBP in versatile peroxidase group sharing catalytic properties of both LiP and MnP. In addition, the RBP enzyme appears to be closely related with the ligninolytic peroxidases from the Trametes versicolor strain.
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Affiliation(s)
- Patrícia R Moreira
- Departamento de Biotecnologia, Instituto Nacional de Engenharia, Tecnologia e Inovação (INETI), Est. Paço do Lumiar, 22, P-1649-038 Lisboa, Portugal
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35
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Zhan X, Giorgianni F, Desiderio DM. Proteomics analysis of growth hormone isoforms in the human pituitary. Proteomics 2005; 5:1228-41. [PMID: 15717326 DOI: 10.1002/pmic.200400987] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In order to elucidate the roles of human growth hormone (hGH) in the normal (control) pituitary and in adenomas, the hGH isoforms in the human pituitary were analyzed with two-dimensional gel electrophoresis, immobilized metal affinity column (Ga(+3)) chromatography, mass spectrometry (MS), and bioinformatics. Twenty-four hGH-containing proteins, with significantly different expression proportions of their isoforms were found. The proportions of isoforms were as follows: isoform 1 (87.5%) > isoform 2 (8.1%) > isoform 3 (3.3%) > isoform 4 (1.1%). Deamidation of asparagine to aspartate was identified with matrix-assisted laser desorption/ionization-time of flight MS. Tandem mass spectrometry data demonstrated that hGH is a phosphoprotein (spot 6); phosphorylation was found at Ser-77 in the tryptic peptide (68)YSFLQNPQTSLCFSESIPTPSNR(90), at Ser-176 in the tryptic peptide (172)FDTNSHNDDALLK(184), and at Ser-132 in the peptide (126)SLVYGASDSNVYDLLK(141). The phosphorylation sites at Ser-77 and Ser-176 were consistent with computer-program predictions (NetPhos). These results provide novel clues for further studies of the functions, and mechanisms of action, of hGH in the human pituitary and in growth hormone-related diseases.
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Affiliation(s)
- Xianquan Zhan
- Charles B. Stout Neuroscience Mass Spectrometry Laboratory, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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36
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Righetti PG. Determination of the isoelectric point of proteins by capillary isoelectric focusing. J Chromatogr A 2004; 1037:491-9. [PMID: 15214685 DOI: 10.1016/j.chroma.2003.11.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Different ways of determining isoelectric points (pI) of proteins in capillary isoelectric focusing are reviewed here. Due to the impossibility of direct pH measurements in the liquid phase, such assessments have to rely on the use of pI markers. Different types of pI markers have been described: dyes, fluorescently labelled peptides, sets of proteins of known pI values. It appears that, perhaps, the best system is a set of 16 synthetic peptides, trimers to hexamers, made to contain each a Trp residue for easy detection at 280 nm. By a careful blend of acidic (Asp, Glu), mildly basic, with pK around neutrality (His), and basic (Lys, Arg) amino acids, it is possible to obtain a series of pI markers with pI values quite evenly distributed along the pH scale, possessing good buffering capacity and conductivity around their pI values and thus focusing as sharp peaks. Another approach to pI determination is the monitoring of the current during mobilization: this allows, with the aid of known pI markers, to calibrate the system with a pI/current graph. Pitfalls and common errors in pI determinations are reviewed here and guidelines given for minimizing such errors in pI estimation.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Agricultural and Industrial Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy.
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37
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Liu Z, Pawliszyn J. Capillary Isoelectric Focusing with Laser-Induced Fluorescence Whole Column Imaging Detection as a Tool To Monitor Reactions of Proteins. J Proteome Res 2004; 3:567-71. [PMID: 15253438 DOI: 10.1021/pr034114w] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Capillary isoelectric focusing (CIEF) with laser-induced fluorescence (LIF) whole column imaging detection (WCID) has the characteristics of high resolution, high speed and high sensitivity for separation of amphoteric biomolecules. These features enable a CIEF-LIF-WCID system to monitor the dynamic process of a protein reaction. The reaction can be a physical change or a chemical reaction, provided that the kinetics of the reaction is slower than the focusing speed or that the intermediates involved have long enough life-span compared to the analysis time. The processes of denaturation (a physical reaction), reduction and carbamylation (both chemical reactions) were dynamically monitored. The CIEF profiles at successive reaction times clearly displayed the formation of different products at different stages. At incomplete denaturation, intermediates with higher apparent pI values relative to the products at complete denaturation were detected. Carbamylation products of a protein were detected when the protein reacted with a urea solution that had prepared three months earlier, exhibiting gradually decreased pI values. Mechanisms involved in these reactions were rationalized. A combined mechanism of denaturation and reduction was suggested to explain the denaturing process under high concentrations of urea. Potential applications and critical factors to manipulate these reactions were also discussed.
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Affiliation(s)
- Zhen Liu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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Kohli E, Gaspari M, Raj HG, Parmar VS, Sharma SK, van der Greef J, Kumari R, Gupta G, Khurana P, Tyagi YK, Watterson AC, Olsen CE. Acetoxy drug: protein transacetylase of buffalo liver—characterization and mass spectrometry of the acetylated protein product. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1698:55-66. [PMID: 15063315 DOI: 10.1016/j.bbapap.2003.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2003] [Revised: 09/29/2003] [Accepted: 10/14/2003] [Indexed: 02/02/2023]
Abstract
The purification and characterization of the buffalo liver microsomal transacetylase (TAase) catalyzing the transfer of acetyl groups from a model acetoxy drug: 7,8-diacetoxy-4-methylcoumarin (DAMC) to GST3-3 has been described here. The enzyme was routinely assayed using DAMC and cytosolic GST as the substrates and was partially purified from microsomes of the buffalo liver. The enzyme was found to have approximate molecular of weight 65 kDa. The action of TAase and DAMC on liver cytosolic GST resulted in the formation of monoacetoxymonohydroxy-4-methylcoumarin (MAMHC) and 7,8-dihydroxy-4-methylcoumarin (DHMC), although the former was the major metabolite. The buffalo liver microsomal TAase exhibited hyperbolic kinetics and yielded K(m) (1667 microM) and V(max) (192 units) when the concentration of DAMC was varied keeping the concentration of GST constant. After having characterized the nature of the substrates and a product of the TAase-catalyzed reaction, we set out to identify the acetylated protein which is another product of the reaction. GST3-3 was used as a model protein substrate for the action of TAase using DAMC as the acetyl donor. The subunit of control and modified GST3-3 were separated by SDS-polyacrylamide gel electrophoresis (PAGE) and digested with trypsin. The tryptic peptides were extracted from the gel pieces and analyzed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOFMS). The data search for calibrated and labeled mass peaks of peptides was performed on the Matrix Science Server using the search engine Mascot. The peptide maps so obtained covered 97% of the GST3-3 sequence. On comparison of MALDI peptide maps of modified and control GST, seven new peaks were recognized corresponding to the potentially acetylated peptides in peptide map. The mass value of each of them was 42 Da higher than the theoretical mass of a non-modified GST3-3 tryptic peptide, strongly suggesting acetylation. By examining the fragmentation patterns and by comparing experimental and predicted values for MS/MS daughter ions, the identity of the seven acetylated GST tryptic peptides could be confirmed by the application of LC/MS/MS. In the modified GST, N-terminal proline and six lysines (Lys(51), Lys(82), Lys(123), Lsy(181), Lys(191) and Lys(210)) were found to be acetylated. The structure of acetylated GST revealed that the lysines that underwent acetylation were peripheral in positions.
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Affiliation(s)
- Ekta Kohli
- Department of Biochemistry, V.P. Chest Institute, University of Delhi, Delhi 110 007, India
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Tang HY, Speicher DW. In Vivo Phosphorylation of Human Erythrocyte Spectrin Occurs in a Sequential Manner. Biochemistry 2004; 43:4251-62. [PMID: 15065869 DOI: 10.1021/bi036092x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spectrin is the major component of the erythrocyte membrane skeleton and exists as a 526 kDa alphabeta heterodimer. The 246 kDa beta-chain of human spectrin is phosphorylated near the C-terminus, but the exact phosphorylation sites are unknown and the role of this phosphorylation is not fully characterized. In this study, we produced a monoclonal antibody, Sp316, capable of recognizing the C-terminal region of beta-spectrin regardless of its phosphorylation state and used it to purify the phosphorylated region after 2-nitro-5-thiocyanobenzoic acid cleavage of spectrin. Two-dimensional gels, mass spectrometry, and reversed-phase high-performance liquid chromatography were used to characterize these phosphorylation states. Only about 1.5% of spectrin isolated from fresh blood is unphosphorylated, about 9% has more than four phosphates per molecule, and the majority of the protein has one to four phosphates per molecule. A total of six phosphorylation sites were identified by tandem mass spectrometry. Quantitative analysis of the phosphorylation states by reversed-phase high-performance liquid chromatography revealed that phosphorylation of beta-spectrin occurs in a sequential manner where each specific site is completely phosphorylated before the next site is modified. The first phosphorylation event occurs on Ser-2114, followed by Ser-2125, Ser-2123, Ser-2128, Ser-2117, and Thr-2110. The identification of the specific phosphorylated beta-spectrin residues and the ordered sequence of phosphorylation events in vivo should provide an invaluable basis for further studies of the role of these posttranslational modifications in spectrin function in situ.
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Affiliation(s)
- Hsin-Yao Tang
- The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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40
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Ikezono T, Shindo S, Li L, Omori A, Ichinose S, Watanabe A, Kobayashi T, Pawankar R, Yagi T. Identification of a novel Cochlin isoform in the perilymph: insights to Cochlin function and the pathogenesis of DFNA9. Biochem Biophys Res Commun 2004; 314:440-6. [PMID: 14733925 DOI: 10.1016/j.bbrc.2003.12.106] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The COCH gene mutated in DFNA9, an autosomal dominant hereditary sensorineural hearing loss and vestibular disorder, encodes Cochlin. Previously, we reported three bovine Cochlin isoforms, p63s, p44s, and p40s, which exhibit significant molecular heterogeneity in vivo. Here we have characterized Cochlin isoforms by generating four isoform-specific anti-Cochlin antibodies. The same three Cochlin isoforms, p63s, p44s, and p40s, were detected in human and cow inner ear tissue; however, p44s and p40s were not detected in perilymph. We identified a novel short 16kDa isoform in human perilymph and a 18-23kDa isoform in cow perilymph, named Cochlin-tomoprotein (CTP), corresponding to the N-terminus of full-length Cochlin (p63s) and the LCCL domain. Notably, CTP contains all of the known mutation sites associated with DFNA9. The pathogenesis of DFNA9 is not fully clarified as yet, and this novel perilymph-associated CTP isoform might provide mechanistic clues to how mutations in the COCH gene damage the inner ear function.
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Affiliation(s)
- Tetsuo Ikezono
- Department of Otorhinolaryngology, Nippon Medical School, Tokyo, Japan.
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41
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Volkin DB, Sanyal G, Burke CJ, Middaugh CR. Preformulation studies as an essential guide to formulation development and manufacture of protein pharmaceuticals. PHARMACEUTICAL BIOTECHNOLOGY 2004; 14:1-46. [PMID: 12189723 DOI: 10.1007/978-1-4615-0549-5_1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- David B Volkin
- Department of Vaccine Pharmaceutical Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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42
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Coulonval K, Bockstaele L, Paternot S, Roger PP. Phosphorylations of cyclin-dependent kinase 2 revisited using two-dimensional gel electrophoresis. J Biol Chem 2003; 278:52052-60. [PMID: 14551212 DOI: 10.1074/jbc.m307012200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To control the G1/S transition and the progression through the S phase, the activation of the cyclin-dependent kinase (CDK) 2 involves the binding of cyclin E then cyclin A, the activating Thr-160 phosphorylation within the T-loop by CDK-activating kinase (CAK), inhibitory phosphorylations within the ATP binding region at Tyr-15 and Thr-14, dephosphorylation of these sites by cdc25A, and release from Cip/Kip family (p27kip1 and p21cip1) CDK inhibitors. To re-assess the precise relationship between the different phosphorylations of CDK2, and the influence of cyclins and CDK inhibitors upon them, we introduce here the use of the high resolution power of two-dimensional gel electrophoresis, combined to Tyr-15- or Thr-160-phosphospecific antibodies. The relative proportions of the potentially active forms of CDK2 (phosphorylated at Thr-160 but not Tyr-15) and inactive forms (non-phosphorylated, phosphorylated only at Tyr-15, or at both Tyr-15 and Thr-160), and their respective association with cyclin E, cyclin A, p21, and p27, were demonstrated during the mitogenic stimulation of normal human fibroblasts. Novel observations modify the current model of the sequential CDK2 activation process: (i) Tyr-15 phosphorylation induced by serum was not restricted to cyclin-bound CDK2; (ii) Thr-160 phosphorylation engaged the entirety of Tyr-15-phosphorylated CDK2 associated not only with a cyclin but also with p27 and p21, suggesting that Cip/Kip proteins do not prevent CDK2 activity by impairing its phosphorylation by CAK; (iii) the potentially active CDK2 phosphorylated at Thr-160 but not Tyr-15 represented a tiny fraction of total CDK2 and a minor fraction of cyclin A-bound CDK2, underscoring the rate-limiting role of Tyr-15 dephosphorylation by cdc25A.
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Affiliation(s)
- Katia Coulonval
- Institute of Interdisciplinary Research and Protein Chemistry Department, Faculté de Médecine, Université Libre de Bruxelles, Campus Erasme, B-1070 Brussels, Belgium.
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43
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Karty JA, Ireland MME, Brun YV, Reilly JP. Artifacts and unassigned masses encountered in peptide mass mapping. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 782:363-83. [PMID: 12458019 DOI: 10.1016/s1570-0232(02)00550-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In peptide mass mapping of isolated proteins, a significant number of the observed mass spectral peaks are often uninterpreted. These peaks derive from a number of sources: errors in the genome that give rise to incorrect peptide mass predictions, undocumented post-translational modifications, sample handling-induced modifications, contaminants in the sample, non-standard protein cleavage sites, and non-protein components of the sample. In a study of the stalk organelle of Caulobacter crescentus, roughly one-third (782/2215) of all observed masses could not be assigned to the proteins identified in the gel spots (Karty et al., J. Proteome Res., 1 (2002) 325). By interpreting these masses, this work illuminates a number of phenomena that may arise in the course of peptide mass mapping of electrophoretically separated proteins and presents results from a number of related studies.
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Affiliation(s)
- Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington 47405, USA
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44
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Kim JY, Kim KW, Kwon HJ, Lee DW, Yoo JS. Probing lysine acetylation with a modification-specific marker ion using high-performance liquid chromatography/electrospray-mass spectrometry with collision-induced dissociation. Anal Chem 2002; 74:5443-9. [PMID: 12433071 DOI: 10.1021/ac0256080] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Posttranslational acetylation of proteins regulates many diverse functions, including DNA recognition, protein-protein interaction, and protein stability. The identification of enzymes that regulate protein acetylation has revealed broader use of this modification than was previously suspected. In this study, we describe a method for identifying protein acetylation at lysine residues by analysis of digested protein using HPLC/ESI-MS with a new modification-specific marker ion. Collision-induced dissociation with capillary or nano-LC/ESI-TOF-MS was used to obtain a fragment ion useful as a marker for acetylated lysine. Although the acetylated lysine immonium ion at m/z 143.1 has been used as a marker ion for detecting acetylated lysine, it can be confused with internal fragment ion in some peptides, producing false positive results. We have found a novel marker ion at m/z 126.1, which is a further fragment ion induced by the loss of NH3 from the acetylated lysine immonium ions at m/z 143.1. This novel marker ion was found to be more specific and approximately 9 times more sensitive than the immonium ion at m/z 143.1. In addition, no interfering ions for acetylated peptides were found in the extracted ion chromatogram at m/z 126.1. The utility of this method was demonstrated with acetylated cytochrome c as a model compound. After the modification was probed by the new marker ion, the acetylated lysine site was determined by the CID-MS spectrum. This method was applied to identify histone H4 acetylation in HeLa cells treated with trichostatin A. Three protein bands separated by acid-urea-Triton gel electrophoresis were confirmed as tetra, tri, and diacetylated histone H4 at lysines 5, 8, 12, and 16. This method may be useful for assaying for lysine acetylation, which is an important regulatory process for a range of biological functions.
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Affiliation(s)
- Jin Young Kim
- Proteome Analysis Team, Korea Basic Science Institute, Daejeon
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45
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Casagrande S, Bonetto V, Fratelli M, Gianazza E, Eberini I, Massignan T, Salmona M, Chang G, Holmgren A, Ghezzi P. Glutathionylation of human thioredoxin: a possible crosstalk between the glutathione and thioredoxin systems. Proc Natl Acad Sci U S A 2002; 99:9745-9. [PMID: 12119401 PMCID: PMC125000 DOI: 10.1073/pnas.152168599] [Citation(s) in RCA: 275] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify proteins undergoing glutathionylation (formation of protein-glutathione mixed disulfides) in human T cell blasts, we radiolabeled the glutathione pool with (35)S, exposed cells to the oxidant diamide, and analyzed cellular proteins by two-dimensional electrophoresis. One of the proteins undergoing glutathionylation was identified by molecular weight, isoelectric point, and immunoblotting as thioredoxin (Trx). Incubation of recombinant human Trx with glutathione disulfide or S-nitrosoglutathione led to the formation of glutathionylated Trx, identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. The glutathionylation site was identified as Cys-72. Glutathionylation of rhTrx abolished its enzymatic activity as insulin disulfide reductase in the presence of NADPH and Trx reductase. Activity was, however, regained with sigmoidal kinetics, indicating a process of autoactivation due to the ability of Trx to de-glutathionylate itself. These data suggest that the intracellular glutathione/glutathione disulfide ratio, an indicator of the redox state of the cell, can regulate Trx functions reversibly through thiol-disulfide exchange reactions.
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Affiliation(s)
- Simona Casagrande
- Mario Negri Institute for Pharmacological Research, Department of Biochemistry, 20157 Milan, Italy
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Tran NT, Cabanes-Macheteau M, Taverna M. Chapter 20 Analysis of glycoproteins and their glycopeptide and glycan fragments by electrophoresis and capillary electrophoresis. JOURNAL OF CHROMATOGRAPHY LIBRARY 2002. [DOI: 10.1016/s0301-4770(02)80045-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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47
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Ikezono T, Omori A, Ichinose S, Pawankar R, Watanabe A, Yagi T. Identification of the protein product of the Coch gene (hereditary deafness gene) as the major component of bovine inner ear protein. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1535:258-65. [PMID: 11278165 DOI: 10.1016/s0925-4439(00)00101-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In order to better understand the cause of hereditary hearing impairment, we have performed a proteomic analysis of the inner ear proteins using two-dimensional gel electrophoresis. In the process of analysis, we have found very unique properties of the bovine homologue of the human COCH gene product. The COCH gene is responsible for one of the hereditary hearing impairments, DFNA9, and was recently suggested to be a possible genetic factor contributing to Ménière's disease. The Coch protein constitutes 70% of bovine inner ear proteins and is composed of 16 different protein spots, with charge and size heterogeneity. Heterogeneity of this protein suggests that the Coch gene is processed in several ways, at the transcriptional and/or posttranslational level. Much knowledge has accumulated about the hereditary hearing impairment genes; however, little research has been done regarding the protein products of those genes. This is the first report to characterize the Coch protein. Study of the Coch protein might provide more information on the mechanism of hearing and vestibular disorders.
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Affiliation(s)
- T Ikezono
- Department of Otorhinolaryngology, Nippon Medical School, Tokyo, Japan.
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48
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Abstract
Protein profiles of developing rat cerebella were analyzed by means of two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). The analysis of adult rat cerebellum gave rise to a protein map comprising approximately 3000 spots detectable by silver staining following high resolution 2-DE with a pH range of 3-10 and a mass range of 8-100 kDa. To obtain landmarks for comparison of developmental profiles of cerebellar proteins, 100 spots were subjected to peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and 67 spots were assigned on the map. Analysis of profiles of the developing cerebella revealed significant changes in the expression of proteins during development. In most cases the expression levels of proteins increased as the cerebellum matured, while the expression of 42 spots appeared specific or remarkably abundant in the immature cerebellum. Peptide mass fingerprinting of these spots allowed us to identify 29 proteins, which include, in addition to proteins of unknown function, many proteins known to have roles in the development of the central nervous system. These results suggest that the proteomic approach is valuable for mass identification of proteins involved in cerebellar morphogenesis.
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Affiliation(s)
- M Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Japan.
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50
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Schenerman MA, Hope JN, Kletke C, Singh JK, Kimura R, Tsao EI, Folena-Wasserman G. Comparability testing of a humanized monoclonal antibody (Synagis) to support cell line stability, process validation, and scale-up for manufacturing. Biologicals 1999; 27:203-15. [PMID: 10652176 DOI: 10.1006/biol.1999.0179] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Biochemical and functional testing of a humanized monoclonal antibody directed against Respiratory Syncytial Virus (Synagis) has been performed to evaluate cell line stability, support process validation, and to demonstrate "comparability" during the course of process development. Using a variety of analytical methods, product manufactured at different sites and in bioreactors from 20 litres to 10,000 litres was shown to be biochemically and functionally equivalent. The biochemical testing for microheterogeneity found on Synagis included evaluation of changes in post-translational modifications such as deamidation, truncation, and carbohydrate structure. Studies were also performed to support cell line stability assessment and cell culture process validation. Cell culture conditions were deliberately varied in an attempt to determine if this would have an impact on the microheterogeneity of the product. In these studies Synagis was produced from cells cultured beyond the population doublings achieved at the maximum manufacturing scale, under conditions of low glucose, and using harvest times outside of the historical manufacturing operating range. Results showed that there was a different pattern of glycosylation during the early stages of bioreactor culture. No other changes in microheterogeneity were apparent for the other culture conditions studied. In summary, comparability assessment demonstrated that the Synagis manufacturing process is robust and consistent resulting in a predictable and reproducible monoclonal antibody product.
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Affiliation(s)
- M A Schenerman
- MedImmune, Inc., 35 W. Watkins Mill Rd., Gaithersburg, MD 20878, USA
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