1
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Menneteau T, Saveliev S, Butré CI, Rivera AKG, Urh M, Delobel A. Addressing common challenges of biotherapeutic protein peptide mapping using recombinant trypsin. J Pharm Biomed Anal 2024; 243:116124. [PMID: 38520959 DOI: 10.1016/j.jpba.2024.116124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
Peptide mapping is the key method for characterization of primary structure of biotherapeutic proteins. This method relies on digestion of proteins into peptides that are then analyzed for amino acid sequence and post-translational modifications. Owing to its high activity and cleavage specificity, trypsin is the protease of choice for peptide mapping. In this study, we investigated critical requirements of peptide mapping and how trypsin affects these requirements. We found that the commonly used MS-grade trypsins contained non-specific, chymotryptic-like cleavage activity causing generation of semi-tryptic peptides and degradation of tryptic-specific peptides. Furthermore, MS-grade trypsins contained pre-existing autoproteolytic peptides and, moreover, additional autoproteolytic peptides were resulting from prominent autoproteolysis during digestion. In our long-standing quest to improve trypsin performance, we developed novel recombinant trypsin and evaluated whether it could address major trypsin drawbacks in peptide mapping. The study showed that the novel trypsin was free of detectable non-specific cleavage activity, had negligible level of autoproteolysis and maintained high activity over the course of digestion reaction. Taking advantage of the novel trypsin advanced properties, especially high cleavage specificity, we established the application for use of large trypsin quantities to digest proteolytically resistant protein sites without negative side effects. We also tested trypsin/Lys-C mix comprising the novel trypsin and showed elimination of non-specific cleavages observed in the digests with the commonly used trypsins. In addition, the improved features of the novel trypsin allowed us to establish the method for accurate and efficient non-enzymatic PTM analysis in biotherapeutic proteins.
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Affiliation(s)
- Thomas Menneteau
- Quality Assistance SA, Technoparc de Thudinie 2, Donstiennes 6536, Belgium
| | - Sergei Saveliev
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, United States
| | - Claire I Butré
- Quality Assistance SA, Technoparc de Thudinie 2, Donstiennes 6536, Belgium
| | | | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, United States
| | - Arnaud Delobel
- Quality Assistance SA, Technoparc de Thudinie 2, Donstiennes 6536, Belgium.
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2
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Kaur J, Mirgane HA, Patil VS, Ahlawat GM, Bhosale SV, Singh PK. Expanding the scope of self-assembled supramolecular biosensors: a highly selective and sensitive enzyme-responsive AIE-based fluorescent biosensor for trypsin detection and inhibitor screening. J Mater Chem B 2024; 12:3786-3796. [PMID: 38546335 DOI: 10.1039/d4tb00264d] [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: 04/18/2024]
Abstract
Trypsin, a pancreatic enzyme associated with diseases like pancreatic cancer and cystic fibrosis, requires effective diagnostic tools. Current detection systems seldom utilize macrocyclic molecules and tetraphenyl ethylene (TPE) derivative-based supramolecular assemblies, known for their biocompatibility and aggregation-induced emission (AIE) properties, for trypsin detection. This study presents an enzyme-responsive, AIE-based fluorescence 'Turn-On' sensing platform for trypsin detection, employing sulfated-β-cyclodextrin (S-βCD), an imidazolium derivative of TPE (TPE-IM), and protamine sulfate (PrS). The anionic S-βCD and cationic TPE-IM formed a strongly fluorescent supramolecular aggregation complex in an aqueous buffer. However, PrS suppresses fluorescence because of its strong binding affinity with S-βCD. The non-fluorescent TPE-IM/S-βCD/PrS supramolecular assembly system exhibits trypsin-responsive properties, as PrS is a known trypsin substrate. Trypsin restores fluorescence in the TPE-IM/S-βCD system through the enzymatic cleavage of PrS, correlating linearly with trypsin catalytic activity in the 0-10 nM concentration range. The limit of detection is 10 pM. This work contributes to the development of self-assembled supramolecular biosensors using charged TPE derivatives and β-cyclodextrin-based host-guest chemistry, offering an innovative fluorescence 'Turn-On' trypsin sensing platform. The sensing system is highly stable under various conditions, selective for trypsin, and demonstrates potential for biological analysis and disease diagnosis in human serum. Additionally, it shows promise for the screening of trypsin inhibitors.
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Affiliation(s)
- Jasvir Kaur
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- University Institute of Biotechnology, Chandigarh University, Panjab 140 413, India
| | - Harshad A Mirgane
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Vrushali S Patil
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- School of Nanoscience & Technology, Shivaji University Kolhapur, Vidya Nagar, Kolhapur 416004, Maharashtra, India
| | - Geetika M Ahlawat
- University Institute of Biotechnology, Chandigarh University, Panjab 140 413, India
| | - Sheshanath V Bhosale
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi 585367, Karnataka, India
| | - Prabhat K Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India
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3
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Qin S, You P, Yu H, Su B. REEP1 Preserves Motor Function in SOD1 G93A Mice by Improving Mitochondrial Function via Interaction with NDUFA4. Neurosci Bull 2023; 39:929-946. [PMID: 36520405 PMCID: PMC10264344 DOI: 10.1007/s12264-022-00995-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/25/2022] [Indexed: 12/23/2022] Open
Abstract
A decline in the activities of oxidative phosphorylation (OXPHOS) complexes has been consistently reported in amyotrophic lateral sclerosis (ALS) patients and animal models of ALS, although the underlying molecular mechanisms are still elusive. Here, we report that receptor expression enhancing protein 1 (REEP1) acts as an important regulator of complex IV assembly, which is pivotal to preserving motor neurons in SOD1G93A mice. We found the expression of REEP1 was greatly reduced in transgenic SOD1G93A mice with ALS. Moreover, forced expression of REEP1 in the spinal cord extended the lifespan, decelerated symptom progression, and improved the motor performance of SOD1G93A mice. The neuromuscular synaptic loss, gliosis, and even motor neuron loss in SOD1G93A mice were alleviated by increased REEP1 through augmentation of mitochondrial function. Mechanistically, REEP1 associates with NDUFA4, and plays an important role in preserving the integrity of mitochondrial complex IV. Our findings offer insights into the pathogenic mechanism of REEP1 deficiency in neurodegenerative diseases and suggest a new therapeutic target for ALS.
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Affiliation(s)
- Siyue Qin
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Pan You
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Hui Yu
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Bo Su
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China.
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4
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von Oesen T, Treblin M, Clawin-Rädecker I, Martin D, Maul R, Hoffmann W, Schrader K, Wegner B, Bode K, Zink R, Rohn S, Fritsche J. Identification of Marker Peptides for the Whey Protein Quantification in Edam-Type Cheese. Foods 2023; 12:foods12102002. [PMID: 37238821 DOI: 10.3390/foods12102002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Several technologies are available for incorporating whey proteins into a cheese matrix. However, there is no valid analytical method available to determine the whey protein content in matured cheese, to date. Consequently, the aim of the present study was to develop a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the quantification of individual whey proteins based on specific marker peptides ('bottom-up' proteomic approach). Therefore, the whey protein-enriched model of the Edam-type cheese was produced in a pilot plant and on an industrial scale. Tryptic hydrolysis experiments were performed to evaluate the suitability of identified potential marker peptides (PMPs) for α-lactalbumin (α-LA) and β-lactoglobulin (β-LG). Based on the findings, α-LA and β-LG appeared to be resistant to proteolytic degradation during six weeks of ripening and no influence on the PMP was observed. Good levels of linearity (R2 > 0.9714), repeatability (CVs < 5%), and recovery rate (80% to 120%) were determined for most PMPs. However, absolute quantification with external peptide and protein standards revealed differences in model cheese depending on the PMP, e.g., 0.50% ± 0.02% to 5.31% ± 0.25% for β-LG. As protein spiking prior to hydrolysis revealed differing digestion behavior of whey proteins, further studies are required to enable valid quantification in various cheese types.
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Affiliation(s)
- Tobias von Oesen
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Mascha Treblin
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Ingrid Clawin-Rädecker
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Dierk Martin
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Ronald Maul
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Wolfgang Hoffmann
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Katrin Schrader
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Benjamin Wegner
- SGS Germany GmbH, Weidenbaumsweg 137, 21035 Hamburg, Germany
| | - Katja Bode
- Center of Expertise Research & Technology (CoE-R&T), DMK Group (Deutsches Milchkontor GmbH), Flughafenallee 17, 28199 Bremen, Germany
| | - Ralf Zink
- Center of Expertise Research & Technology (CoE-R&T), DMK Group (Deutsches Milchkontor GmbH), Flughafenallee 17, 28199 Bremen, Germany
| | - Sascha Rohn
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Department of Food Chemistry and Analysis, Institute of Food Technology and Food Chemistry, Technische Universität Berlin, TIB 4/3 1, Gustav Meyer Allee 25, 13355 Berlin, Germany
| | - Jan Fritsche
- Department of Safety and Quality of Milk and Fish Products, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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5
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Gao J, Wang L, Ren X, Dunn JR, Peters A, Miyagi M, Fujioka H, Zhao F, Askwith C, Liang J, Wang X. Translational regulation in the brain by TDP-43 phase separation. J Cell Biol 2021; 220:e202101019. [PMID: 34427634 PMCID: PMC8404466 DOI: 10.1083/jcb.202101019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/03/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023] Open
Abstract
The in vivo physiological function of liquid-liquid phase separation (LLPS) that governs non-membrane-bound structures remains elusive. Among LLPS-prone proteins, TAR DNA-binding protein of 43 kD (TDP-43) is under intense investigation because of its close association with neurological disorders. Here, we generated mice expressing endogenous LLPS-deficient murine TDP-43. LLPS-deficient TDP-43 mice demonstrate impaired neuronal function and behavioral abnormalities specifically related to brain function. Brain neurons of these mice, however, did not show TDP-43 proteinopathy or neurodegeneration. Instead, the global rate of protein synthesis was found to be greatly enhanced by TDP-43 LLPS loss. Mechanistically, TDP-43 LLPS ablation increased its association with PABPC4, RPS6, RPL7, and other translational factors. The physical interactions between TDP-43 and translational factors relies on a motif, the deletion of which abolished the impact of LLPS-deficient TDP-43 on translation. Our findings show a specific physiological role for TDP-43 LLPS in the regulation of brain function and uncover an intriguing novel molecular mechanism of translational control by LLPS.
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Affiliation(s)
- Ju Gao
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Luwen Wang
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Xiaojia Ren
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Justin R. Dunn
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Ariele Peters
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
| | - Hisashi Fujioka
- Electron Microscopy Core Facility, Case Western Reserve University, Cleveland, OH
| | - Fangli Zhao
- Department of Neuroscience, The Ohio State University, Columbus, OH
| | - Candice Askwith
- Department of Neuroscience, The Ohio State University, Columbus, OH
| | - Jingjing Liang
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Xinglong Wang
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
- Department of Pathology, Case Western Reserve University, Cleveland, OH
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6
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Kaur J, Malegaonkar JN, Bhosale SV, Singh PK. An anionic tetraphenyl ethylene based simple and rapid fluorescent probe for detection of trypsin and paraoxon methyl. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115980] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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7
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A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field. Proteomes 2020; 8:proteomes8030014. [PMID: 32640657 PMCID: PMC7564415 DOI: 10.3390/proteomes8030014] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.
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8
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Tavano OL, Berenguer-Murcia A, Secundo F, Fernandez-Lafuente R. Biotechnological Applications of Proteases in Food Technology. Compr Rev Food Sci Food Saf 2018; 17:412-436. [DOI: 10.1111/1541-4337.12326] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Olga Luisa Tavano
- Faculty of Nutrition; Alfenas Federal Univ.; 700 Gabriel Monteiro da Silva St Alfenas MG 37130-000 Brazil
| | - Angel Berenguer-Murcia
- Inorganic Chemistry Dept. and Materials Science Inst.; Alicante Univ.; Ap. 99 E-03080 Alicante Spain
| | - Francesco Secundo
- Istit. di Chimica del Riconoscimento Molecolare; CNR; v. Mario Bianco 9 20131 Milan Italy
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9
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Methylene blue decreases mitochondrial lysine acetylation in the diabetic heart. Mol Cell Biochem 2017; 432:7-24. [PMID: 28303408 PMCID: PMC5532421 DOI: 10.1007/s11010-017-2993-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/24/2017] [Indexed: 12/31/2022]
Abstract
Diabetic cardiomyopathy is preceded by mitochondrial alterations, and progresses to heart failure. We studied whether treatment with methylene blue (MB), a compound that was reported to serve as an alternate electron carrier within the mitochondrial electron transport chain (ETC), improves mitochondrial metabolism and cardiac function in type 1 diabetes. MB was administered at 10 mg/kg/day to control and diabetic rats. Both echocardiography and hemodynamic studies were performed to assess cardiac function. Mitochondrial studies comprised the measurement of oxidative phosphorylation and specific activities of fatty acid oxidation enzymes. Proteomic studies were employed to compare the level of lysine acetylation on cardiac mitochondrial proteins between the experimental groups. We found that MB facilitates NADH oxidation, increases NAD+, and the activity of deacetylase Sirtuin 3, and reduces protein lysine acetylation in diabetic cardiac mitochondria. We identified that lysine acetylation on 83 sites in 34 proteins is lower in the MB-treated diabetic group compared to the same sites in the untreated diabetic group. These changes occur across critical mitochondrial metabolic pathways including fatty acid transport and oxidation, amino acid metabolism, tricarboxylic acid cycle, ETC, transport, and regulatory proteins. While the MB treatment has no effect on the activities of acyl-CoA dehydrogenases, it decreases 3-hydroxyacyl-CoA dehydrogenase activity and long-chain fatty acid oxidation, and improves cardiac function. Providing an alternative route for mitochondrial electron transport is a novel therapeutic approach to decrease lysine acetylation, alleviate cardiac metabolic inflexibility, and improve cardiac function in diabetes.
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10
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Metaproteomic evidence of changes in protein expression following a change in electrode potential in a robust biocathode microbiome. Proteomics 2015; 15:3486-96. [DOI: 10.1002/pmic.201400585] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 07/23/2015] [Accepted: 08/05/2015] [Indexed: 11/07/2022]
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11
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Manes NP, Mann JM, Nita-Lazar A. Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification. J Vis Exp 2015:e52959. [PMID: 26325288 DOI: 10.3791/52959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Absolute quantification of target proteins within complex biological samples is critical to a wide range of research and clinical applications. This protocol provides step-by-step instructions for the development and application of quantitative assays using selected reaction monitoring (SRM) mass spectrometry (MS). First, likely quantotypic target peptides are identified based on numerous criteria. This includes identifying proteotypic peptides, avoiding sites of posttranslational modification, and analyzing the uniqueness of the target peptide to the target protein. Next, crude external peptide standards are synthesized and used to develop SRM assays, and the resulting assays are used to perform qualitative analyses of the biological samples. Finally, purified, quantified, heavy isotope labeled internal peptide standards are prepared and used to perform isotope dilution series SRM assays. Analysis of all of the resulting MS data is presented. This protocol was used to accurately assay the absolute abundance of proteins of the chemotaxis signaling pathway within RAW 264.7 cells (a mouse monocyte/macrophage cell line). The quantification of Gi2 (a heterotrimeric G-protein α-subunit) is described in detail.
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Affiliation(s)
- Nathan P Manes
- Cellular Networks Proteomics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Jessica M Mann
- Cellular Networks Proteomics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Aleksandra Nita-Lazar
- Cellular Networks Proteomics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health;
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12
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Blankenship E, Vukoti K, Miyagi M, Lodowski DT. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:833-40. [PMID: 24598752 PMCID: PMC3949523 DOI: 10.1107/s1399004713033658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/12/2013] [Indexed: 05/20/2024]
Abstract
With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.
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Affiliation(s)
- Elise Blankenship
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Krishna Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Opthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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13
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Davidsen JM, Bartley DM, Townsend CA. Non-ribosomal propeptide precursor in nocardicin A biosynthesis predicted from adenylation domain specificity dependent on the MbtH family protein NocI. J Am Chem Soc 2013; 135:1749-59. [PMID: 23330869 DOI: 10.1021/ja307710d] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nocardicin A is a monocyclic β-lactam isolated from the actinomycete Nocardia uniformis that shows moderate antibiotic activity against a broad spectrum of gram-negative bacteria. The monobactams are of renewed interest due to emerging gram-negative strains resistant to clinically available penicillins and cephalosporins. Like isopenicillin N, nocardicin A has a tripeptide core of non-ribosomal origin. Paradoxically, the nocardicin A gene cluster encodes two non-ribosomal peptide synthetases (NRPSs), NocA and NocB, predicted to encode five modules pointing to a pentapeptide precursor in nocardicin A biosynthesis, unless module skipping or other nonlinear reactions are occurring. Previous radiochemical incorporation experiments and bioinformatic analyses predict the incorporation of p-hydroxy-L-phenylglycine (L-pHPG) into positions 1, 3, and 5 and L-serine into position 4. No prediction could be made for position 2. Multidomain constructs of each module were heterologous expressed in Escherichia coli for determination of the adenylation domain (A-domain) substrate specificity using the ATP/PPi exchange assay. Three of the five A-domains, from modules 1, 2, and 4, required the addition of stoichiometric amounts of MbtH family protein NocI to detect exchange activity. On the basis of these analyses, the predicted product of the NocA and NocB NRPSs is L-pHPG-L-Arg-D-pHPG-L-Ser-L-pHPG, a pentapeptide. Despite being flanked by non-proteinogenic amino acids, proteolysis of this pentapeptide by trypsin yields two fragments from cleavage at the C terminus of the L-Arg residue. Thus, a proteolytic step is likely involved in the biosynthesis of nocardicin A, a rare but precedented editing event in the formation of non-ribosomal natural products that is supported by the identification of trypsin-encoding genes in N. uniformis.
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Affiliation(s)
- Jeanne M Davidsen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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14
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Vukoti KM, Kadiyala CSR, Miyagi M. Streptomyces erythraeus trypsin inactivates α1-antitrypsin. FEBS Lett 2011; 585:3898-902. [PMID: 22115549 PMCID: PMC3236438 DOI: 10.1016/j.febslet.2011.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 11/06/2011] [Accepted: 11/08/2011] [Indexed: 11/16/2022]
Abstract
Streptomyces erythraeus trypsin (SET) is a serine protease that is secreted extracellularly by S. erythraeus. We investigated the inhibitory effect of α(1)-antitrypsin on the catalytic activity of SET. Intriguingly, we found that SET is not inhibited by α(1)-antitrypsin. Our investigations into the molecular mechanism underlying this observation revealed that SET hydrolyzes the Met-Ser bond in the reaction center loop of α(1)-antitrypsin. However, SET somehow avoids entrapment by α(1)-antitrypsin. We also confirmed that α(1)-antitrypsin loses its inhibitory activity after incubation with SET. Thus, our study demonstrates that SET is not only resistant to α(1)-antitrypsin but also inactivates α(1)-antitrypsin.
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Affiliation(s)
- Krishna M. Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106
| | - Chandra Sekhar Rao Kadiyala
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106
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15
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Chamrád I, Strouhal O, Řehulka P, Lenobel R, Šebela M. Microscale affinity purification of trypsin reduces background peptides in matrix-assisted laser desorption/ionization mass spectrometry of protein digests. J Proteomics 2011; 74:948-57. [DOI: 10.1016/j.jprot.2011.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 01/26/2011] [Accepted: 02/09/2011] [Indexed: 11/24/2022]
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16
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Abstract
Here, we describe the novel use of a volatile surfactant, perfluorooctanoic acid (PFOA), for shotgun proteomics. PFOA was found to solubilize membrane proteins as effectively as sodium dodecyl sulfate (SDS). PFOA concentrations up to 0.5% (w/v) did not significantly inhibit trypsin activity. The unique features of PFOA allowed us to develop a single-tube shotgun proteomics method that used all volatile chemicals that could easily be removed by evaporation prior to mass spectrometry analysis. The experimental procedures involved: 1) extraction of proteins in 2% PFOA; 2) reduction of cystine residues with triethyl phosphine and their S-alkylation with iodoethanol; 3) trypsin digestion of proteins in 0.5% PFOA; 4) removal of PFOA by evaporation; and 5) LC-MS/MS analysis of the resulting peptides. The general applicability of the method was demonstrated with the membrane preparation of photoreceptor outer segments. We identified 75 proteins from 1 µg of the tryptic peptides in a single, 1-hour, LC-MS/MS run. About 67% of the proteins identified were classified as membrane proteins. We also demonstrate that a proteolytic 18O labeling procedure can be incorporated after the PFOA removal step for quantitative proteomic experiments. The present method does not require sample clean-up devices such as solid-phase extractions and membrane filters, so no proteins/peptides are lost in any experimental steps. Thus, this single-tube shotgun proteomics method overcomes the major drawbacks of surfactant use in proteomic experiments.
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Tian G, Zhou Y, Hajkova D, Miyagi M, Dinculescu A, Hauswirth WW, Palczewski K, Geng R, Alagramam KN, Isosomppi J, Sankila EM, Flannery JG, Imanishi Y. Clarin-1, encoded by the Usher Syndrome III causative gene, forms a membranous microdomain: possible role of clarin-1 in organizing the actin cytoskeleton. J Biol Chem 2009; 284:18980-93. [PMID: 19423712 DOI: 10.1074/jbc.m109.003160] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clarin-1 is the protein product encoded by the gene mutated in Usher syndrome III. Although the molecular function of clarin-1 is unknown, its primary structure predicts four transmembrane domains similar to a large family of membrane proteins that include tetraspanins. Here we investigated the role of clarin-1 by using heterologous expression and in vivo model systems. When expressed in HEK293 cells, clarin-1 localized to the plasma membrane and concentrated in low density compartments distinct from lipid rafts. Clarin-1 reorganized actin filament structures and induced lamellipodia. This actin-reorganizing function was absent in the modified protein encoded by the most prevalent North American Usher syndrome III mutation, the N48K form of clarin-1 deficient in N-linked glycosylation. Proteomics analyses revealed a number of clarin-1-interacting proteins involved in cell-cell adhesion, focal adhesions, cell migration, tight junctions, and regulation of the actin cytoskeleton. Consistent with the hypothesized role of clarin-1 in actin organization, F-actin-enriched stereocilia of auditory hair cells evidenced structural disorganization in Clrn1(-/-) mice. These observations suggest a possible role for clarin-1 in the regulation and homeostasis of actin filaments, and link clarin-1 to the interactive network of Usher syndrome gene products.
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Affiliation(s)
- Guilian Tian
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4965, USA
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