1
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Schairer J, Römer J, Neusüß C. CE-MS and CE-MS/MS for the multiattribute analysis of monoclonal antibody variants at the subunit level. J Pharm Biomed Anal 2024; 252:116495. [PMID: 39368136 DOI: 10.1016/j.jpba.2024.116495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/21/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]
Abstract
The analysis of product-related substances and impurities is a critical step in the biopharmaceutical quality control of multiattribute monoclonal antibodies (mAbs), as posttranslational modifications or other variants can influence the product's biological activity. Many approaches are available for variant analysis; however, they are either variant-specific, mAb-specific, time-consuming, or require expensive equipment. Here, we present a generic capillary electrophoretic method based on a neutral-coated capillary which was coupled to mass spectrometry (MS) via the nanoCEasy interface for mAb variant analysis at the subunit level (enzymatically digested and reduced mAb). The method enabled the separation of several (i) size variants (e.g. glycosylation variants) and (ii) charge variants (e.g. c-terminal lysin clipping) as well as (iii) multiple other proteoforms (e.g. additional glycation) and (iv) incompletely reduced subunits. Separated variants were confirmed by MS/MS fragmentation even for small mass deviations like deamidation or open disulfide bridges. The system, initially developed for one mAb, was tested with nine other IgG1s to show the general applicability of the system. The presented multiattribute method enables fast and detailed characterization of mAb variants with little sample preparation and relatively simple separation equipment enabling the separation of a large set of mAb variants.
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Affiliation(s)
- Jasmin Schairer
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, Aalen 73430, Germany; Faculty of Science, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Jennifer Römer
- Rentschler Biopharma SE, Erwin-Rentschler-Straße 21, Laupheim 88471, Germany
| | - Christian Neusüß
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, Aalen 73430, Germany.
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2
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Hibbert JE, Jorgenson KW, Zhu WG, Steinert ND, Hornberger TA. Protocol for quantifying the in vivo rate of protein degradation in mice using a pulse-chase technique. STAR Protoc 2023; 4:102574. [PMID: 37729055 PMCID: PMC10517276 DOI: 10.1016/j.xpro.2023.102574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
The ability to measure the in vivo rate of protein degradation is a major limitation in numerous fields of biology. Here, we present a protocol for quantifying this rate in mice using a pulse-chase technique that utilizes an azide-bearing non-canonical amino acid called azidohomoalanine (AHA). We describe steps for using chow containing AHA to pulse-label the animal's proteome. We then detail the quantification of AHA-labeled proteins in whole-tissue lysates or histological sections using a copper-catalyzed azide-alkyne cycloaddition 'click' reaction. For complete details on the use and execution of this protocol, please refer to Steinert et al. (2023).1.
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Affiliation(s)
- Jamie E Hibbert
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI 53706, USA; School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA.
| | - Kent W Jorgenson
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI 53706, USA; School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Wenyuan G Zhu
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI 53706, USA; School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Nathaniel D Steinert
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI 53706, USA; School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Troy A Hornberger
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI 53706, USA; School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI 53706, USA.
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3
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Wei B, Lantz C, Liu W, Viner R, Loo RRO, Campuzano IDG, Loo JA. Added Value of Internal Fragments for Top-Down Mass Spectrometry of Intact Monoclonal Antibodies and Antibody-Drug Conjugates. Anal Chem 2023; 95:9347-9356. [PMID: 37278738 PMCID: PMC10954349 DOI: 10.1021/acs.analchem.3c01426] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) are two of the most important therapeutic drug classes that require extensive characterization, whereas their large size and structural complexity make them challenging to characterize and demand the use of advanced analytical methods. Top-down mass spectrometry (TD-MS) is an emerging technique that minimizes sample preparation and preserves endogenous post-translational modifications (PTMs); however, TD-MS of large proteins suffers from low fragmentation efficiency, limiting the sequence and structure information that can be obtained. Here, we show that including the assignment of internal fragments in native TD-MS of an intact mAb and an ADC can improve their molecular characterization. For the NIST mAb, internal fragments can access the sequence region constrained by disulfide bonds to increase the TD-MS sequence coverage to over 75%. Important PTM information, including intrachain disulfide connectivity and N-glycosylation sites, can be revealed after including internal fragments. For a heterogeneous lysine-linked ADC, we show that assigning internal fragments improves the identification of drug conjugation sites to achieve a coverage of 58% of all putative conjugation sites. This proof-of-principle study demonstrates the potential value of including internal fragments in native TD-MS of intact mAbs and ADCs, and this analytical strategy can be extended to bottom-up and middle-down MS approaches to achieve even more comprehensive characterization of important therapeutic molecules.
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Affiliation(s)
- Benqian Wei
- Department of Chemistry and Biochemistry, University of California Los Angeles-Los Angeles, CA, 90095 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California Los Angeles-Los Angeles, CA, 90095 USA
| | - Weijing Liu
- Thermo Fisher Scientific, San Jose, CA, 95134 USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, 95134 USA
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles-Los Angeles, CA, 90095 USA
- UCLA-DOE Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
| | - Iain D. G. Campuzano
- Amgen Research, Center for Research Acceleration and Digital Innovation, Molecular Analytics, Thousand Oaks, CA, 91320 USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles-Los Angeles, CA, 90095 USA
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA, 90095 USA
- UCLA-DOE Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
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4
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The aminopeptidase B (Ap-B) is phosphorylated in HEK293 cells. Biochimie 2022; 201:204-212. [PMID: 35952945 DOI: 10.1016/j.biochi.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/22/2022]
Abstract
Proteolysis is a post-translational modification (PTM) that affects the whole proteome. First regarded as only destructive, it is more precise than expected. It is finely regulated by other PTMs like phosphorylation. Aminopeptidase B (Ap-B), a M1 metallopeptidase, hydrolyses the peptide bond on the carbonyl side of basic residues at the NH2-terminus of peptides. 2D electrophoresis (2DE) was used to show that Ap-B is modified by phosphorylation. Detection of Ap-B by western blot after 2DE reveals several isoforms with different isoelectric points. Using alkaline phosphatase, Pro-Q Diamond phosphorylation-specific dye and kinase-specific inhibitors, we confirmed that Ap-B is phosphorylated. Phosphorylation can alter the structure of proteins leading to changes in their activity, localization, stability and association with other interacting molecules. We showed that Ap-B phosphorylation might delay its turnover. Our study illustrates the central role of the crosstalk between kinases and proteases in the regulation of many biological processes.
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5
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King DT, Zhu S, Hardie DB, Serrano-Negrón JE, Madden Z, Kolappan S, Vocadlo DJ. Chemoproteomic identification of CO 2-dependent lysine carboxylation in proteins. Nat Chem Biol 2022; 18:782-791. [PMID: 35710617 DOI: 10.1038/s41589-022-01043-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/15/2022] [Indexed: 01/09/2023]
Abstract
Carbon dioxide is an omnipresent gas that drives adaptive responses within organisms from all domains of life. The molecular mechanisms by which proteins serve as sensors of CO2 are, accordingly, of great interest. Because CO2 is electrophilic, one way it can modulate protein biochemistry is by carboxylation of the amine group of lysine residues. However, the resulting CO2-carboxylated lysines spontaneously decompose, giving off CO2, which makes studying this modification difficult. Here we describe a method to stably mimic CO2-carboxylated lysine residues in proteins. We leverage this method to develop a quantitative approach to identify CO2-carboxylated lysines of proteins and explore the lysine 'carboxylome' of the CO2-responsive cyanobacterium Synechocystis sp. We uncover one CO2-carboxylated lysine within the effector binding pocket of the metabolic signaling protein PII. CO2-carboxylatation of this lysine markedly lowers the affinity of PII for its regulatory effector ligand ATP, illuminating a negative molecular control mechanism mediated by CO2.
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Affiliation(s)
- Dustin T King
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Darryl B Hardie
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Jesús E Serrano-Negrón
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zarina Madden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Subramania Kolappan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. .,Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
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6
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Cejkov M, Greer T, Johnson RO, Zheng X, Li N. Electron Transfer Dissociation Parameter Optimization Using Design of Experiments Increases Sequence Coverage of Monoclonal Antibodies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:762-771. [PMID: 33596068 DOI: 10.1021/jasms.0c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Middle-down analysis of monoclonal antibodies (mAbs) by tandem mass spectrometry (MS2) can provide detailed insight into their primary structure with minimal sample preparation. The middle-down approach uses an enzyme to cleave mAbs into Fc/2, LC, and Fd subunits that are then analyzed by reversed phase liquid chromatography tandem mass spectrometry (RPLC-MS2). As maximum sequence coverage is desired to obtain meaningful structural information at the subunit level, a host of dissociation methods have been developed, and sometimes combined, to bolster fragmentation and increase the number of identified fragments. Here, we present a design of experiments (DOE) approach to optimize MS2 parameters, in particular those that may influence electron transfer dissociation (ETD) efficiency to increase the sequence coverage of antibody subunits. Applying this approach to the NIST monoclonal antibody standard (NISTmAb) using three RPLC-MS2 runs resulted in high sequence coverages of 67%, 67%, and 52% for Fc/2, LC, and Fd subunits, respectively. In addition, we apply this DOE strategy to model the parameters required to maximize the number of fragments produced in "low", "medium", and "high" mass ranges, which ultimately resulted in even higher sequence coverages of NISTmAb subunits (75%, 78%, and 64% for Fc/2, LC, and Fd subunits, respectively). The DOE approach provides high sequence coverage percentages utilizing only one fragmentation method, ETD, and could be extended to other state-of-the-art techniques that combine multiple fragmentation mechanisms to increase coverage.
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Affiliation(s)
- Milos Cejkov
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Reid O'Brien Johnson
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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7
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Huang P, Kong Q, Gao W, Chu B, Li H, Mao Y, Cai Z, Xu R, Tian R. Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics. Anal Chim Acta 2020; 1127:140-148. [PMID: 32800117 DOI: 10.1016/j.aca.2020.06.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022]
Abstract
Understanding the tumor heterogeneity through spatially resolved proteome profiling is important for biomedical research and clinical application. Laser capture microdissection (LCM) is a powerful technology for exploring local cell populations without losing spatial information. Conventionally, tissue sections are stained with hematoxylin and eosin (H&E) for cell-type identification before LCM. However, it generally requires experienced pathologists to distinguish different cell types, which limits the application of LCM to broad cancer research field. Here, we designed an immunohistochemistry (IHC)-based workflow for cell type-resolved proteome analysis of tissue samples. Firstly, targeted cell type was marked by IHC using antibody targeting cell-type specific marker to improve accuracy and efficiency of LCM. Secondly, to increase protein recovery from chemically crosslinked IHC tissues, we optimized a decrosslinking procedure to seamlessly combine with the integrated spintip-based sample preparation technology SISPROT. This newly developed approach, termed IHC-SISPROT, has comparable performance as H&E staining-based proteomic analysis. High sensitivity and reproducibility of IHC-SISPROT were achieved by combining with data independent acquisition proteomics. More than 3500 proteins were identified from only 0.2 mm2 and 12 μm thickness of hepatocellular carcinoma (HCC) tissue section. Furthermore, using 5 mm2 and 12 μm thickness of HCC tissue section, 6660 and 6052 protein groups were quantified from cancer cells and cancer-associated fibroblasts (CAFs) by the IHC-SISPROT workflow. Bioinformatic analysis revealed the enrichment of cell type-specific ligands and receptors and potentially new communications between cancer cells and CAFs by these signaling proteins. Therefore, IHC-SISPROT is a sensitive and accurate proteomic approach for spatial profiling of cell type-specific proteome from tissues.
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Affiliation(s)
- Peiwu Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Qian Kong
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Weina Gao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Bizhu Chu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hua Li
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China; SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yiheng Mao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Ruilian Xu
- Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518020, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, 518055, China.
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8
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Wang D, Nowak C, Mason B, Katiyar A, Liu H. Analytical artifacts in characterization of recombinant monoclonal antibody therapeutics. J Pharm Biomed Anal 2020; 183:113131. [DOI: 10.1016/j.jpba.2020.113131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 01/12/2023]
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9
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10
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Tang HY, Speicher DW. Experimental Assignment of Disulfide-Bonds in Purified Proteins. ACTA ACUST UNITED AC 2019; 96:e86. [PMID: 30747488 DOI: 10.1002/cpps.86] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The formation of disulfide bonds in proteins is an important post-translational modification that is critical for stabilizing the native structures of proteins, particularly proteins exposed to oxidizing environments. For this reason, most cysteines in secreted proteins or protein domains on the surface of the cell are in disulfides, whereas most cysteines in the cytoplasm are in the unmodified -SH form. Disulfide linkages must be experimentally determined, as they cannot be predicted from amino acid sequence. These assignments provide insights into three-dimensional structure and contribute to the understanding of structural-functional relationships. This unit details a series of protocols that have been applied successfully to map disulfide bonds in proteins. The general strategy involves chemical or proteolytic cleavage of the protein followed by chromatographic separation of the resultant peptides. Mass spectrometry is used to identify disulfide-containing peptides and determine sites of disulfide linkage. A partial reduction and alkylation strategy for mapping disulfide linkages in peptides with multiple disulfide bonds is also presented. © 2019 by John Wiley & Sons, Inc.
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11
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Guo C, Guo X, Zhao L, Chen D, Wang J, Sun J. Optimization of carbamylation conditions and study on the effects on the product ions of carbamylation and dual modification of the peptide by Q-TOF MS. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:384-396. [PMID: 30041545 DOI: 10.1177/1469066718788665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Modified peptides fragmented by collision-induced dissociation can offer additional sequence information, which is beneficial for the de novo sequencing of peptides. Here, the model peptide VQGESNDLK was carbamylated. The optimal conditions were as follows: temperature of 90℃, pH of 7, and the time of 60 min. Then, we studied the b- and y-series ions of the native, carbamylated, and dual-modified peptides. The results were as follows. The short carbamylated peptides (≤10 amino acid residues) produced more b-series ions (including b1 ion). The long carbamylated peptides (>10 amino acid residues) produced additional b1 ion but fewer y-series ions (especially in the high-mass region). The short dual-modified peptides produced more b-series ions (including b1 ion) and more y-series ions, and their peptide sequence coverage was almost 100%. The long dual-modified peptides produce b1 ion and more y-series ions, and their peptide sequence coverage was nearly above 90%. Therefore, both carbamylation and the dual modification method could be used to identify the N-terminal amino acid, and the dual modification method was also excellent for the de novo sequencing of the tryptic peptides.
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Affiliation(s)
- Cheng Guo
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan, Beijing, China
| | - Xuefeng Guo
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan, Beijing, China
| | - Lei Zhao
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan, Beijing, China
| | - Dandan Chen
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan, Beijing, China
| | - Jin Wang
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan, Beijing, China
| | - Jia Sun
- State Forestry Administration Key Open Laboratory, International Centre for Bamboo and Rattan, Beijing, China
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12
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De Backer J, Razzokov J, Hammerschmid D, Mensch C, Hafideddine Z, Kumar N, van Raemdonck G, Yusupov M, Van Doorslaer S, Johannessen C, Sobott F, Bogaerts A, Dewilde S. The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor. Redox Biol 2018; 19:1-10. [PMID: 30081385 PMCID: PMC6084017 DOI: 10.1016/j.redox.2018.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 12/12/2022] Open
Abstract
Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
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Affiliation(s)
- Joey De Backer
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium.
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Dietmar Hammerschmid
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium; Biomolecular & Analytical Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Carl Mensch
- Research Group Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Zainab Hafideddine
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium; The Laboratory of Biophysics and Biomedical Physics, Department of Physics, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Naresh Kumar
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Geert van Raemdonck
- Center for Proteomics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Sabine Van Doorslaer
- The Laboratory of Biophysics and Biomedical Physics, Department of Physics, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Christian Johannessen
- Research Group Molecular Spectroscopy, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium
| | - Sylvia Dewilde
- Research Group PPES, Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, Wilrijk, 1610 Antwerp, Belgium.
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13
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Ivleva VB, Schneck NA, Gollapudi D, Arnold F, Cooper JW, Lei QP. Investigation of Sequence Clipping and Structural Heterogeneity of an HIV Broadly Neutralizing Antibody by a Comprehensive LC-MS Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1512-1523. [PMID: 29736600 PMCID: PMC6652184 DOI: 10.1007/s13361-018-1968-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/07/2018] [Accepted: 04/14/2018] [Indexed: 05/11/2023]
Abstract
CAP256 is one of the highly potent, broadly neutralizing monoclonal antibodies (bNAb) designed for HIV-1 therapy. During the process development of one of the constructs, an unexpected product-related impurity was observed via microfluidics gel electrophoresis. A panel of complementary LC-MS analyses was applied for the comprehensive characterization of CAP256 which included the analysis of the intact and reduced protein, the middle-up approach, and a set of complementary peptide mapping techniques and verification of the disulfide bonds. The designed workflow allowed to identify a clip within a protruding acidic loop in the CDR-H3 region of the heavy chain, which can lead to the decrease of bNAb potency. This characterization explained the origin of the additional species reflected by the reducing gel profile. An intra-loop disulfide bond linking the two fragments was identified, which explained why the non-reducing capillary electrophoresis (CE) profile was not affected. The extensive characterization of CAP256 post-translational modifications was performed to investigate a possible cause of CE profile complexity and to illustrate other structural details related to this molecule's biological function. Two sites of the engineered Tyr sulfation were verified in the antigen-binding loop, and pyroglutamate formation was used as a tool for monitoring the extent of antibody clipping. Overall, the comprehensive LC-MS study was crucial to (1) identify the impurity as sequence clipping, (2) pinpoint the clipping location and justify its susceptibility relative to the molecular structure, (3) lead to an upstream process optimization to mitigate product quality risk, and (4) ultimately re-engineer the sequence to be clip-resistant. Graphical Abstract ᅟ.
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Affiliation(s)
- Vera B Ivleva
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA.
| | - Nicole A Schneck
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Deepika Gollapudi
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Frank Arnold
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Jonathan W Cooper
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA
| | - Q Paula Lei
- Vaccine Production Program, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9 West Watkins Mill Rd., Gaithersburg, MD, 20878, USA.
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14
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Machuca MA, Roujeinikova A. Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain. J Vis Exp 2017. [PMID: 29286481 DOI: 10.3791/57092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.
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Affiliation(s)
- Mayra A Machuca
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University;
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University; Department of Biochemistry and Molecular Biology, Monash University;
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15
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Fresnais M, Richardin P, Sepúlveda M, Leize-Wagner E, Charrié-Duhaut A. Omics for Precious Rare Biosamples: Characterization of Ancient Human Hair by a Proteomic Approach. ACTA ACUST UNITED AC 2017; 21:361-370. [DOI: 10.1089/omi.2017.0067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Margaux Fresnais
- Laboratoire de spectrométrie de masse des interactions et des systèmes (LSMIS), Université de Strasbourg, CNRS, CMC UMR 7140, Strasbourg, France
| | - Pascale Richardin
- Centre de recherche et de restauration des musées de France (C2RMF), Palais du Louvre, Paris, France
| | - Marcela Sepúlveda
- Laboratorio de Análisis e Investigación Arqueométricas y Laboratorio de Arqueologia y Paleoambiente, Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Emmanuelle Leize-Wagner
- Laboratoire de spectrométrie de masse des interactions et des systèmes (LSMIS), Université de Strasbourg, CNRS, CMC UMR 7140, Strasbourg, France
| | - Armelle Charrié-Duhaut
- Laboratoire de spectrométrie de masse des interactions et des systèmes (LSMIS), Université de Strasbourg, CNRS, CMC UMR 7140, Strasbourg, France
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16
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Jersie-Christensen RR, Sultan A, Olsen JV. Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity. Methods Mol Biol 2016; 1355:251-260. [PMID: 26584931 DOI: 10.1007/978-1-4939-3049-4_17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The traditional sample preparation workflow for mass spectrometry (MS)-based phosphoproteomics is time consuming and usually requires multiple steps, e.g., lysis, protein precipitation, reduction, alkylation, digestion, fractionation, and phosphopeptide enrichment. Each step can introduce chemical artifacts, in vitro protein and peptide modifications, and contaminations. Those often result in sample loss and affect the sensitivity, dynamic range and accuracy of the mass spectrometric analysis. Here we describe a simple and reproducible phosphoproteomics protocol, where lysis, denaturation, reduction, and alkylation are performed in a single step, thus reducing sample loss and increasing reproducibility. Moreover, unlike standard cell lysis procedures the cell harvesting is performed at high temperatures (99 °C) and without detergents and subsequent need for protein precipitation. Phosphopeptides are enriched using TiO2 beads and the orbitrap mass spectrometer is operated in a sensitive mode with higher energy collisional dissociation (HCD).
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Affiliation(s)
- Rosa R Jersie-Christensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Abida Sultan
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
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17
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Hedrick VE, LaLand MN, Nakayasu ES, Paul LN. Digestion, Purification, and Enrichment of Protein Samples for Mass Spectrometry. ACTA ACUST UNITED AC 2015; 7:201-222. [PMID: 26331527 DOI: 10.1002/9780470559277.ch140272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Victoria E. Hedrick
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Mercedes N. LaLand
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Ernesto S. Nakayasu
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
| | - Lake N. Paul
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University; West Lafayette Indiana
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18
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Ji Y, Liu M, Bachschmid MM, Costello CE, Lin C. Surfactant-Induced Artifacts during Proteomic Sample Preparation. Anal Chem 2015; 87:5500-4. [PMID: 25945600 DOI: 10.1021/acs.analchem.5b00249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bottom-up proteomics is a powerful tool for characterization of protein post-translational modifications (PTMs), where PTMs are identified at the peptide level by mass spectrometry (MS) following protein digestion. However, enzymatic digestion is associated with additional sample processing steps that may potentially introduce artifactual modifications. Here, during an MS study of the PTMs of the regulator of G-protein signaling 4, we discovered that the use of ProteaseMAX, which is an acid-labile surfactant commonly used to improve protein solubilization and digestion efficiency, can lead to in vitro modifications on cysteine residues. These hydrophobic modifications resemble S-palmitoylation and hydroxyfarnesylation, thus discouraging the use of ProteaseMAX in studies of lipid modifications of proteins. Furthermore, since they target the cysteine thiol group, the presence of these artifacts will inevitably lead to inaccuracies in quantitative analysis of cysteine modifications.
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19
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An Y, Zhang Y, Mueller HM, Shameem M, Chen X. A new tool for monoclonal antibody analysis: application of IdeS proteolysis in IgG domain-specific characterization. MAbs 2015; 6:879-93. [PMID: 24927271 DOI: 10.4161/mabs.28762] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Monoclonal antibody (mAb) products are extraordinarily heterogeneous due to the presence of a variety of enzymatic and chemical modifications, such as deamidation, isomerization, oxidation, glycosylation, glycation, and terminal cyclization. The modifications in different domains of the antibody molecule can result in different biological consequences. Therefore, characterization and routine monitoring of domain-specific modifications are essential to ensure the quality of the therapeutic antibody products. For this purpose, a rapid and informative methodology was developed to examine the heterogeneity of individual domains in mAb products. A recently discovered endopeptidase, IdeS, cleaves heavy chains below the hinge region, producing F(ab') 2 and Fc fragments. Following reduction of disulfide bonds, three antibody domains (LC, Fd, and Fc/2) can be released for further characterization. Subsequent analyses by liquid chromatography/mass spectrometry, capillary isoelectric focusing, and glycan mapping enable domain-specific profiling of oxidation, charge heterogeneity, and glycoform distribution. When coupled with reversed phase chromatography, the unique chromatographic profile of each molecule offers a simple strategy for an identity test, which is an important formal test for biopharmaceutical quality control purposes. This methodology is demonstrated for a number of IgGs of different subclasses (IgG1, IgG2, IgG4), as well as an Fc fusion protein. The presented technique provides a convenient platform approach for scientific and formal therapeutic mAb product characterization. It can also be applied in regulated drug substance batch release and stability testing of antibody and Fc fusion protein products, in particular for identity and routine monitoring of domain-specific modifications.
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Affiliation(s)
- Yan An
- Sterile Product and Analytical Development; Merck Research Laboratories; Kenilworth, NJ USA
| | - Ying Zhang
- Sterile Product and Analytical Development; Merck Research Laboratories; Kenilworth, NJ USA
| | - Hans-Martin Mueller
- Sterile Product and Analytical Development; Merck Research Laboratories; Kenilworth, NJ USA
| | - Mohammed Shameem
- Sterile Product and Analytical Development; Merck Research Laboratories; Kenilworth, NJ USA
| | - Xiaoyu Chen
- Sterile Product and Analytical Development; Merck Research Laboratories; Kenilworth, NJ USA
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20
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Cho HR, Park JS, Wood TD, Choi YS. Longitudinal Assessment of Peptide Recoveries from a Sample Solution in an Autosampler Vial for Proteomics. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ha Ra Cho
- College of Pharmacy; Dankook University; Chungnam 330-714 South Korea
| | - Jun Seo Park
- College of Pharmacy; Dankook University; Chungnam 330-714 South Korea
| | - Troy D. Wood
- Department of Chemistry; State University of New York at Buffalo; Buffalo NY 14260-3000 USA
| | - Yong Seok Choi
- College of Pharmacy; Dankook University; Chungnam 330-714 South Korea
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21
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Dong Q, Yan X, Kilpatrick LE, Liang Y, Mirokhin YA, Roth JS, Rudnick PA, Stein SE. Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA). Mol Cell Proteomics 2014; 13:2435-49. [PMID: 24889059 DOI: 10.1074/mcp.o113.037135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This work presents a method for creating a mass spectral library containing tandem spectra of identifiable peptide ions in the tryptic digestion of a single protein. Human serum albumin (HSA(1)) was selected for this purpose owing to its ubiquity, high level of characterization and availability of digest data. The underlying experimental data consisted of ∼3000 one-dimensional LC-ESI-MS/MS runs with ion-trap fragmentation. In order to generate a wide range of peptides, studies covered a broad set of instrument and digestion conditions using multiple sources of HSA and trypsin. Computer methods were developed to enable the reliable identification and reference spectrum extraction of all peptide ions identifiable by current sequence search methods. This process made use of both MS2 (tandem) spectra and MS1 (electrospray) data. Identified spectra were generated for 2918 different peptide ions, using a variety of manually-validated filters to ensure spectrum quality and identification reliability. The resulting library was composed of 10% conventional tryptic and 29% semitryptic peptide ions, along with 42% tryptic peptide ions with known or unknown modifications, which included both analytical artifacts and post-translational modifications (PTMs) present in the original HSA. The remaining 19% contained unexpected missed-cleavages or were under/over alkylated. The methods described can be extended to create equivalent spectral libraries for any target protein. Such libraries have a number of applications in addition to their known advantages of speed and sensitivity, including the ready re-identification of known PTMs, rejection of artifact spectra and a means of assessing sample and digestion quality.
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Affiliation(s)
- Qian Dong
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Xinjian Yan
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Lisa E Kilpatrick
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Yuxue Liang
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Yuri A Mirokhin
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Jeri S Roth
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Paul A Rudnick
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
| | - Stephen E Stein
- From the ‡Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8362, Gaithersburg, Maryland 20899, United States
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22
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Autoantibodies to posttranslational modifications in rheumatoid arthritis. Mediators Inflamm 2014; 2014:492873. [PMID: 24782594 PMCID: PMC3981057 DOI: 10.1155/2014/492873] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/10/2014] [Indexed: 12/11/2022] Open
Abstract
Autoantibodies have been associated with human pathologies for a long time, particularly with autoimmune diseases (AIDs). Rheumatoid factor (RF) is known since the late 1930s to be associated with rheumatoid arthritis (RA). The discovery of anticitrullinated protein antibodies in the last century has changed this and other posttranslational modifications (PTM) relevant to RA have since been described. Such PTM introduce neoepitopes in proteins that can generate novel autoantibody specificities. The recent recognition of these novel specificities in RA provides a unique opportunity to understand human B-cell development in vivo. In this paper, we will review the three of the main classes of PTMs already associated with RA: citrullination, carbamylation, and oxidation. With the advancement of research methodologies it should be expected that other autoantibodies against PTM proteins could be discovered in patients with autoimmune diseases. Many of such autoantibodies may provide significant biomarker potential.
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23
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Traum AZ. Urine proteomic profiling to identify biomarkers of steroid resistance in pediatric nephrotic syndrome. Expert Rev Proteomics 2014; 5:715-9. [DOI: 10.1586/14789450.5.5.715] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Expression, purification and improved antigenicity of the Mycobacterium tuberculosis PstS1 antigen for serodiagnosis. Protein Expr Purif 2013; 95:77-83. [PMID: 24326191 DOI: 10.1016/j.pep.2013.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/18/2013] [Accepted: 11/21/2013] [Indexed: 11/22/2022]
Abstract
The phosphate-specific transport substrate binding protein-1 (PstS1) is a potential antigen used for the serological diagnosis of tuberculosis. For a highly specific diagnostic result, it is important that the recombinant PstS1 be highly pure and correctly folded. In this study, the PstS1 was expressed as fusion protein with glutathione-S-transferase (PstS1-GST) and Escherichia coli trigger factor (PstS1-TF) and their immunodiagnostic potentials were evaluated. The insoluble PstS1-GST was denatured and refolded to the native conformation by a step-gradient dilution, followed by purification with affinity chromatography on immobilized glutathione whereas the soluble PstS1-TF was directly purified by Ni-NTA affinity and size-exclusion chromatographies. The levels of antibody responses to PstS1-TF and PstS1-GST were measured by enzyme-linked immunosorbent assay (ELISA) in the sera of 22 tuberculosis patients with smear-positive and culture-positive tuberculosis as well as 20 healthy individuals; the antigenicities of the samples were evaluated in terms of sensitivity and specificity. To determine the diagnostic accuracy, receiver operation characteristic (ROC) curves were constructed and then the areas under the ROC curves (AUC) were calculated; the AUC values for PstS1-TF and PstS1-GST were 0.971 and 0.877 with 95% confidence intervals (CI) of 0.927-1.000 and 0.768-0.986, respectively. The specificity of PstS1-TF was reduced from 89.5% to 84.2%, but in case of PstS1-GST it dropped drastically from 78.9% to 26.3% when the sensitivity was raised from 86.4% up to 95.5%. These results indicate that PstS1-TF is capable of producing more accurate and consistent serodiagnostic results than PstS1-GST, possibly due to its conformation being closer to the native state.
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25
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Al-Majdoub M, Opuni KFM, Koy C, Glocker MO. Facile Fabrication and Instant Application of Miniaturized Antibody-Decorated Affinity Columns for Higher-Order Structure and Functional Characterization of TRIM21 Epitope Peptides. Anal Chem 2013; 85:10479-87. [DOI: 10.1021/ac402559m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M. Al-Majdoub
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - K. F. M. Opuni
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - C. Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - M. O. Glocker
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
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26
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Hsp70 is a novel posttranscriptional regulator of gene expression that binds and stabilizes selected mRNAs containing AU-rich elements. Mol Cell Biol 2012; 33:71-84. [PMID: 23109422 DOI: 10.1128/mcb.01275-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The AU-rich elements (AREs) encoded within many mRNA 3' untranslated regions (3'UTRs) are targets for factors that control transcript longevity and translational efficiency. Hsp70, best known as a protein chaperone with well-defined peptide-refolding properties, is known to interact with ARE-like RNA substrates in vitro. Here, we show that cofactor-free preparations of Hsp70 form direct, high-affinity complexes with ARE substrates based on specific recognition of U-rich sequences by both the ATP- and peptide-binding domains. Suppressing Hsp70 in HeLa cells destabilized an ARE reporter mRNA, indicating a novel ARE-directed mRNA-stabilizing role for this protein. Hsp70 also bound and stabilized endogenous ARE-containing mRNAs encoding vascular endothelial growth factor (VEGF) and Cox-2, which involved a mechanism that was unaffected by an inhibitor of its protein chaperone function. Hsp70 recognition and stabilization of VEGF mRNA was mediated by an ARE-like sequence in the proximal 3'UTR. Finally, stabilization of VEGF mRNA coincided with the accumulation of Hsp70 protein in HL60 promyelocytic leukemia cells recovering from acute thermal stress. We propose that the binding and stabilization of selected ARE-containing mRNAs may contribute to the cytoprotective effects of Hsp70 following cellular stress but may also provide a novel mechanism linking constitutively elevated Hsp70 expression to the development of aggressive neoplastic phenotypes.
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27
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Abstract
Outer membrane protein A (OmpA) of Escherichia coli is a paradigm for the biogenesis of outer membrane proteins; however, the structure and assembly of OmpA have remained controversial. A review of studies to date supports the hypothesis that native OmpA is a single-domain large pore, while a two-domain narrow-pore structure is a folding intermediate or minor conformer. The in vitro refolding of OmpA to the large-pore conformation requires isolation of the protein from outer membranes with retention of an intact disulfide bond followed by sufficient incubation in lipids at temperatures of ≥ 26 °C to overcome the high energy of activation for refolding. The in vivo maturation of the protein involves covalent modification of serines in the eighth β-barrel of the N-terminal domain by oligo-(R)-3-hydroxybutyrates as the protein is escorted across the cytoplasm by SecB for post-translational secretion across the secretory translocase in the inner membrane. After cleavage of the signal sequence, protein chaperones, such as Skp, DegP and SurA, guide OmpA across the periplasm to the β-barrel assembly machinery (BAM) complex in the outer membrane. During this passage, a disulfide bond is formed between C290 and C302 by DsbA, and the hydrophobicity of segments of the C-terminal domain, which are destined for incorporation as β-barrels in the outer membrane bilayer, is increased by covalent attachment of oligo-(R)-3-hydroxybutyrates. With the aid of the BAM complex, OmpA is then assembled into the outer membrane as a single-domain large pore.
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Affiliation(s)
- Rosetta N Reusch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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28
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Deng X, Hahne T, Schröder S, Redweik S, Nebija D, Schmidt H, Janssen O, Lachmann B, Wätzig H. The challenge to quantify proteins with charge trains due to isoforms or conformers. Electrophoresis 2011; 33:263-9. [DOI: 10.1002/elps.201100321] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/30/2011] [Accepted: 08/05/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Xi Deng
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Hahne
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simone Schröder
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sabine Redweik
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dashnor Nebija
- Department of Medicinal and Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Hendrik Schmidt
- Laboratory for Molecular Immunology, Institute for Immunology, University Hospital Schleswig‐Holstein, Kiel, Germany
| | - Ottmar Janssen
- Laboratory for Molecular Immunology, Institute for Immunology, University Hospital Schleswig‐Holstein, Kiel, Germany
| | - Bodo Lachmann
- Department of Medicinal and Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Hermann Wätzig
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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29
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Chesnik M, Halligan B, Olivier M, Mirza SP. Sequential abundant ion fragmentation analysis (SAIFA): an alternative approach for phosphopeptide identification using an ion trap mass spectrometer. Anal Biochem 2011; 418:197-203. [PMID: 21855524 PMCID: PMC3188319 DOI: 10.1016/j.ab.2011.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 10/17/2022]
Abstract
Phosphorylation has been the most studied of all the posttranslational modifications of proteins. Mass spectrometry has emerged as a powerful tool for phosphomapping on proteins/peptides. Collision-induced dissociation (CID) of phosphopeptides leads to the loss of phosphoric or metaphosphoric acid as a neutral molecule, giving an intense neutral loss product ion in the mass spectrum. Dissociation of the neutral loss product ion identifies peptide sequence. This method of data-dependent constant neutral loss (DDNL) scanning analysis has been commonly used for mapping phosphopeptides. However, preferential losses of groups other than phosphate are frequently observed during CID of phosphopeptides. Ions that result from such losses are not identified during DDNL analysis due to predetermined scanning for phosphate loss. In this study, we describe an alternative approach for improved identification of phosphopeptides by sequential abundant ion fragmentation analysis (SAIFA). In this approach, there is no predetermined neutral loss molecule, thereby undergoing sequential fragmentation of abundant peak, irrespective of the moiety lost during CID. In addition to improved phosphomapping, the method increases the sequence coverage of the proteins identified, thereby increasing the confidence of protein identification. To the best of our knowledge, this is the first report to use SAIFA for phosphopeptide identification.
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Affiliation(s)
- Marla Chesnik
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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30
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Heyda J, Kožíšek M, Bednárova L, Thompson G, Konvalinka J, Vondrášek J, Jungwirth P. Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein. J Phys Chem B 2011; 115:8910-24. [DOI: 10.1021/jp200790h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Heyda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Lucie Bednárova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Gary Thompson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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31
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Choi HS, Lee SK, Kwon KH, Yoo JS, Ji K, Kim JY. Pressure Cycling Technology-assisted Protein Digestion for Efficient Proteomic Analysis. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.2.599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Schreier SM, Steinkellner H, Jirovetz L, Hermann M, Exner M, Gmeiner BMK, Kapiotis S, Laggner H. S-carbamoylation impairs the oxidant scavenging activity of cysteine: its possible impact on increased LDL modification in uraemia. Biochimie 2011; 93:772-7. [PMID: 21277933 DOI: 10.1016/j.biochi.2011.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
Abstract
Carbamoylation is the non-enzymatic reaction of cyanate with amino-, hydroxy- or thiol groups. In vivo, amino group modification (N-carbamoylation) resulting in altered function of proteins/amino acids has been observed in patients suffering from uraemia due to urea-derived cyanate. Uraemia has been linked to impaired antioxidant defense. As thiol-compounds like cysteine, N-acetyl cysteine and GSH have oxidant scavenging properties one may speculate that thiol-group carbamoylation (S-carbamoylation) may impair their protective activity. Here we report on the effect of S-carbamoylation on the ABTS free radical and HOCl scavenging property of cysteine as well on its ability to protect LDL from atherogenic modification induced by AAPH generated peroxylradicals or HOCl. The results show that S-carbamoylation impaired the ABTS free radical and HOCl scavenging property of the thiol-compounds tested. The ability of the thiols to protect LDL from lipid oxidation and apolipoprotein modification was strongly diminished by S-carbamoylation. The data indicate that S-carbamoylation could impair the free radical and HOCl scavenging of thiol-amino acids reducing their protective property against LDL atherogenic modification by these oxidant species. As S-carbamoylation is most effective at pH 7 to 5 in vivo thiol-carbamoylation may especially occur at sites of acidic extracellular pH as in hypoxic/inflammatory macrophage rich areas like the atherosclerotic plaque where increased LDL oxidation has been found and may contribute to the higher oxidative stress in uraemia.
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Affiliation(s)
- Sabine M Schreier
- Center of Pathobiochemistry and Genetics, Department of Medical Chemistry and Pathobiochemistry, Medical University of Vienna, Vienna, Austria
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Delporte C, Van Antwerpen P, Zouaoui Boudjeltia K, Noyon C, Abts F, Métral F, Vanhamme L, Reyé F, Rousseau A, Vanhaeverbeek M, Ducobu J, Nève J. Optimization of apolipoprotein-B-100 sequence coverage by liquid chromatography-tandem mass spectrometry for the future study of its posttranslational modifications. Anal Biochem 2010; 411:129-38. [PMID: 21129357 DOI: 10.1016/j.ab.2010.11.039] [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] [Received: 10/29/2010] [Revised: 11/24/2010] [Accepted: 11/24/2010] [Indexed: 11/18/2022]
Abstract
Proteomic applications have been increasingly used to study posttranslational modifications of proteins (PTMs). For the purpose of identifying and localizing specific but unknown PTMs on huge proteins, improving their sequence coverage is fundamental. Using liquid chromatography coupled to mass spectrometry (LC-MS/MS), peptide mapping of the native apolipoprotein-B-100 was performed to further document the effects of oxidation. Apolipoprotein-B-100 is the main protein of low-density lipoprotein particles and its oxidation could play a role in atherogenesis. Because it is one of the largest human proteins, the sequence recovery rate of apolipoprotein-B-100 only reached 1% when conventional analysis parameters were used. The different steps of the peptide mapping process-from protein treatment to data analysis-were therefore reappraised and optimized. These optimizations allowed a protein sequence recovery rate of 79%, a rate which has never been achieved previously for such a large human protein. The key points for improving peptide mapping were optimization of the data analysis software; peptide separation by LC; sample preparation; and MS acquisition. The new protocol has allowed us to increase by a factor of 4 the detection of modified peptides in apolipoprotein-B-100. This approach could easily be transferred to any study of PTMs using LC-MS/MS.
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Olajuyigbe FM, Demitri N, Ajele JO, Maurizio E, Randaccio L, Geremia S. Carbamylation of N-terminal proline. ACS Med Chem Lett 2010; 1:254-7. [PMID: 24900204 DOI: 10.1021/ml100046d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 05/26/2010] [Indexed: 11/29/2022] Open
Abstract
Protein carbamylation is of great concern both in vivo and in vitro. Here, we report the first structural characterization of a protein carbamylated at the N-terminal proline. The unexpected carbamylation of the α-amino group of the least reactive codified amino acid has been detected in high-resolution electron density maps of a new crystal form of the HIV-1 protease/saquinavir complex. The carbamyl group is found coplanar to the proline ring with a trans conformation. The reaction of N-terminal with cyanate ion derived from the chaotropic agent urea was confirmed by mass spectra analysis on protease single crystals. Implications of carbamylation process in vitro and in vivo are discussed.
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Affiliation(s)
- Folasade M. Olajuyigbe
- Department of Chemical Sciences
- Department of Biochemistry, Federal University of Technology, 340001 Akure, Nigeria
| | | | - Joshua O. Ajele
- Department of Biochemistry, Federal University of Technology, 340001 Akure, Nigeria
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Ackrill T, Anderson DW, Macmillan D. Towards biomolecular assembly employing extended native chemical ligation in combination with thioester synthesis using an N→S acyl shift. Biopolymers 2010; 94:495-503. [DOI: 10.1002/bip.21473] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Bolivar JM, Rocha-Martin J, Godoy C, Rodrigues RC, Guisan JM. Complete reactivation of immobilized derivatives of a trimeric glutamate dehydrogenase from Thermus thermophillus. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.08.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Alvarez LA, Merola F, Erard M, Rusconi F. Mass Spectrometry-Based Structural Dissection of Fluorescent Proteins. Biochemistry 2009; 48:3810-2. [DOI: 10.1021/bi900327f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis A. Alvarez
- Laboratoire de Chimie Physique,
Université Paris-Sud 11, UMR 8000 CNRS, F-91405 Orsay Cedex,
France
| | - Fabienne Merola
- Laboratoire de Chimie Physique,
Université Paris-Sud 11, UMR 8000 CNRS, F-91405 Orsay Cedex,
France
| | - Marie Erard
- Laboratoire de Chimie Physique,
Université Paris-Sud 11, UMR 8000 CNRS, F-91405 Orsay Cedex,
France
| | - Filippo Rusconi
- Laboratoire de biophysique, Muséum national d’Histoire naturelle, CNRS UMR5153-INSERM U565-MNHN USM0503, 57 rue Cuvier, Case postale 26, F-75231 Paris Cedex 05, France
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Bartkowiak K, Wieczorek M, Buck F, Harder S, Moldenhauer J, Effenberger KE, Pantel K, Peter-Katalinic J, Brandt BH. Two-Dimensional Differential Gel Electrophoresis of a Cell Line Derived from a Breast Cancer Micrometastasis Revealed a Stem/Progenitor Cell Protein Profile. J Proteome Res 2009; 8:2004-14. [DOI: 10.1021/pr8009758] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Bartkowiak
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Marek Wieczorek
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Friedrich Buck
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Sönke Harder
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Jennifer Moldenhauer
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Katharina E. Effenberger
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Klaus Pantel
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Jasna Peter-Katalinic
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
| | - Burkhard H. Brandt
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany, Department of Plant Biochemistry and Biotechnology, Westphalian Wilhelm’s-University Münster, Hindenburgplatz 55, 48143 Münster, Germany, and Institute of Medical Physics and Biophysics, Westphalian Wilhelm’s-University Münster, Robert-Koch Str. 31, D-48149 Münster, Germany
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Abstract
HPLC-chip/MS is a novel nanoflow analytical technology conducted on a microfabricated chip that allows for highly efficient HPLC separation and superior sensitive MS detection of complex proteomic mixtures. This is possible through on-chip preconcentration and separation with fluidic connection made automatically in a leak-tight fashion. Minimum precolumn and postcolumn peak dispersion and uncompromised ease of use result in compounds eluting in bands of only a few nanoliters. The chip is fabricated out of bio-inert polyimide-containing channels and integrated chip structures, such as an electrospray emitter, columns, and frits manufactured by laser ablation technology. Meanwhile, a variety of HPLC-chips differing in design and stationary phase are commercially available, which provide a comprehensive solution for applications in proteomics, glycomics, biomarker, and pharmaceutical discovery. The HPLC-chip can also be easily integrated into a multidimensional separation workflow where different orthogonal separation techniques are combined to solve a highly complex separation problems. In this chapter, we describe in detail the methodological chip usage and functionality and its application in the elucidation of the protein profile of human nucleoli.
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Affiliation(s)
- Martin Vollmer
- Agilent Technologies, Hewlett Packard-Strasse 8, 76337, Waldbronn, Germany.
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Dick LW, Mahon D, Qiu D, Cheng KC. Peptide mapping of therapeutic monoclonal antibodies: Improvements for increased speed and fewer artifacts. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:230-6. [DOI: 10.1016/j.jchromb.2008.12.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 11/14/2008] [Accepted: 12/04/2008] [Indexed: 10/21/2022]
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Martinez A, Traverso JA, Valot B, Ferro M, Espagne C, Ephritikhine G, Zivy M, Giglione C, Meinnel T. Extent of N-terminal modifications in cytosolic proteins from eukaryotes. Proteomics 2008; 8:2809-31. [PMID: 18655050 DOI: 10.1002/pmic.200701191] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Most proteins in all organisms undergo crucial N-terminal modifications involving N-terminal methionine excision, N-alpha-acetylation or N-myristoylation (N-Myr), or S-palmitoylation. We investigated the occurrence of these poorly annotated but essential modifications in proteomes, focusing on eukaryotes. Experimental data for the N-terminal sequences of animal, fungi, and archaeal proteins, were used to build dedicated predictive modules in a new software. In vitro N-Myr experiments were performed with both plant and animal N-myristoyltransferases, for accurate prediction of the modification. N-terminal modifications from the fully sequenced genome of Arabidopsis thaliana were determined by MS. We identified 105 new modified protein N-termini, which were used to check the accuracy of predictive data. An accuracy of more than 95% was achieved, demonstrating (i) overall conservation of the specificity of the modification machinery in higher eukaryotes and (ii) robustness of the prediction tool. Predictions were made for various proteomes. Proteins that had undergone both N-terminal methionine (Met) cleavage and N-acetylation were found to be strongly overrepresented among the most abundant proteins, in contrast to those retaining their genuine unblocked Met. Here we propose that the nature of the second residue of an ORF is a key marker of the abundance of the mature protein in eukaryotes.
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Affiliation(s)
- Aude Martinez
- Institut des Sciences du Végétal, UPR2355, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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Oberhuber C, Ma Y, Marsh J, Rigby N, Smole U, Radauer C, Alessandri S, Briza P, Zuidmeer L, Maderegger B, Himly M, Sancho AI, van Ree R, Knulst A, Ebner C, Shewry P, Mills ENC, Wellner K, Breiteneder H, Hoffmann-Sommergruber K, Bublin M. Purification and characterisation of relevant natural and recombinant apple allergens. Mol Nutr Food Res 2008; 52 Suppl 2:S208-19. [DOI: 10.1002/mnfr.200700522] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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44
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Ruan Y, Wan M. An optimized procedure for solubilization, reduction, and transfer of human breast cancer membrane-enriched fraction by 2-DE. Electrophoresis 2007; 28:3333-40. [PMID: 17722185 DOI: 10.1002/elps.200700035] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The separation of integral and peripheral membrane proteins is still a challenge, although many achievements have been made in the 2-DE-based membrane proteomics. Using a human breast cancer cell line, MCF-7, we investigated the influences of Tris, reducing reagents, cup loading, and SDS on membrane protein solubilization and separation by 2-DE. The addition of Tris to the sample solution improved the solubilization of the membrane-enriched fraction, and the best-quality gel patterns were obtained at 20 mM Tris. Tributylphosphine (TBP), a reducing agent, was not optimum in the 2-DE process because it not only decreased the solubilization of hydrophobic proteins but also caused some proteins, such as hsp60, prohibitin, and actin, to be resolved to a string of spots. However, when combined with DTT, TBP could improve the resolution of 2-DE patterns. Cup loading significantly facilitated the entrance of membrane proteins into IPG strips and over 1000 protein spots with high resolution were visualized. Adopting this strategy, an ATP synthase alpha chain was resolved into two adjacent spots for the first time in 2-DE gel patterns through the adding DTT in the middle of the IEF. A high SDS concentration in the equilibration buffer enhanced the transfer and increased the staining intensity of 50% of the protein spots in the gels, but also resulted in losses of some spots.
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Affiliation(s)
- Yusong Ruan
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi' an Jiaotong University, Xi' an, PR China
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45
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46
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Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genes Dev 2007; 17:1362-77. [PMID: 17690205 PMCID: PMC1950905 DOI: 10.1101/gr.6427907] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 06/12/2007] [Indexed: 11/24/2022]
Abstract
While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.
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Affiliation(s)
- Nitin Gupta
- Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA.
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47
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Chen EI, Cociorva D, Norris JL, Yates JR. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J Proteome Res 2007; 6:2529-38. [PMID: 17530876 PMCID: PMC2570269 DOI: 10.1021/pr060682a] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An optimization and comparison of trypsin digestion strategies for peptide/protein identifications by microLC-MS/MS with or without MS compatible detergents in mixed organic-aqueous and aqueous systems was carried out in this study. We determine that adding MS-compatible detergents to proteolytic digestion protocols dramatically increases peptide and protein identifications in complex protein mixtures by shotgun proteomics. Protein solubilization and proteolytic efficiency are increased by including MS-compatible detergents in trypsin digestion buffers. A modified trypsin digestion protocol incorporating the MS compatible detergents consistently identifies over 300 proteins from 5 microg of pancreatic cell lysates and generates a greater number of peptide identifications than trypsin digestion with urea when using LC-MS/MS. Furthermore, over 700 proteins were identified by merging protein identifications from trypsin digestion with three different MS-compatible detergents. We also observe that the use of mixed aqueous and organic solvent systems can influence protein identifications in combinations with different MS-compatible detergents. Peptide mixtures generated from different MS-compatible detergents and buffer combinations show a significant difference in hydrophobicity. Our results show that protein digestion schemes incorporating MS-compatible detergents generate quantitative as well as qualitative changes in observed peptide identifications, which lead to increased protein identifications overall and potentially increased identification of low-abundance proteins.
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Affiliation(s)
- Emily I. Chen
- Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037
| | - Daniel Cociorva
- Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037
| | | | - John R. Yates
- Department of Cell Biology, 10550 North Torrey Pines Road, SR11, The Scripps Research Institute, La Jolla, CA 92037
- Correspondence: John R. III Yates, , Phone: (858) 784-8862, Fax (858) 784-8883, The Scripps Research Institute, 10550 North Torrey Pines Road, SR 11, La Jolla, CA92037
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Angel PM, Orlando R. Quantitative carbamylation as a stable isotopic labeling method for comparative proteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:1623-34. [PMID: 17465008 DOI: 10.1002/rcm.2990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A method was developed that uses urea to both solublize and isotopically label biological samples for comparative proteomics. This approach uses either light or heavy urea ((12)CH(4)(14)N(2)O or (13)CH(4)(15)N(2)O, respectively) at a concentration of 8 M and a pH of 7 to dissolve the samples prior to digestion. After the sample is digested using standard proteomic protocols and dried, isotopic labeling is completed by resuspending the sample in a solution of 8 M urea at a pH of 8.5, using the same isotopic species of urea as used for digestion and incubating for 4 h at 80 degrees C. Under these conditions, carbamylation occurs only on the primary amines of the peptides. The effects of complete carbamylation on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS) (collision-induced dissociation (CID)) were examined. Peptides that had a C-terminal carbamylated lysine residue were found to have a reduced intensity when viewed by MALDI-TOFMS. CID of a tryptic peptide that was carbamylated on both the N-terminus and the C-terminus was found to have a more uniform distribution of b- and y-ions, as well as prominent ions from loss of water. Reversed-phase chromatography coupled to ESI-MS/MS was used to identify and quantify the isotopically labeled standard proteins, bovine serum albumin (BSA), bovine transferrin, and bovine alpha-casein. Quantitative error between theoretical and observed data ranged from 1.7-10.0%. Relative standard deviations for protein quantitation ranged from 5.2-27.8% over a dynamic range from 0.1-10 (L/H). The development of a method utilizing urea-assisted carbamylation of lysines and N-termini to globally labeled samples for comparative proteomics may prove useful for samples that require a strong chaotrope prior to proteolysis.
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Affiliation(s)
- Peggi M Angel
- Complex Carbohydrate Research Center, The Departments of Biochemistry & Molecular Biology and Chemistry, University of Georgia, 315 Riverbend Road, Athens, GA 30302-4712, USA
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Leong SSJ, Middelberg APJ. A simplified bioprocess for human alpha-fetoprotein production from inclusion bodies. Biotechnol Bioeng 2007; 97:99-117. [PMID: 17115449 DOI: 10.1002/bit.21271] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A simple and effective Escherichia coli (E. coli) bioprocess is demonstrated for the preparation of recombinant human alpha-fetoprotein (rhAFP), a pharmaceutically promising protein that has important immunomodulatory functions. The new rhAFP process employs only unit operations that are easy to scale and validate, and reduces the complexity embedded in existing inclusion body processing methods. A key requirement in the establishment of this process was the attainment of high purity rhAFP prior to protein refolding because (i) rhAFP binds easily to hydrophobic contaminants once refolded, and (ii) rhAFP aggregates during renaturation, in a contaminant- dependent way. In this work, direct protein extraction from cell suspension was coupled with a DNA precipitation-centrifugation step prior to purification using two simple chromatographic steps. Refolding was conducted using a single-step, redox-optimized dilution refolding protocol, with refolding success determined by reversed phase HPLC analysis, ELISA, and circular dichroism spectroscopy. Quantitation of DNA and protein contaminant loads after each unit operation showed that contaminant levels were reduced to levels comparable to traditional flowsheets. Protein microchemical modification due to carbamylation in this urea-based process was identified and minimized, yielding a final refolded and purified product that was significantly purified from carbamylated variants. Importantly, this work conclusively demonstrates, for the first time, that a chemical extraction process can substitute the more complex traditional inclusion body processing flowsheet, without compromising product purity and yield. This highly intensified and simplified process is expected to be of general utility for the preparation of other therapeutic candidates expressed as inclusion bodies.
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Affiliation(s)
- Susanna S J Leong
- Centre for Biomolecular Engineering, Division of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
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50
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The study of three extraction methods for pre-separation and enrichment: Application to the complex proteome separation in rat liver. Sep Purif Technol 2006. [DOI: 10.1016/j.seppur.2006.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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