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Sun J, Liu X, Guo J, Zhao W, Gao W. Pyridine-2,6-dicarboxaldehyde-Enabled N-Terminal In Situ Growth of Polymer-Interferon α Conjugates with Significantly Improved Pharmacokinetics and In Vivo Bioactivity. ACS APPLIED MATERIALS & INTERFACES 2021; 13:88-96. [PMID: 33382581 DOI: 10.1021/acsami.0c15786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymer-protein conjugates are a class of biohybrids with unique properties that are highly useful in biomedicine ranging from protein therapeutics to biomedical imaging; however, it remains a considerable challenge to conjugate polymers to proteins in a site-specific, mild, and efficient way to form polymer-protein conjugates with uniform structures and properties and optimal functions. Herein we report pyridine-2,6-dicarboxaldehyde (PDA)-enabled N-terminal modification of proteins with polymerization initiators for in situ growth of poly(oligo(ethylene glycol)methyl ether methacrylate) (POEGMA) conjugates uniquely at the N-termini of a range of natural and recombinant proteins in a mild and efficient fashion. The formed POEGMA-protein conjugates showed highly retained in vitro bioactivity as compared with free proteins. Notably, the in vitro bioactivity of a POEGMA-interferon α (IFN) conjugate synthesized by this new chemistry is 8.1-fold higher than that of PEGASYS that is a commercially available and Food and Drug Administration (FDA) approved PEGylated IFN. The circulation half-life of the conjugate is similar to that of PEGASYS but is 46.2 times longer than that of free IFN. Consequently, the conjugate exhibits considerably improved antiviral bioactivity over free IFN and even PEGASYS in a mouse model. These results indicate that the PDA-enabled N-terminal grafting-from method is applicable to a number of proteins whose active sites are far away from the N-terminus for the synthesis of N-terminal polymer-protein conjugates with high yield, well-retained activity, and considerably improved pharmacology for biomedical applications.
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Affiliation(s)
- Jiawei Sun
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinyu Liu
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology, Beijing 100081, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
| | - Jianwen Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenguo Zhao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Weiping Gao
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology, Beijing 100081, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
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2
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Lorenzatto KR, Kim K, Ntai I, Paludo GP, Camargo de Lima J, Thomas PM, Kelleher NL, Ferreira HB. Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage. J Proteome Res 2015; 14:4805-14. [PMID: 26465659 DOI: 10.1021/acs.jproteome.5b00642] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Echinococcus granulosus is the causative agent of cystic hydatid disease, a neglected zoonosis responsible for high morbidity and mortality. Several molecular mechanisms underlying parasite biology remain poorly understood. Here, E. granulosus subcellular fractions were analyzed by top down and bottom up proteomics for protein identification and characterization of co-translational and post-translational modifications (CTMs and PTMs, respectively). Nuclear and cytosolic extracts of E. granulosus protoscoleces were fractionated by 10% GELFrEE and proteins under 30 kDa were analyzed by LC-MS/MS. By top down analysis, 186 proteins and 207 proteoforms were identified, of which 122 and 52 proteoforms were exclusively detected in nuclear and cytosolic fractions, respectively. CTMs were evident as 71% of the proteoforms had methionine excised and 47% were N-terminal acetylated. In addition, in silico internal acetylation prediction coupled with top down MS allowed the characterization of 9 proteins differentially acetylated, including histones. Bottom up analysis increased the overall number of identified proteins in nuclear and cytosolic fractions to 154 and 112, respectively. Overall, our results provided the first description of the low mass proteome of E. granulosus subcellular fractions and highlighted proteoforms with CTMs and PTMS whose characterization may lead to another level of understanding about molecular mechanisms controlling parasitic flatworm biology.
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Affiliation(s)
- Karina R Lorenzatto
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Kyunggon Kim
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Ioanna Ntai
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Gabriela P Paludo
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson Camargo de Lima
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrique B Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
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3
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Erdmann I, Marter K, Kobler O, Niehues S, Abele J, Müller A, Bussmann J, Storkebaum E, Ziv T, Thomas U, Dieterich DC. Cell-selective labelling of proteomes in Drosophila melanogaster. Nat Commun 2015; 6:7521. [PMID: 26138272 PMCID: PMC4507001 DOI: 10.1038/ncomms8521] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 05/16/2015] [Indexed: 01/06/2023] Open
Abstract
The specification and adaptability of cells rely on changes in protein composition. Nonetheless, uncovering proteome dynamics with cell-type-specific resolution remains challenging. Here we introduce a strategy for cell-specific analysis of newly synthesized proteomes by combining targeted expression of a mutated methionyl-tRNA synthetase (MetRS) with bioorthogonal or fluorescent non-canonical amino-acid-tagging techniques (BONCAT or FUNCAT). Substituting leucine by glycine within the MetRS-binding pocket (MetRSLtoG) enables incorporation of the non-canonical amino acid azidonorleucine (ANL) instead of methionine during translation. Newly synthesized proteins can thus be labelled by coupling the azide group of ANL to alkyne-bearing tags through ‘click chemistry'. To test these methods for applicability in vivo, we expressed MetRSLtoG cell specifically in Drosophila. FUNCAT and BONCAT reveal ANL incorporation into proteins selectively in cells expressing the mutated enzyme. Cell-type-specific FUNCAT and BONCAT, thus, constitute eligible techniques to study protein synthesis-dependent processes in complex and behaving organisms. Mutated tRNA synthetases can incorporate non-canonical amino acids into proteins. Erdmann et al. exploit this property to metabolically label newly synthesized proteins in selected cell types in Drosophila, and demonstrate their detection using proteomics (BONCAT) and fluorescence imaging (FUNCAT).
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Affiliation(s)
- Ines Erdmann
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Kathrin Marter
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Oliver Kobler
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Sven Niehues
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Julia Abele
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Anke Müller
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Julia Bussmann
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Erik Storkebaum
- 1] Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany [2] Faculty of Medicine, University of Münster, Münster 48149, Germany
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion, Haifa 32000, Israel
| | - Ulrich Thomas
- Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Daniela C Dieterich
- 1] Research Group Neuronal Plasticity and Communication, Institute for Pharmacology and Toxicology, Otto-von-Guericke-University Magdeburg, Magdeburg 39120, Germany [2] Research Group Neuralomics, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany [3] Center for Behavioral Brain Sciences, Magdeburg 39118, Germany
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4
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Banday AR, Azim S, Hussain MA, Nehar S, Tabish M. Computational prediction and characterisation of ubiquitously expressed new splice variant of Prkaca gene in mouse. Cell Biol Int 2013; 37:687-93. [PMID: 23456795 DOI: 10.1002/cbin.10080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/13/2013] [Indexed: 11/11/2022]
Abstract
Prkaca gene of mouse encodes for a cAMP dependent protein kinase catalytic alpha subunit. PKA occurs naturally as a 4-membered structure having two regulatory (R) and two catalytic (C) subunits each encoded by separate gene. Alternatively spliced two transcript variants are known for the Prkaca gene, which encode for two isoforms of PKA C-subunits, namely Cα1 and Cα2. These isoforms arise as a result of alternative splicing of the first coding exon with the internal exons. We have identified a new transcript variant using combinatorial approach of bioinformatics and molecular biology techniques involving RT-PCR, semi-nested PCR and sequencing. The new transcript variant encoding Cα3 isoform has N-terminus that differs from Cα1 and Cα2 isoforms. Cα3 isoform also arise as a result of alternative splicing of first coding exon with the internal exon. Newly identified transcript is expressed ubiquitously in different tissues examined.
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Affiliation(s)
- Abdul Rouf Banday
- Faculty of Life Sciences, Department of Biochemistry, A.M. University, Aligarh 202 002, Uttar Pradesh, India
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5
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Banday AR, Azim S, Rehman SU, Tabish M. Two novel N-terminal coding exons of Prkar1b gene of mouse: Identified using a novel approach of in silico and molecular biology techniques. Gene 2012; 500:73-9. [DOI: 10.1016/j.gene.2012.02.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 02/29/2012] [Accepted: 02/29/2012] [Indexed: 11/25/2022]
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6
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Banday AR, Azim S, Tabish M. Identification and expression analysis of three novel splice variants of protein kinase A catalytic β subunit gene in the mouse using combinatorial in silico and molecular biology approaches. FEBS J 2012; 279:572-85. [DOI: 10.1111/j.1742-4658.2011.08446.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Zhang X, Ye J, Engholm-Keller K, Højrup P. A proteome-scale study on in vivo protein Nα
-acetylation using an optimized method. Proteomics 2010; 11:81-93. [DOI: 10.1002/pmic.201000453] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 08/11/2010] [Accepted: 09/29/2010] [Indexed: 12/26/2022]
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8
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A proteomics approach to study in vivo protein Nα-modifications. J Proteomics 2009; 73:240-51. [DOI: 10.1016/j.jprot.2009.09.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/21/2009] [Accepted: 09/09/2009] [Indexed: 11/22/2022]
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9
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Tags for labeling protein N-termini with subtiligase for proteomics. Bioorg Med Chem Lett 2008; 18:6000-3. [PMID: 18762420 DOI: 10.1016/j.bmcl.2008.08.044] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 08/11/2008] [Accepted: 08/12/2008] [Indexed: 11/22/2022]
Abstract
The peptide ligase subtiligase, derived from subtilisin, has been employed in the identification of protein N-termini in complex mixtures. Here, the peptide ester substrates for the ligation reaction were optimized with respect to solubility, resulting in greater incorporation of the N-terminal tags. Additionally, the quantitation of the incorporated tags was explored, and a 'click' chemistry-based derivatization provided the ability to quantitate the tag to low nanomolar concentrations by sandwich ELISA. These new tags should expand the utility of subtiligase for the proteomic study of N-termini.
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10
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Kanno T, Kitano M, Kato R, Omori A, Endo Y, Tozawa Y. Sequence specificity and efficiency of protein N-terminal methionine elimination in wheat-embryo cell-free system. Protein Expr Purif 2006; 52:59-65. [PMID: 17123829 DOI: 10.1016/j.pep.2006.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2006] [Revised: 09/06/2006] [Accepted: 09/12/2006] [Indexed: 10/24/2022]
Abstract
Recent improvements in wheat-embryo cell-free translation resulted in a highly productive system for protein preparation. To clarify N-terminal processing of the cell-free system in a preparative-scale (> mg protein product per ml), 20 mutant variants of maltose-binding protein (MalE), each having a different penultimate residue in the sequence Met-Xaa-Ile-Glu-, and 20 glutathione S-transferase (GST) variants, having Met-Xaa-Pro-Ile-sequence, were designed and synthesized. The MalE and GST proteins were purified by amylose-resin and glutathione columns, respectively, followed by analysis of their N-terminal sequences. These investigations revealed that sequence specificity and efficiency of the N-terminal Met (N-Met) elimination in the cell-free system are similar to those reported from investigations in cellular systems or in the wheat-embryo cell-free protein expression system in analytical scale (approximately 10 microg protein product per ml). Cleavage of the N-Met is basically determined by the penultimate amino acid in the polypeptide sequence. In the case of MalE, the cleavage was efficient when the penultimate residue was Ala, Cys, Gly, Pro, Ser or Thr. But, in the case of GST with Pro as the antepenultimate residue, the efficiency was significantly reduced when the penultimate residue was Gly or Thr. We also confirmed that substitution of the antepenultimate residue in MalE to Pro drastically reduced the efficiency of N-Met cleavage when the penultimate residue was Ala, Gly, Pro, Ser or Thr, indicating inhibitory effects of antepenultimate residue Pro on N-Met elimination. These results clarified sequence-specific functions of the endogenous N-terminal processing machinery in the scaled-up wheat-embryo cell-free translation system.
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Affiliation(s)
- Takuya Kanno
- Cell-Free Science and Technology Research Center, Ehime University, Matsuyama 790-8577, Japan
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11
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Frottin F, Martinez A, Peynot P, Mitra S, Holz RC, Giglione C, Meinnel T. The proteomics of N-terminal methionine cleavage. Mol Cell Proteomics 2006; 5:2336-49. [PMID: 16963780 DOI: 10.1074/mcp.m600225-mcp200] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1'), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (>120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1' were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues at P2', P3', and P4' strongly slowed the reaction, and some proteins with Val and Thr at P1' could not undergo Met cleavage. These in vitro data were fully consistent with data for 862 E. coli proteins with known N-terminal sequences in vivo. The specificity sites were found to be identical to those for the other type of MAPs, MAP2s, and a dedicated prediction tool for Met cleavage is now available. Taking into account the rules of MAP cleavage and leader peptide removal, the N termini of all proteins were predicted from the annotated genome and compared with data obtained in vivo. This analysis showed that proteins displaying N-Met cleavage are overrepresented in vivo. We conclude that protein secretion involving leader peptide cleavage is more frequent than generally thought.
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Affiliation(s)
- Frédéric Frottin
- Protein Maturation, Cell Fate, and Therapeutics, Institut des Sciences du Végétal, UPR2355, CNRS, Bâtiment 23, 1 avenue de la Terrasse, F-91198 Gif-sur-Yvette cedex, France
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12
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Iida T, Kamo M, Uozumi N, Inui T, Imai K. Further application of a two-step heparin affinity chromatography method using divalent cations as eluents: Purification and identification of membrane-bound heparin binding proteins from the mitochondrial fraction of HL-60 cells. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 823:209-12. [PMID: 16019269 DOI: 10.1016/j.jchromb.2005.06.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 06/07/2005] [Accepted: 06/09/2005] [Indexed: 10/25/2022]
Abstract
Membrane proteins were obtained from the mitochondrial fraction of HL-60 cells by solubilization with octyl glucoside and bound to heparin-gels. Bound proteins were successively eluted with solutions containing increasing concentrations of Mg(2+) in the first and increasing concentrations of Ca(2+) in the second chromatography. After SDS-PAGE and subsequent N-terminal amino acid analysis of proteins on each band, 13 proteins were identified. Fifteen out of the 37 proteins analysed were modified at their N-termini. These results show that this two-step affinity chromatography method using divalent cations as eluents can be applied to a variety of membranes for the isolation of specific proteins.
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Affiliation(s)
- Tsukimi Iida
- Department of Science of Human Life, City College of Mie, 157, Ishinnden-nakano, Tsu, Mie 514-0112, Japan.
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13
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Lapko VN, Smith DL, Smith JB. Methylation and carbamylation of human gamma-crystallins. Protein Sci 2003; 12:1762-74. [PMID: 12876325 PMCID: PMC2323962 DOI: 10.1110/ps.0305403] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2003] [Revised: 05/01/2003] [Accepted: 05/01/2003] [Indexed: 10/26/2022]
Abstract
Accessible sulfhydryls of cysteine residues are likely sites of reaction in long-lived proteins such as human lens crystallins. Disulfide bonding between cysteines is a major contributor to intermolecular cross-linking and aggregation of crystallins. A recently reported modification of gammaS-crystallins, S-methylation of cysteine residues, can prevent disulfide formation. The aim of this study was to determine whether cysteines in gammaC-, gammaD-, and gammaB-crystallins are also S-methylated. Our data show that all the gamma-crystallins are S-methylated, but only at specific cysteines. In gammaD-crystallin, methylation is exclusively at Cys 110, whereas in gammaC- and gammaB-crystallins, the principal methylation site is Cys 22 with minor methylation at Cys 79. gammaD-crystallin is the most heavily methylated gamma-crystallin. gammaD-Crystallins from adult lenses are 37%-70% methylated, whereas gammaC and gammaB are approximately 12% methylated. The specificity of gamma-crystallin methylation and its occurrence in young clear lenses supports the idea that inhibition of disulfide bonding by S-methylation may play a protective role against cataract. Another modification, not reported previously, is carbamylation of the N termini of gammaB-, gammaC-, gammaD-crystallins. N-terminal carbamylation is likely a developmentally related modification that does not negatively impact crystallin function.
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Affiliation(s)
- Veniamin N Lapko
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
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14
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Imai K, Iida T, Takano Y, Uozumi N. Membrane-bound heparin binding proteins from HL-60 cells purified in a two-step affinity chromatography differentially eluted with divalent cations. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 780:1-12. [PMID: 12383474 DOI: 10.1016/s1570-0232(02)00404-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Solubilized membrane proteins from HL-60 cells were separated by two-step affinity chromatography. Proteins eluted with MgCl2 in the first heparin-gel were applied to the second heparin-gel and eluted with CaCl2. The eluted proteins were analysed and purified by electrophoresis. N-terminal amino acid sequences of eight proteins on the characteristic bands were determined. Homology search for the sequences indicated that three microsomal proteins, two nuclear proteins and a glycolytic enzyme were eluted with divalent cations, whereas a nuclear ribonucleoprotein and a membrane-cytoskelton linker protein were not dissociated with divalent cations, but with 2 M NaCl. Heparin affinity chromatography combined with differential elution with divalent cations can be a useful method for separation of membrane proteins.
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Affiliation(s)
- Katsuyuki Imai
- Department of Science of Human Life, City College of Mie, Issinden-Nakano, Tsu-shi, Mie 514-0112, Japan. imai_
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15
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Banbula A, Mak P, Smoluch M, Travis J, Potempa J. Arginine-specific cysteine proteinase from porphyromonas gingivalis as a convenient tool in protein chemistry. Biol Chem 2001; 382:1399-404. [PMID: 11688723 DOI: 10.1515/bc.2001.172] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
RgpB, a cysteine proteinase produced by Porphyromonas gingivalis, exhibits proteolytic activity selectively directed against peptide bonds containing an arginine residue in the P1 position. Here we show that this enzyme can be used for very efficient and specific protein cleavage. RgpB is highly active even at high concentrations of denaturing agents, including urea (up to 6 M) and SDS (0.1%), both of them being commonly used for solubilization of insoluble proteins and peptides. Moreover, RgpB is able to digest polypeptide chains in buffers supplemented with 1% Triton X-100, 1% octyl or decylpyranoside, detergents employed for the enzymatic digestion of proteins transferred onto nitrocellulose membranes. These features render RgpB a suitable tool for use in protein chemistry.
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Affiliation(s)
- A Banbula
- Institute of Molecular Biology, Jagiellonian University, Krakow, Poland
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16
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Utsumi T, Sato M, Nakano K, Takemura D, Iwata H, Ishisaka R. Amino acid residue penultimate to the amino-terminal gly residue strongly affects two cotranslational protein modifications, N-myristoylation and N-acetylation. J Biol Chem 2001; 276:10505-13. [PMID: 11124252 DOI: 10.1074/jbc.m006134200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To examine the amino-terminal sequence requirements for cotranslational protein N-myristoylation, a series of site-directed mutagenesis of N-terminal region were performed using tumor necrosis factor as a nonmyristoylated model protein. Subsequently, the susceptibility of these mutants to protein N-myristoylation was evaluated by metabolic labeling in an in vitro translation system or in transfected cells. It was found that the amino acid residue at position 3 in an N-myristoylation consensus motif, Met-Gly-X-X-X-Ser-X-X-X, strongly affected the susceptibility of the protein to two different cotranslational protein modifications, N-myristoylation and N-acetylation; 10 amino acids (Ala, Ser, Cys, Thr, Val, Asn, Leu, Ile, Gln, and His) with a radius of gyration smaller than 1.80 A directed N-myristoylation, two negatively charged residues (Asp and Glu) directed N-acetylation, and two amino acids (Gly and Met) directed heterogeneous modification with both N-myristoylation and N-acetylation. The amino acid requirements at this position for the two modifications were dramatically changed when Ser at position 6 in the consensus motif was replaced with Ala. Thus, the amino acid residue penultimate to the N-terminal Gly residue strongly affected two cotranslational protein modifications, N-myristoylation and N-acetylation, and the amino acid requirements at this position for these two modifications were significantly affected by downstream residues.
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Affiliation(s)
- T Utsumi
- Department of Biological Chemistry and Department of Veterinary Medicine, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan.
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17
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Bradshaw RA, Brickey WW, Walker KW. N-terminal processing: the methionine aminopeptidase and N alpha-acetyl transferase families. Trends Biochem Sci 1998; 23:263-7. [PMID: 9697417 DOI: 10.1016/s0968-0004(98)01227-4] [Citation(s) in RCA: 364] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Removal of the initiator methionine and/or acetylation of the alpha-amino group are among the earliest possible chemical modifications that occur during protein synthesis in eukaryotes. These events are catalyzed by methionine aminopeptidase and N alpha-acetyltransferase, respectively. Recent advances in the isolation and characterization of these enzymes indicate that they exist as isoforms that vary in cellular location, function, and evolutionary origins.
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Affiliation(s)
- R A Bradshaw
- Dept of Physiology and Biophysics, College of Medicine, University of California, Irvine 92697, USA
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Gu QM, Sih CJ. Isolation and identification of C-terminal peptides of proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1995; 46:366-71. [PMID: 8567180 DOI: 10.1111/j.1399-3011.1995.tb01070.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A method for the isolation and identification of C-terminal peptides of proteins has been developed. The procedure entails the racemization of the C-terminal amino acid by reaction of the N-trifluoroacetylated protein with acetic anhydride and pyridine. After deprotection, the protein is fragmented to yield a mixture of peptides, which in turn are digested with carboxypeptidases. All peptides are hydrolyzed to L-amino acids except the C-terminal peptide with the terminal D-amino-acid residue. It is resistant to the action of carboxypeptidases and is readily identified by peptide mapping.
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Affiliation(s)
- Q M Gu
- School of Pharmacy, University of Wisconsin, Madison, USA
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19
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Vergères G, Winterhalter KH, Richter C. Localization of the N-terminal methionine of rat liver cytochrome P-450 in the lumen of the endoplasmic reticulum. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1063:235-41. [PMID: 1901499 DOI: 10.1016/0005-2736(91)90376-j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recent cumulative evidence suggests that liver microsomal cytochrome P-450 (P-450) is exposed to the cytosol with the exception of the N-terminal peptide (amino acid residues 1 to 21), or two peptides (residues 1 to 60). We tested the localization of the N-terminal methionine residue of P-450IIB1 of rat liver microsomes in the natural membrane with the site-specific reagent fluorescein isothiocyanate. The N-terminus of isolated P-450 was stoichiometrically modified in solution with fluorescein isothiocyanate. In intact microsomes, the N-terminus was not modified but became accessible to the reagent when the membrane was dissolved with Triton X-100. Our results indicate that the N-terminus faces the lumen of the endoplasmic reticulum, and we propose that P-450 spans the membrane only once with amino acid residues 1 to 21.
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Affiliation(s)
- G Vergères
- Laboratorium für Biochemie, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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20
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Chang YH, Teichert U, Smith JA. Purification and characterization of a methionine aminopeptidase from Saccharomyces cerevisiae. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)45456-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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21
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Levin MS, Li E, Gordon JI. Structure-function analyses of mammalian cellular retinol-binding proteins by expression in Escherichia coli. Methods Enzymol 1990; 189:506-20. [PMID: 2292966 DOI: 10.1016/0076-6879(90)89329-g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Lowe J, Sacchettini J, Laposata M, McQuillan J, Gordon J. Expression of rat intestinal fatty acid-binding protein in Escherichia coli. Purification and comparison of ligand binding characteristics with that of Escherichia coli-derived rat liver fatty acid-binding protein. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45664-5] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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23
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Driessen HP, de Jong WW, Tesser GI, Bloemendal H. The mechanism of N-terminal acetylation of proteins. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1985; 18:281-325. [PMID: 3902358 DOI: 10.3109/10409238509086784] [Citation(s) in RCA: 192] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
N alpha-acetylation is almost exclusively restricted to eukaryotic structural proteins. As a rule it is a post-initiational process, requiring the presence of the enzyme N alpha-acetyltransferase and the acetyl donor acetylcoenzyme A. N alpha-acetyltransferases appear to have a narrow substrate specificity, which is very similar for enzymes from different tissues and species. Amino acids predominantly present at the N terminus of N alpha-acetylated proteins are alanine, serine, and methionine. The occurrence of these residues is apparently a prerequisite for acetylation. The region following these amino acids is also important. If methionine is at the N terminus, the second position is always occupied by a strongly hydrophilic amino acid. Two- and three-dimensional structural characteristics of the protein do not seem to play a major role in N alpha-acetylation. Up to now the exact function for N alpha-acetylation is not known.
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Brown J. A comparison of the turnover of alpha-N-acetylated and nonacetylated mouse L-cell proteins. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37787-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Deutch CE, Scarpulla RC, Soffer RL. Posttranslational NH2-terminal aminoacylation. CURRENT TOPICS IN CELLULAR REGULATION 1978; 13:1-28. [PMID: 352619 DOI: 10.1016/b978-0-12-152813-3.50005-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Evidence that approximately eighty per cent of the soluble proteins from Ehrlich ascites cells are Nalpha-acetylated. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33793-6] [Citation(s) in RCA: 222] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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Black JA, Stenzel P, Harkins RN. The terminal amino acids of protein sequences and protein maturation. J Theor Biol 1975; 50:161-6. [PMID: 1127955 DOI: 10.1016/0022-5193(75)90030-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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Johnson GL, Brown JL. Partial purification and characterization of two peptidases from Neurospora crassa. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 370:530-40. [PMID: 4280316 DOI: 10.1016/0005-2744(74)90114-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Abstract
A methionyl-specific dipeptidase from Streptococcus pneumoniae has been described. This enzyme and the pneumococcal tripeptidase have been shown to be intracellular, soluble, and constitutive. In addition to their function in cleavage of peptide nutrients, these peptidases may play a role in protein synthesis and turnover.
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31
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Koffer-Gutmann A, Arnstein HR. The presence of N-terminal methionine on nascent protein of rat liver and rabbit reticulocytes and its cleavage during polypeptide-chain elongation. Biochem J 1973; 134:969-83. [PMID: 4762764 PMCID: PMC1177905 DOI: 10.1042/bj1340969] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
1. The size of nascent globin peptides from which the N-terminal methionine residue is cleaved has been investigated by comparing the proportion of N-terminal methionine and valine in short and long chains. Nascent chains were labelled in rabbit reticulocyte lysates, fractionated according to length by chromatography on Sephadex G-50, and analysed by the Edman degradation of selected pooled fractions. It was found that different peptide fractions contained either methionine or valine, but not both, as the N-terminal residue. Methionine was present at the N-terminus of globin chains containing up to approx. 50 amino acids whereas valine was found to be the N-terminal amino acid of longer peptides. 2. In similar experiments with nascent proteins of rat liver, labelled either in vivo or in a cell-free system containing microsomal material and cell sap, evidence was obtained for the presence of methionine at the N-terminus of nascent chains up to approx. 65 amino acid residues long. Thus protein synthesis in liver appears to be initiated also by methionine, but in this case cleavage takes place somewhat later during peptide elongation than in globin synthesis.
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Brown JL. The modification of the amino terminal region of Escherichia coli proteins after initiation with methionine analogues. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 294:527-9. [PMID: 4574657 DOI: 10.1016/0005-2787(73)90108-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Arginyl Transfer Ribonucleic Acid Protein Transferase and Endogenous Acceptor Proteins in Cultured Mammalian Cells. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)44842-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Abstract
There is 50% identity in the sequences of the first 50 residues of the alpha chains of Escherichia coli and Pseudomonas putida. No deletions or additions of residues are found in this region, except for the N-terminal methionine residue which is missing in the polypeptide isolated from P. putida. Most of the residues which differ are chemically dissimilar, and half of them are specified by codons which differ by more than a single base. The two residues known by mutational analysis to be essential for catalysis in E. coli are conserved in P. putida. The potential taxonomic usefulness of information of this sort is analyzed.
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36
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Brown JL, Krall JF. Studies on the substrate specificity of an Escherichia coli peptidase. Biochem Biophys Res Commun 1971; 42:390-7. [PMID: 5542886 DOI: 10.1016/0006-291x(71)90383-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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