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Inter-chain disulfide bond improved protein trans-splicing increases plasma coagulation activity in C57BL/6 mice following portal vein FVIII gene delivery by dual vectors. SCIENCE CHINA-LIFE SCIENCES 2013; 56:262-7. [DOI: 10.1007/s11427-013-4455-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 01/30/2013] [Indexed: 11/25/2022]
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102
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Abstract
Successful completion of diverse cellular functions, such as mitosis, positioning organelles, and assembling cilia, depends on the proper assembly of microtubule-based structures. While essentially all of the proteins needed to assemble these structures are now known, we cannot explain how even simple features such as size and shape are determined. As steps toward filling this knowledge gap, there have been several recent efforts toward reconstituting, with purified proteins, the basic structural motifs that recur in diverse cytoskeletal arrays. We discuss these studies and highlight how they shed light on the self-organized assembly of complex and dynamic cytoskeleton-based cellular structures.
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103
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Callahan BP, Stanger M, Belfort M. A redox trap to augment the intein toolbox. Biotechnol Bioeng 2013; 110:1565-73. [PMID: 23280506 DOI: 10.1002/bit.24821] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/14/2012] [Accepted: 12/11/2012] [Indexed: 11/11/2022]
Abstract
The unregulated activity of inteins during expression and consequent side reactions during work-up limits their widespread use in biotechnology and chemical biology. Therefore, we exploited a mechanism-based approach to regulate intein autocatalysis for biotechnological application. The system, inspired by our previous structural studies, is based on reversible trapping of the intein's catalytic cysteine residue through a disulfide bond. Using standard mutagenesis, the disulfide trap can be implemented to impart redox control over different inteins and for a variety of applications both in vitro and in Escherichia coli. Thereby, we first enhanced the output for bioconjugation in intein-mediated protein ligation, also referred to as expressed protein ligation, where precursor recovery and product yield were augmented fourfold to sixfold. Second, in bioseparation experiments, the redox trap boosted precursor recovery and product yield twofold. Finally, the disulfide-trap intein technology stimulated development of a novel bacterial redox sensor. This sensor reliably identified hyperoxic E. coli harboring mutations that disrupt the reductive pathways for thioredoxin and glutathione, against a background of wild-type cells.
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Affiliation(s)
- Brian P Callahan
- Department of Biological Sciences, University at Albany, Life Sciences Building 2061, 1400 Washington Avenue, Albany, New York 12222, USA.
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104
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Intein-Fused Lucine Zippers Increase Plasma Coagulation Activity by Improving Protein Trans-Splicing in Dual-Vector Factor Ⅷ Gene Delivered Mice*. PROG BIOCHEM BIOPHYS 2013. [DOI: 10.3724/sp.j.1206.2012.00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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105
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Vila-Perelló M, Liu Z, Shah NH, Willis JA, Idoyaga J, Muir TW. Streamlined expressed protein ligation using split inteins. J Am Chem Soc 2012; 135:286-92. [PMID: 23265282 PMCID: PMC3544275 DOI: 10.1021/ja309126m] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified proteins are invaluable tools for studying the molecular details of biological processes, and they also hold great potential as new therapeutic agents. Several methods have been developed for the site-specific modification of proteins, one of the most widely used being expressed protein ligation (EPL) in which a recombinant α-thioester is ligated to an N-terminal Cys-containing peptide. Despite the widespread use of EPL, the generation and isolation of the required recombinant protein α-thioesters remain challenging. We describe here a new method for the preparation and purification of recombinant protein α-thioesters using engineered versions of naturally split DnaE inteins. This family of autoprocessing enzymes is closely related to the inteins currently used for protein α-thioester generation, but they feature faster kinetics and are split into two inactive polypeptides that need to associate to become active. Taking advantage of the strong affinity between the two split intein fragments, we devised a streamlined procedure for the purification and generation of protein α-thioesters from cell lysates and applied this strategy for the semisynthesis of a variety of proteins including an acetylated histone and a site-specifically modified monoclonal antibody.
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Affiliation(s)
- Miquel Vila-Perelló
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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106
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Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS One 2012; 7:e43820. [PMID: 22937103 PMCID: PMC3427171 DOI: 10.1371/journal.pone.0043820] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/26/2012] [Indexed: 01/30/2023] Open
Abstract
Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self-association. Since split intein is exploited in protein semi-synthesis, we tested the related protein trans-splicing (PTS) activities of the corresponding split inteins. Notably, a novel functional split intein composed of the N-terminal 36 residues combined with the remaining C-terminal fragment was identified. Its PTS activity was shown to be better than current reported two-piece intein with a short N-terminal segment. Thus, the incorporation of in silico CP prediction facilitated the design of split intein as well as circular permutants.
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107
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Otaka A, Sato K, Ding H, Shigenaga A. One-Pot/Sequential Native Chemical Ligation UsingN-Sulfanylethylanilide Peptide. CHEM REC 2012; 12:479-90. [DOI: 10.1002/tcr.201200007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Indexed: 01/05/2023]
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108
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Matsumoto T, Tanaka T, Kondo A. Enzyme-mediated methodologies for protein modification and bioconjugate synthesis. Biotechnol J 2012; 7:1137-46. [DOI: 10.1002/biot.201200022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 12/14/2022]
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109
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Ling J, Policarpo RL, Rabideau AE, Liao X, Pentelute BL. Protein thioester synthesis enabled by sortase. J Am Chem Soc 2012; 134:10749-52. [PMID: 22686546 PMCID: PMC3465687 DOI: 10.1021/ja302354v] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteins containing a C-terminal thioester are important intermediates in semisynthesis. Currently there is one main method for the synthesis of protein thioesters that relies upon the use of engineered inteins. Here we report a simple strategy, utilizing sortase A, for routine preparation of recombinant proteins containing a C-terminal (α)thioester. We used our method to prepare two different anthrax toxin cargo proteins: one containing an (α)thioester and another containing a D-polypeptide segment situated between two protein domains. We show that both variants can translocate through protective antigen pore. This new method to synthesize a protein thioester allows for interfacing of sortase-mediated ligation and native chemical ligation.
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Affiliation(s)
- Jingjing Ling
- Department of Chemistry, Massachusetts Institute of Technology, 16-573a, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Rocco L. Policarpo
- Department of Chemistry, Massachusetts Institute of Technology, 16-573a, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Amy E. Rabideau
- Department of Chemistry, Massachusetts Institute of Technology, 16-573a, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Xiaoli Liao
- Department of Chemistry, Massachusetts Institute of Technology, 16-573a, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 16-573a, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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110
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Shah NH, Dann GP, Vila-Perelló M, Liu Z, Muir TW. Ultrafast protein splicing is common among cyanobacterial split inteins: implications for protein engineering. J Am Chem Soc 2012; 134:11338-41. [PMID: 22734434 DOI: 10.1021/ja303226x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe the first systematic study of a family of inteins, the split DnaE inteins from cyanobacteria. By measuring in vivo splicing efficiencies and in vitro kinetics, we demonstrate that several inteins can catalyze protein trans-splicing in tens of seconds rather than hours, as is commonly observed for this autoprocessing protein family. Furthermore, we show that when artificially fused, these inteins can be used for rapid generation of protein α-thioesters for expressed protein ligation. This comprehensive survey of split inteins provides indispensable information for the development and improvement of intein-based tools for chemical biology.
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Affiliation(s)
- Neel H Shah
- Department of Chemistry, Princeton University, 325 Frick Chemistry Laboratory, Princeton, New Jersey 08544, USA
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111
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Abstract
Circular proteins, once thought to be rare, are now commonly found in plants. Their chemical synthesis, once thought to be difficult, is now readily achievable. The enabling methodology is largely due to the advances in entropic chemical ligation to overcome the entropy barrier in coupling the N- and C-terminal ends of large peptide segments for either intermolecular ligation or intramolecular ligation in end-to-end cyclization. Key elements of an entropic chemical ligation consist of a chemoselective capture step merging the N and C termini as a covalently linked O/S-ester intermediate to permit the subsequent step of an intramolecular O/S-N acyl shift to form an amide. Many ligation methods exploit the supernucleophilicity of a thiol side chain at the N terminus for the capture reaction, which makes cysteine-rich peptides ideal candidates for the entropy-driven macrocyclization. Advances in desulfurization and modification of the thiol-containing amino acids at the ligation sites to other amino acids add extra dimensions to the entropy-driven ligation methods. This minireview describes recent advances of entropy-driven ligation to prepare circular proteins with or without a cysteinyl side chain.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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112
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113
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Spasser L, Brik A. Chemistry and Biology of the Ubiquitin Signal. Angew Chem Int Ed Engl 2012; 51:6840-62. [DOI: 10.1002/anie.201200020] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 01/07/2023]
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114
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Sun Y, Cao S, Yang M, Wu S, Wang Z, Lin X, Song X, Liao DJ. Basic anatomy and tumor biology of the RPS6KA6 gene that encodes the p90 ribosomal S6 kinase-4. Oncogene 2012; 32:1794-810. [PMID: 22614021 PMCID: PMC3427418 DOI: 10.1038/onc.2012.200] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RPS6KA6 gene encodes the p90 ribosomal S6 kinase-4 (RSK4) that is still largely uncharacterized. In this study we identified a new RSK4 transcription initiation site and several alternative splice sites with a 5’RACE approach. The resulting mRNA variants encompass four possible first start codons. The first 15 nucleotides (nt) of exon 22 in mouse and the penultimate exon in both human (exon 21) and mouse (exon 24) RSK4 underwent alternative splicing, although the penultimate exon deleted variant appeared mainly in cell clines, but not in most normal tissues. Demethylation agent 5-azacytidine inhibited the deletion of the penultimate exon whereas two indolocarbazole-derived inhibitors of cyclin dependent kinase 4 or 6 induced deletion of the first 39 nt from exon 21 of human RSK4. In all human cancer cell lines studied, the 90-kD wild type RSK4 was sparse but, surprisingly, several isoforms at or smaller than 72-kD were expressed as detected by seven different antibodies. On immunoblots, each of these smaller isoforms often appeared as a duplet or triplet and the levels of these isoforms varied greatly among different cell lines and culture conditions. Cyclin D1 inhibited RSK4 expression and serum starvation enhanced the inhibition, whereas c-Myc and RSK4 inhibited cyclin D1. The effects of RSK4 on cell growth, cell death and chemoresponse depended on the mRNA variant or the protein isoform expressed, on the specificity of the cell lines, as well as on the anchorage-dependent or -independent growth conditions and the in vivo situation. Moreover, we also observed that even a given cDNA might be expressed to multiple proteins; therefore, when using a cDNA, one needs to exclude this possibility before attribution of the biological results from the cDNA to the anticipated protein. Collectively, our results suggest that whether RSK4 is oncogenic or tumor suppressive depends on many factors.
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Affiliation(s)
- Y Sun
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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115
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Thompson AD, Makley LN, McMenimen K, Gestwicki JE. The three cornerstones of chemical biology: innovative probes, new discoveries, and enabling tools. ACS Chem Biol 2012; 7:791-6. [PMID: 22594530 DOI: 10.1021/cb3001827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea D. Thompson
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leah N. Makley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kathryn McMenimen
- Department of Chemistry, Mt. Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Jason E. Gestwicki
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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116
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Pavic K, Köhn M. Chemical Biology Techniques Unlock the Secrets of Casein Kinase 2 Regulation by Phosphorylation and Glycosylation. Chembiochem 2012; 13:1253-5. [DOI: 10.1002/cbic.201200235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Indexed: 01/17/2023]
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117
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Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 2012; 13:168-82. [DOI: 10.1038/nrm3286] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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118
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Tarrant MK, Rho HS, Xie Z, Jiang YL, Gross C, Culhane JC, Yan G, Qian J, Ichikawa Y, Matsuoka T, Zachara N, Etzkorn FA, Hart GW, Jeong JS, Blackshaw S, Zhu H, Cole PA. Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat Chem Biol 2012; 8:262-9. [PMID: 22267120 PMCID: PMC3288285 DOI: 10.1038/nchembio.771] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 10/24/2011] [Indexed: 01/08/2023]
Abstract
Protein Ser/Thr kinase CK2 (casein kinase II) is involved in a myriad of cellular processes including cell growth and proliferation by phosphorylating hundreds of substrates, yet the regulation process of CK2 function is poorly understood. Here we report that the CK2 catalytic subunit CK2α is modified by O-GlcNAc on Ser347, proximal to a cyclin-dependent kinase phosphorylation site (Thr344) on the same protein. We use protein semisynthesis to show that Thr344 phosphorylation increases CK2α cellular stability via Pin1 interaction whereas Ser347 glycosylation appears to be antagonistic to Thr344 phosphorylation and permissive to proteasomal degradation. By performing kinase assays with the site-specifically modified phospho- and glyco-modified CK2α in combination with CK2β and Pin1 binding partners on human protein microarrays, we show that CK2 kinase substrate selectivity is modulated by these specific posttranslational modifications. This study suggests how a promiscuous protein kinase can be regulated at multiple levels to achieve particular biological outputs.
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Affiliation(s)
- Mary Katherine Tarrant
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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119
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Schwarzer D, Ludwig C, Thiel IV, Mootz HD. Probing intein-catalyzed thioester formation by unnatural amino acid substitutions in the active site. Biochemistry 2011; 51:233-42. [PMID: 22182201 DOI: 10.1021/bi2014823] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inteins are single-turnover catalysts that splice themselves out of a precursor polypeptide chain. For most inteins, the first step of protein splicing is the formation of a thioester through an N-S acyl shift at the upstream splice junction. However, the mechanism by which this reaction is achieved and the impact of mutations in and close to the active site remain unclear on the atomic level. To investigate these questions, we have further explored a split variant of the Ssp DnaB intein by introducing substitutions with unnatural amino acids within the short synthetic N-terminal fragment. A previously reported collapse of the oxythiazolidine anion intermediate into a thiazoline ring was found to be specificially dependent on the methyl side chain of the flanking Ala(-1). The stereoisomer d-Ala and the constitutional isomers β-Ala and sarcosine did not lead to this side reaction but rather supported splicing. Substitution of the catalytic Cys1 with homocysteine strongly inhibited protein splicing; however, thioester formation was not impaired. These results argue against the requirement of a base to deprotonate the catalytic thiol group prior to the N-S acyl shift, because it should be misaligned for optimal proton abstraction. A previously described mutant intein evolved for more general splicing in different sequence contexts could even rather efficiently splice with this homocysteine. Our findings show the large impact of some subtle structural changes on the protein splicing pathway, but also the remarkable tolerance toward other changes. Such insights will also be important for the biotechnological exploitation of inteins.
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Affiliation(s)
- Dirk Schwarzer
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149 Münster, Germany
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120
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Bavikar SN, Spasser L, Haj-Yahya M, Karthikeyan SV, Moyal T, Ajish Kumar KS, Brik A. Chemical Synthesis of Ubiquitinated Peptides with Varying Lengths and Types of Ubiquitin Chains to Explore the Activity of Deubiquitinases. Angew Chem Int Ed Engl 2011; 51:758-63. [DOI: 10.1002/anie.201106430] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Revised: 10/12/2011] [Indexed: 01/27/2023]
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121
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Bavikar SN, Spasser L, Haj-Yahya M, Karthikeyan SV, Moyal T, Ajish Kumar KS, Brik A. Chemical Synthesis of Ubiquitinated Peptides with Varying Lengths and Types of Ubiquitin Chains to Explore the Activity of Deubiquitinases. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106430] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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122
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Ramsden R, Arms L, Davis TN, Muller EGD. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP. BMC Biotechnol 2011; 11:71. [PMID: 21708017 PMCID: PMC3141402 DOI: 10.1186/1472-6750-11-71] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/27/2011] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein. RESULTS The Pch PRP8 mini-intein of Penicillium chrysogenum was modified to include: 1) aminoglycoside phosphotransferase; 2) imidazoleglycerol-phosphate dehydratase, His5 from S. pombe ; 3) hygromycin B phosphotransferase; and 4) the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in E. coli, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in S. cerevisiae. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene CMD1. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker. CONCLUSIONS Inteins continue to show their flexibility as tools in molecular biology. The Pch PRP8 intein can successfully tolerate a variety of genetic markers and still retain high splicing efficiency. We have shown that a genetically marked intein can be used to insert GFP in one-step within a target protein in vivo.
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Affiliation(s)
- Richard Ramsden
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Luther Arms
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Eric GD Muller
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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123
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Shah NH, Vila-Perelló M, Muir TW. Kinetic control of one-pot trans-splicing reactions by using a wild-type and designed split intein. Angew Chem Int Ed Engl 2011; 50:6511-5. [PMID: 21656885 DOI: 10.1002/anie.201102909] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Indexed: 01/28/2023]
Affiliation(s)
- Neel H Shah
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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124
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Shah NH, Vila-Perelló M, Muir TW. Kinetic Control of One-Pot Trans-Splicing Reactions by Using a Wild-Type and Designed Split Intein. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102909] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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125
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Fang GM, Li YM, Shen F, Huang YC, Li JB, Lin Y, Cui HK, Liu L. Protein Chemical Synthesis by Ligation of Peptide Hydrazides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100996] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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126
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Fang GM, Li YM, Shen F, Huang YC, Li JB, Lin Y, Cui HK, Liu L. Protein chemical synthesis by ligation of peptide hydrazides. Angew Chem Int Ed Engl 2011; 50:7645-9. [PMID: 21648030 DOI: 10.1002/anie.201100996] [Citation(s) in RCA: 577] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Ge-Min Fang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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127
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Popp MWL, Ploegh HL. Bilden und Brechen von Peptidbindungen: Protein-Engineering mithilfe von Sortase. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008267] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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128
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Popp MWL, Ploegh HL. Making and breaking peptide bonds: protein engineering using sortase. Angew Chem Int Ed Engl 2011; 50:5024-32. [PMID: 21538739 DOI: 10.1002/anie.201008267] [Citation(s) in RCA: 221] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Indexed: 01/31/2023]
Abstract
Sortases are a class of bacterial enzymes that possess transpeptidase activity. It is their ability to site-specifically break a peptide bond and then reform a new bond with an incoming nucleophile that makes sortase an attractive tool for protein engineering. This technique has been adopted for a range of applications, from chemistry-based to cell biology and technology. In this Minireview we provide a brief overview of the biology of sortase enzymes and current applications in protein engineering. We identify areas that lend themselves to further innovation and that suggest new applications.
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129
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Abstract
Epigenetics, broadly defined as the inheritance of non-Mendelian phenotypic traits, can be more narrowly defined as heritable alterations in states of gene expression ("on" versus "off") that are not linked to changes in DNA sequence. Moreover, these alterations can persist in the absence of the signals that initiate them, thus suggesting some kind of "memory" to epigenetic forms of regulation. How, for example, during early female mammalian development, is one X chromosome selected to be kept in an active state, while the genetically identical sister X chromosome is "marked" to be inactive, even though they reside in the same nucleus, exposed to the same collection of shared trans-factors? Once X inactivation occurs, how are these contrasting chromatin states maintained and inherited faithfully through subsequent cell divisions? Chromatin states, whether active (euchromatic) or silent (heterochromatic) are established, maintained, and propagated with remarkable precision during normal development and differentiation. However, mistakes made in establishing and maintaining these chromatin states, often executed by a variety of chromatin-remodeling activities, can lead to mis-expression or mis-silencing of critical downstream gene targets with far-reaching implications for human biology and disease, notably cancer. Though chromatin biologists have identified many of the "inputs" that are important for controlling chromatin states, the detailed mechanisms by which these processes work remain largely opaque, in part due to the staggering complexity of the chromatin polymer, the physiologically relevant form of our genome. The primary objective of this article is to serve as a "call to arms" for chemists to contribute to the development of the precision tools needed to answer pressing molecular problems in this rapidly moving field.
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Affiliation(s)
- C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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130
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Frederiks F, Stulemeijer IJE, Ovaa H, van Leeuwen F. A modified epigenetics toolbox to study histone modifications on the nucleosome core. Chembiochem 2010; 12:308-13. [PMID: 21243718 DOI: 10.1002/cbic.201000617] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Indexed: 11/06/2022]
Abstract
In the eukaryotic cell nucleus, the DNA is packaged in a structure called chromatin. The fundamental building block of chromatin is the nucleosome, which is composed of DNA wrapped around an octamer of four distinct histone proteins. Post-translational modifications (PTMs) of histone proteins can affect chromatin structure and function and thereby play critical roles in regulating gene expression. Most histone PTMs are found in unstructured histone tails that protrude from the nucleosome core. As a consequence, (synthetic) peptide truncations of these tails provide convenient substrates for the analysis of histone binding proteins and modifying enzymes. Modifications located on residues that reside in the nucleosome core are more difficult to study because short peptides do not recapitulate this defined structured state well. Methylation of histone H3 on Lys79 (H3K79), mediated by the Dot1 enzyme, is an example of such a core PTM. This modification, which is highly conserved, is linked to human leukemia, and pharmacological modulation of Dot1 activity could be a strategy to treat leukemia. Here we review the available and emerging genetic, biochemical, and chemical methods that together are starting to reveal the function and regulation of this and other histone modifications on the nucleosome core.
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Affiliation(s)
- Floor Frederiks
- Division of Gene Regulation, Netherlands Cancer Institute, Netherlands Proteomics Centre, Amsterdam, The Netherlands
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131
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Pereira B, Shemella PT, Amitai G, Belfort G, Nayak SK, Belfort M. Spontaneous proton transfer to a conserved intein residue determines on-pathway protein splicing. J Mol Biol 2010; 406:430-42. [PMID: 21185311 DOI: 10.1016/j.jmb.2010.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 12/16/2010] [Indexed: 02/06/2023]
Abstract
The discovery of inteins, which are protein-splicing elements, has stimulated interest for various applications in chemical biology, bioseparations, drug delivery, and sensor development. However, for inteins to effectively contribute to these applications, an increased mechanistic understanding of cleavage and splicing reactions is required. While the multistep chemical reaction that leads to splicing is often explored and utilized, it is not clear how the intein navigates through the reaction space. The sequence of reaction steps must progress in concert in order to yield efficient splicing while minimizing off-pathway cleavage reactions. In this study, we demonstrate that formation of a previously identified branched intermediate is the critical step for determining splicing over cleavage products. By combining experimental assays and quantum mechanical simulations, we identify the electrostatic interactions that are important to the dynamics of the reaction steps. We illustrate, via an animated simulation trajectory, a proton transfer from the first C-terminal extein residue to a conserved aspartate, which synchronizes the multistep enzymatic reaction that is key to splicing. This work provides new insights into the complex interplay between critical active-site residues in the protein splicing mechanism, thereby facilitating biotechnological application while shedding light on multistep enzyme activity.
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Affiliation(s)
- Brian Pereira
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
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