1
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Liu XY, Yang YL, Dang Y, Marek I, Zhang FG, Ma JA. Tetrazole Diversification of Amino Acids and Peptides via Silver-Catalyzed Intermolecular Cycloaddition with Aryldiazonium Salts. Angew Chem Int Ed Engl 2023; 62:e202304740. [PMID: 37212541 DOI: 10.1002/anie.202304740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/23/2023]
Abstract
Selective structural modification of amino acids and peptides is a central strategy in organic chemistry, chemical biology but also in pharmacology and material science. In this context, the formation of tetrazole rings, known to possess significant therapeutic properties, would expand the chemical space of unnatural amino acids but has received less attention. In this study, we demonstrated that the classic unimolecular Wolff rearrangement of α-amino acid-derived diazoketones could be replaced by a faster intermolecular cycloaddition reaction with aryldiazonium salts under identical practical conditions. This strategy provides an efficient synthetic platform that could transform proteinogenic α-amino acids into a plethora of unprecedented tetrazole-decorated amino acid derivatives with preservation of the stereocenters. Density functional theory studies shed some light on the reaction mechanism and provided information regarding the origins of the chemo- and regioselectivity. Furthermore, this diazo-cycloaddition protocol was applied to construct tetrazole-modified peptidomimetics and drug-like amino acid derivatives.
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Affiliation(s)
- Xuan-Yu Liu
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yi-Lin Yang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yanfeng Dang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Ilan Marek
- Schulich Faculty of Chemistry and the Resnick Sustainability Center for Catalysis, Technion-Israel Institute of Technology, Haifa, 3200009, Israel
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
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2
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Aoun P, Nyssen N, Richard S, Zhurkin F, Jabin I, Colasson B, Reinaud O. Selective Metal-ion Complexation of a Biomimetic Calix[6]arene Funnel Cavity Functionalized with Phenol or Quinone. Chemistry 2023; 29:e202202934. [PMID: 36321640 PMCID: PMC10107959 DOI: 10.1002/chem.202202934] [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: 09/19/2022] [Indexed: 11/06/2022]
Abstract
In the biomimetic context, many studies have evidenced the importance of the 1st and 2nd coordination sphere of a metal ion for controlling its properties. Here, we propose to evaluate a yet poorly explored aspect, which is the nature of the cavity that surrounds the metal labile site. Three calix[6]arene-based aza-ligands are compared, that differ only by the nature of cavity walls, anisole, phenol or quinone (LOMe , LOH and LQ ). Monitoring ligand exchange of their ZnII complexes evidenced important differences in the metal ion relative affinities for nitriles, halides or carboxylates. It also showed a possible sharp kinetic control on both, metal ion binding and ligand exchange. Hence, this study supports the observations reported on biological systems, highlighting that the substitution of an amino-acid residue of the enzyme active site, at remote distance of the metal ion, can have strong impacts on metal ion lability, substrate/product exchange or selectivity.
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Affiliation(s)
- Pamela Aoun
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Cité, 45 Rue des Saints Pères, 75006, Paris, France
| | - Nicolas Nyssen
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Cité, 45 Rue des Saints Pères, 75006, Paris, France.,Laboratoire de Chimie Organique, Université libre de Bruxelles (ULB), Avenue F. D. Roosevelt 50, CP160/06, B 1050, Brussels, Belgium
| | - Sarah Richard
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Cité, 45 Rue des Saints Pères, 75006, Paris, France
| | - Fedor Zhurkin
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Cité, 45 Rue des Saints Pères, 75006, Paris, France
| | - Ivan Jabin
- Laboratoire de Chimie Organique, Université libre de Bruxelles (ULB), Avenue F. D. Roosevelt 50, CP160/06, B 1050, Brussels, Belgium
| | - Benoit Colasson
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Cité, 45 Rue des Saints Pères, 75006, Paris, France
| | - Olivia Reinaud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 Université Paris Cité, 45 Rue des Saints Pères, 75006, Paris, France
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3
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Post-Translational Modification of ZEB Family Members in Cancer Progression. Int J Mol Sci 2022; 23:ijms232315127. [PMID: 36499447 PMCID: PMC9737314 DOI: 10.3390/ijms232315127] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Post-translational modification (PTM), the essential regulatory mechanisms of proteins, play essential roles in physiological and pathological processes. In addition, PTM functions in tumour development and progression. Zinc finger E-box binding homeobox (ZEB) family homeodomain transcription factors, such as ZEB1 and ZEB2, play a pivotal role in tumour progression and metastasis by induction epithelial-mesenchymal transition (EMT), with activation of stem cell traits, immune evasion and epigenetic reprogramming. However, the relationship between ZEB family members' post-translational modification (PTM) and tumourigenesis remains largely unknown. Therefore, we focussed on the PTM of ZEBs and potential therapeutic approaches in cancer progression. This review provides an overview of the diverse functions of ZEBs in cancer and the mechanisms and therapeutic implications that target ZEB family members' PTMs.
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4
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Wang X, Lin Z, Bustin KA, McKnight NR, Parsons WH, Matthews ML. Discovery of Potent and Selective Inhibitors against Protein-Derived Electrophilic Cofactors. J Am Chem Soc 2022; 144:5377-5388. [PMID: 35235319 PMCID: PMC10159212 DOI: 10.1021/jacs.1c12748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Electrophilic cofactors are widely distributed in nature and play important roles in many physiological and disease processes, yet they have remained blind spots in traditional activity-based protein profiling (ABPP) approaches that target nucleophiles. More recently, reverse-polarity (RP)-ABPP using hydrazine probes identified an electrophilic N-terminal glyoxylyl (Glox) group for the first time in secernin-3 (SCRN3). The biological function(s) of both the protein and Glox as a cofactor has not yet been pharmacologically validated because of the lack of selective inhibitors that could disrupt and therefore identify its activity. Here, we present the first platform for analyzing the reactivity and selectivity of an expanded nucleophilic probe library toward main-chain carbonyl cofactors such as Glox and pyruvoyl (Pyvl) groups. We first applied the library proteome-wide to profile and confirm engagement with various electrophilic protein targets, including secernin-2 (SCRN2), shown here also to possess a Glox group. A broadly reactive indole ethylhydrazine probe was used for a competitive in vitro RP-ABPP assay to screen for selective inhibitors against such cofactors from a set of commercially available nucleophilic fragments. Using Glox-containing SCRN proteins as a case study, naphthyl hydrazine was identified as a potent and selective SCRN3 inhibitor, showing complete inhibition in cell lysates with no significant cross-reactivity detected for other enzymes. Moving forward, this platform provides the fundamental basis for the development of selective Glox inhibitors and represents a starting point to advance small molecules that modulate electrophile-dependent function.
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Affiliation(s)
- Xie Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zongtao Lin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Katelyn A Bustin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nate R McKnight
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Megan L Matthews
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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5
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Zhu HQ, Tang XL, Zheng RC, Zheng YG. Recent advancements in enzyme engineering via site-specific incorporation of unnatural amino acids. World J Microbiol Biotechnol 2021; 37:213. [PMID: 34741210 DOI: 10.1007/s11274-021-03177-1] [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: 08/28/2021] [Accepted: 10/23/2021] [Indexed: 11/28/2022]
Abstract
With increased attention to excellent biocatalysts, evolving methods based on nature or unnatural amino acid (UAAs) mutagenesis have become an important part of enzyme engineering. The emergence of powerful method through expanding the genetic code allows to incorporate UAAs with unique chemical functionalities into proteins, endowing proteins with more structural and functional features. To date, over 200 diverse UAAs have been incorporated site-specifically into proteins via this methodology and many of them have been widely exploited in the field of enzyme engineering, making this genetic code expansion approach possible to be a promising tool for modulating the properties of enzymes. In this context, we focus on how this robust method to specifically incorporate UAAs into proteins and summarize their applications in enzyme engineering for tuning and expanding the functional properties of enzymes. Meanwhile, we aim to discuss how the benefits can be achieved by using the genetically encoded UAAs. We hope that this method will become an integral part of the field of enzyme engineering in the future.
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Affiliation(s)
- Hang-Qin Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ren-Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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6
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Xiong W, Liu B, Shen Y, Jing K, Savage TR. Protein engineering design from directed evolution to de novo synthesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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7
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Dettling SE, Ahmadi M, Lin Z, He L, Matthews ML. Discovery of Electrophiles and Profiling of Enzyme Cofactors. ACTA ACUST UNITED AC 2020; 12:e86. [PMID: 33197155 PMCID: PMC9285064 DOI: 10.1002/cpch.86] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Reverse‐polarity activity‐based protein profiling (RP‐ABPP) is a chemical proteomics approach that uses nucleophilic probes amenable to “click” chemistry deployed into living cells in culture to capture, immunoprecipitate, and identify protein‐bound electrophiles. RP‐ABPP is used to characterize the structure and function of reactive electrophilic post‐translational modifications (PTMs) and the proteins harboring them, which may uncover unknown or novel functions. RP‐ABPP has demonstrated utility as a versatile method to monitor the metabolic regulation of electrophilic cofactors, using a pyruvoyl cofactor in S‐adenosyl‐l‐methionine decarboxylase (AMD1), and to discover novel types of electrophilic modifications on proteins in human cells, such as the glyoxylyl modification on secernin‐3 (SCRN3). These cofactors cannot be predicted by sequence, and therefore this area is relatively undeveloped. RP‐ABPP is the only global, unbiased approach to discover such electrophiles. Here, we describe the utility of these experiments and provide a detailed protocol for de novo discovery, quantitation, and global profiling of electrophilic functionality of proteins. © 2020 The Authors. Basic Protocol 1: Identification and quantification of probe‐reactive proteins Basic Protocol 2: Characterization of the site of probe labeling Basic Protocol 3: Determination and quantitation of electrophile structure
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Affiliation(s)
- Suzanne E Dettling
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mina Ahmadi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zongtao Lin
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lin He
- Zenagem, LLC, Philadelphia, Pennsylvania
| | - Megan L Matthews
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania.,Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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8
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Yuan Z, Liao J, Jiang H, Cao P, Li Y. Aldehyde catalysis - from simple aldehydes to artificial enzymes. RSC Adv 2020; 10:35433-35448. [PMID: 35515689 PMCID: PMC9056934 DOI: 10.1039/d0ra06651f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/16/2020] [Indexed: 12/22/2022] Open
Abstract
Chemists have been learning and mimicking enzymatic catalysis in various aspects of organic synthesis. One of the major goals is to develop versatile catalysts that inherit the high catalytic efficiency of enzymatic processes, while being effective for a broad scope of substrates. In this field, the study of aldehyde catalysts has achieved significant progress. This review summarizes the application of aldehydes as sustainable and effective catalysts in different reactions. The fields, in which the aldehydes successfully mimic enzymatic systems, include light energy absorption/transfer, intramolecularity introduction through tether formation, metal binding for activation/orientation and substrate activation via aldimine formation. Enantioselective aldehyde catalysis has been achieved with the development of chiral aldehyde catalysts. Direct simplification of aldehyde-dependent enzymes has also been investigated for the synthesis of noncanonical chiral amino acids. Further development in aldehyde catalysis is expected, which might also promote exploration in fields related to prebiotic chemistry, early enzyme evolution, etc.
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Affiliation(s)
- Zeqin Yuan
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
| | - Jun Liao
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
| | - Hao Jiang
- Undisclosed Pharmaceutical Company Copenhagen Denmark
| | - Peng Cao
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
| | - Yang Li
- College of Chemistry and Materials Science, Sichuan Normal University Chengdu 610068 China
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9
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Drienovská I, Gajdoš M, Kindler A, Takhtehchian M, Darnhofer B, Birner-Gruenberger R, Dörr M, Bornscheuer UT, Kourist R. Folding Assessment of Incorporation of Noncanonical Amino Acids Facilitates Expansion of Functional-Group Diversity for Enzyme Engineering. Chemistry 2020; 26:12338-12342. [PMID: 32347609 PMCID: PMC7590180 DOI: 10.1002/chem.202002077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 12/31/2022]
Abstract
Protein design is limited by the diversity of functional groups provided by the canonical protein „building blocks“. Incorporating noncanonical amino acids (ncAAs) into enzymes enables a dramatic expansion of their catalytic features. For this, quick identification of fully translated and correctly folded variants is decisive. Herein, we report the engineering of the enantioselectivity of an esterase utilizing several ncAAs. Key for the identification of active and soluble protein variants was the use of the split‐GFP method, which is crucial as it allows simple determination of the expression levels of enzyme variants with ncAA incorporations by fluorescence. Several identified variants led to improved enantioselectivity or even inverted enantiopreference in the kinetic resolution of ethyl 3‐phenylbutyrate.
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Affiliation(s)
- Ivana Drienovská
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Matúš Gajdoš
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Alexia Kindler
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Mahsa Takhtehchian
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Patholoy, Diagnostic and Research Center of Molecular Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstraße 24, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Patholoy, Diagnostic and Research Center of Molecular Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060, Wien, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstraße 24, 8010, Graz, Austria
| | - Mark Dörr
- Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
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10
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Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:97-125. [PMID: 32951817 PMCID: PMC7320668 DOI: 10.1016/bs.apcsb.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein composition is restricted by the genetic code to a relatively small number of natural amino acids. Similarly, the known three-dimensional structures adopt a limited number of protein folds. However, proteins exert a large variety of functions and show a remarkable ability for regulation and immediate response to intracellular and extracellular stimuli. To some degree, the wide variability of protein function can be attributed to the post-translational modifications. Post-translational modifications have been observed in all kingdoms of life and give to proteins a significant degree of chemical and consequently functional and structural diversity. Their importance is partly reflected in the large number of genes dedicated to their regulation. So far, hundreds of post-translational modifications have been observed while it is believed that many more are to be discovered along with the technological advances in sequencing, proteomics, mass spectrometry and structural biology. Indeed, the number of studies which report novel post translational modifications is getting larger supporting the notion that their space is still largely unexplored. In this review we explore the impact of post-translational modifications on protein structure and function with emphasis on catalytic activity regulation. We present examples of proteins and protein families whose catalytic activity is substantially affected by the presence of post translational modifications and we describe the molecular basis which underlies the regulation of the protein function through these modifications. When available, we also summarize the current state of knowledge on the mechanisms which introduce these modifications to protein sites.
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Abstract
AbstractThe goal of sustainable development has been accepted as a common policy in current society. In response to this challenge, the development of green processes which utilize environmentally benign oxidants, reduce chemical waste and handling costs, is highly desirable. Given the widespread importance of imines as pivotal synthetic intermediates and essential pharmacophores in numerous biologically active compounds, various catalytic methods allowing the aerobic oxidation of amines to imines have been developed. Recently, noticeable progress has arisen from the discovery of various quinone-based catalytic systems, inspired by copper amine oxidase enzymes (CuAOs), which are able to reproduce the selectivity of CuAOs for primary amines and even to expand the amine substrates scope. However, the need for synthesizing these catalysts prior use adversely affects the economics as well as the eco-friendly nature of the method. To surpass these drawbacks, the “second-order” biomimicry idea has been recently advanced to describe a system in which in situ modification of pre-catalyst components affords the active biomimetic catalyst. This minireview especially covers our recent contribution to the design of bioinspired quinone-based catalysts for the aerobic oxidation of amines to imines which has culminated in a dual bioinspired protocol as an example of “second-order” biomimicry.
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Affiliation(s)
- Martine Largeron
- UMR 8038 CNRS-Université Paris Descartes (Paris 5), Sorbonne Paris Cité, Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire, 75270 Paris cedex 06, France
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12
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Drienovská I, Roelfes G. Expanding the enzyme universe with genetically encoded unnatural amino acids. Nat Catal 2020. [DOI: 10.1038/s41929-019-0410-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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13
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Fujieda N. His-Cys and Trp-Cys cross-links generated by post-translational chemical modification. Biosci Biotechnol Biochem 2019; 84:445-454. [PMID: 31771431 DOI: 10.1080/09168451.2019.1696178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Galactose oxidase and amine oxidase contain a cofactor which is generated by post-translational chemical modification to the corresponding amino acid side chains near the copper active center. Such cofactors provide proteins unusual catalytic ability that canonical amino acids cannot exert as well as their structural stability, and thereby are called as protein-derived cofactors. These cofactors and modifications are mostly derived from aromatic amino acid residues, especially Tyr, Trp, and His. Current information about unusual cofactors derived from two of those, heteroaromatic residues (Trp and His) is summarized, especially chemical properties and maturation process of the cross-links between cysteine and heteroaromatic amino acids (His-Cys and Trp-Cys cross-links).Abbreviations: FMN: flavin mononucleotide; FAD: flavin adenine nucleotide; RNA: ribonucleic acid; PDC: protein-derived cofactor; GFP: green fluorescent protein; MIO: 3,5-dihydro-5-methylidene-4-imidazol-4-one; LTQ: lysyl tyrosylquinone; CTQ: cysteine tryptophylquinone; TTQ: tryptophan tryptophylquinone; E.coli: Escherichia coli; WT: wild type.
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Affiliation(s)
- Nobutaka Fujieda
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
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14
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Investigation into isomerization reaction of phenylalanine aminomutase from Pantoea agglomerans. Enzyme Microb Technol 2019; 132:109428. [PMID: 31731949 DOI: 10.1016/j.enzmictec.2019.109428] [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] [Received: 07/07/2019] [Revised: 08/30/2019] [Accepted: 09/10/2019] [Indexed: 11/23/2022]
Abstract
Phenylalanine aminomutase (PaPAM) from Pantoea agglomerans is a member of the MIO (4-methylene-imidazol-5-one) family of enzymes, which isomerizes α-phenylalanine to β-phenylalanine, and could be used to synthesize unnatural β-arylalanine. However, the mechanism of isomerization reaction is not clear. To investigate the mechanism, the gene (pam), which encodes PaPAM, was first expressed in E.coli, and recombinant PaPAM was prepared using affinity chromatography. Then, 15N-(2S)-α-phenylalanine, (2S)-(3-2H2)-α-phenylalanine and (2S,3S)-[2,3-2H2]-α-phenylalanine were used as substrates to analyze the mechanism of isomerization reaction. The results of MS and NMR showed that the isomerization reaction was performed through the intramolecular exchange of NH2 with pro-3R hydrogen of α-phenylalanine. The PaPAM shuttles the α-NH2 of α-phenylalanine to β site to replace the pro-3R hydrogen. Simultaneously, the pro-3R hydrogen is shifted to α site to produce β-phenylalanine. Furthermore, a key residue, Phe at position 455 in the active site, was determined to control the exchange way using molecular docking and sequence alignment of MIO family enzymes. The results indicated that the key 455 Phe residue is involved in changing the binding orientation of the carboxyl group of the intermediate trans-cinnamic acid to control the NH2-H pair exchange.
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15
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Mayer C. Selection, Addiction and Catalysis: Emerging Trends for the Incorporation of Noncanonical Amino Acids into Peptides and Proteins in Vivo. Chembiochem 2019; 20:1357-1364. [PMID: 30618145 PMCID: PMC6563710 DOI: 10.1002/cbic.201800733] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 12/22/2022]
Abstract
Expanding the genetic code of organisms by incorporating noncanonical amino acids (ncAAs) into target proteins through the suppression of stop codons in vivo has profoundly impacted how we perform protein modification or detect proteins and their interaction partners in their native environment. Yet, with genetic code expansion strategies maturing over the past 15 years, new applications that make use—or indeed repurpose—these techniques are beginning to emerge. This Concept article highlights three of these developments: 1) The incorporation of ncAAs for the biosynthesis and selection of bioactive macrocyclic peptides with novel ring architectures, 2) synthetic biocontainment strategies based on the addiction of microorganisms to ncAAs, and 3) enzyme design strategies, in which ncAAs with unique functionalities enable the catalysis of new‐to‐nature reactions. Key advances in all three areas are presented and potential future applications discussed.
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Affiliation(s)
- Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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16
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Mayer C, Dulson C, Reddem E, Thunnissen AWH, Roelfes G. Directed Evolution of a Designer Enzyme Featuring an Unnatural Catalytic Amino Acid. Angew Chem Int Ed Engl 2019; 58:2083-2087. [PMID: 30575260 PMCID: PMC6519144 DOI: 10.1002/anie.201813499] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/15/2022]
Abstract
The impressive rate accelerations that enzymes display in nature often result from boosting the inherent catalytic activities of side chains by their precise positioning inside a protein binding pocket. Such fine-tuning is also possible for catalytic unnatural amino acids. Specifically, the directed evolution of a recently described designer enzyme, which utilizes an aniline side chain to promote a model hydrazone formation reaction, is reported. Consecutive rounds of directed evolution identified several mutations in the promiscuous binding pocket, in which the unnatural amino acid is embedded in the starting catalyst. When combined, these mutations boost the turnover frequency (kcat ) of the designer enzyme by almost 100-fold. This results from strengthening the catalytic contribution of the unnatural amino acid, as the engineered designer enzymes outperform variants, in which the aniline side chain is replaced with a catalytically inactive tyrosine residue, by more than 200-fold.
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Affiliation(s)
- Clemens Mayer
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
| | - Christopher Dulson
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
| | - Eswar Reddem
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
| | - Andy‐Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474AGGroningenThe Netherlands
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17
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Mayer C, Dulson C, Reddem E, Thunnissen AMWH, Roelfes G. Directed Evolution of a Designer Enzyme Featuring an Unnatural Catalytic Amino Acid. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Clemens Mayer
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
| | - Christopher Dulson
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
| | - Eswar Reddem
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9474 AG Groningen The Netherlands
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18
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Affiliation(s)
- Zheng Huang
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Jean-Philip Lumb
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
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19
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A designer enzyme for hydrazone and oxime formation featuring an unnatural catalytic aniline residue. Nat Chem 2018; 10:946-952. [PMID: 29967395 DOI: 10.1038/s41557-018-0082-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 05/15/2018] [Indexed: 11/08/2022]
Abstract
Creating designer enzymes with the ability to catalyse abiological transformations is a formidable challenge. Efforts toward this goal typically consider only canonical amino acids in the initial design process. However, incorporating unnatural amino acids that feature uniquely reactive side chains could significantly expand the catalytic repertoire of designer enzymes. To explore the potential of such artificial building blocks for enzyme design, here we selected p-aminophenylalanine as a potentially novel catalytic residue. We demonstrate that the catalytic activity of the aniline side chain for hydrazone and oxime formation reactions is increased by embedding p-aminophenylalanine into the hydrophobic pore of the multidrug transcriptional regulator from Lactococcus lactis. Both the recruitment of reactants by the promiscuous binding pocket and a judiciously placed aniline that functions as a catalytic residue contribute to the success of the identified artificial enzyme. We anticipate that our design strategy will prove rewarding to significantly expand the catalytic repertoire of designer enzymes in the future.
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20
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McCann S, Lumb JP, Arndtsen BA, Stahl SS. Second-Order Biomimicry: In Situ Oxidative Self-Processing Converts Copper(I)/Diamine Precursor into a Highly Active Aerobic Oxidation Catalyst. ACS CENTRAL SCIENCE 2017; 3:314-321. [PMID: 28470049 PMCID: PMC5408333 DOI: 10.1021/acscentsci.7b00022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Indexed: 05/11/2023]
Abstract
A homogeneous Cu-based catalyst system consisting of [Cu(MeCN)4]PF6, N,N'-di-tert-butylethylenediamine (DBED), and p-(N,N-dimethylamino)pyridine (DMAP) mediates efficient aerobic oxidation of alcohols. Mechanistic study of this reaction shows that the catalyst undergoes an in situ oxidative self-processing step, resulting in conversion of DBED into a nitroxyl that serves as an efficient cocatalyst for aerobic alcohol oxidation. Insights into this behavior are gained from kinetic studies, which reveal an induction period at the beginning of the reaction that correlates with the oxidative self-processing step, EPR spectroscopic analysis of the catalytic reaction mixture, which shows the buildup of the organic nitroxyl species during steady state turnover, and independent synthesis of oxygenated DBED derivatives, which are shown to serve as effective cocatalysts and eliminate the induction period in the reaction. The overall mechanism bears considerable resemblance to enzymatic reactivity. Most notable is the "oxygenase"-type self-processing step that mirrors generation of catalytic cofactors in enzymes via post-translational modification of amino acid side chains. This higher-order function within a synthetic catalyst system presents new opportunities for the discovery and development of biomimetic catalysts.
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Affiliation(s)
- Scott
D. McCann
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jean-Philip Lumb
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8 Canada
- E-mail:
| | - Bruce A. Arndtsen
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8 Canada
- E-mail:
| | - Shannon S. Stahl
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- E-mail:
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21
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Matthews ML, He L, Horning BD, Olson EJ, Correia BE, Yates JR, Dawson PE, Cravatt BF. Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat Chem 2016; 9:234-243. [PMID: 28221344 PMCID: PMC5325178 DOI: 10.1038/nchem.2645] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. We show here that "reverse-polarity" (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells, including the pyruvoyl cofactor of S-adenosyl-l-methionine decarboxylase (AMD1), which we find is dynamically controlled by intracellular methionine concentrations, and a heretofore unknown modification – an N-terminally bound glyoxylyl group – in the poorly characterized protein secernin-3. RP-ABPP thus provides a versatile method to monitor the metabolic regulation of electrophilic cofactors and discover novel types of electrophilic modifications on proteins in human cells. A chemical proteomic strategy is described for the discovery of protein-bound electrophilic groups in human cells and used to characterize dynamic regulation of the pyruvoyl catalytic cofactor in S-adenosyl-l-methionine decarboxylase and to discover an N-terminal glyoxylyl modification on Secernin proteins.
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Affiliation(s)
- Megan L Matthews
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Lin He
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.,Bioinformatics Solutions Inc., Waterloo, Ontario N2L 6J2, Canada
| | - Benjamin D Horning
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Erika J Olson
- Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Bruno E Correia
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.,École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - John R Yates
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Philip E Dawson
- Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Benjamin F Cravatt
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
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22
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Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate. Sci Rep 2015; 5:11870. [PMID: 26149121 PMCID: PMC4493562 DOI: 10.1038/srep11870] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/09/2015] [Indexed: 12/29/2022] Open
Abstract
Ergothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond formation reaction and a PLP-mediated C-S lyase (EgtE) reaction results in a net sulfur transfer from cysteine to histidine side-chain. This demonstrates a new sulfur transfer strategy in the biosynthesis of sulfur-containing natural products. Due to difficulties associated with the overexpression of Mycobacterium smegmatis EgtE protein, the proposed EgtE functionality remained to be verified biochemically. In this study, we have successfully overexpressed and purified M. smegmatis EgtE enzyme and evaluated its activities under different in vitro conditions: C-S lyase reaction using either thioether or sulfoxide as a substrate in the presence or absence of reductants. Results from our biochemical characterizations support the assignment of sulfoxide 4 as the native EgtE substrate and the involvement of a sulfenic acid intermediate in the ergothioneine C-S lyase reaction.
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23
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Nauser T, Carreras A. Carbon-centered radicals add reversibly to histidine--implications. Chem Commun (Camb) 2015; 50:14349-51. [PMID: 25292330 DOI: 10.1039/c4cc05316h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbon-centered radicals of alcohols commonly used as hydroxyl radical scavengers (MeOH, EtOH, i-PrOH and t-BuOH) add reversibly to histidine with equilibrium constants up to 3 × 10(3) M(-1) and rate constants on the order of 10(9) M(-1) s(-1). Similar equilibria may compromise determinations of one-electron (radical) electrode potentials.
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Affiliation(s)
- Thomas Nauser
- Laboratorium für Anorganische Chemie, Departement für Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog Weg 2, CH-8093 Zürich, Switzerland.
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24
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Appel MJ, Bertozzi CR. Formylglycine, a post-translationally generated residue with unique catalytic capabilities and biotechnology applications. ACS Chem Biol 2015; 10:72-84. [PMID: 25514000 PMCID: PMC4492166 DOI: 10.1021/cb500897w] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Formylglycine (fGly) is a catalytically essential residue found almost exclusively in the active sites of type I sulfatases. Formed by post-translational oxidation of cysteine or serine side chains, this aldehyde-functionalized residue participates in a unique and highly efficient catalytic mechanism for sulfate ester hydrolysis. The enzymes that produce fGly, formylglycine-generating enzyme (FGE) and anaerobic sulfatase-maturating enzyme (anSME), are as unique and specialized as fGly itself. FGE especially is structurally and mechanistically distinct, and serves the sole function of activating type I sulfatase targets. This review summarizes the current state of knowledge regarding the mechanism by which fGly contributes to sulfate ester hydrolysis, the molecular details of fGly biogenesis by FGE and anSME, and finally, recent biotechnology applications of fGly beyond its natural catalytic function.
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Affiliation(s)
- Mason J. Appel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
| | - Carolyn R. Bertozzi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California 94720, United States
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25
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Hu W, Song H, Sae Her A, Bak DW, Naowarojna N, Elliott SJ, Qin L, Chen X, Liu P. Bioinformatic and biochemical characterizations of C-S bond formation and cleavage enzymes in the fungus Neurospora crassa ergothioneine biosynthetic pathway. Org Lett 2014; 16:5382-5. [PMID: 25275953 PMCID: PMC4201327 DOI: 10.1021/ol502596z] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 01/03/2023]
Abstract
Ergothioneine is a histidine thiol derivative. Its mycobacterial biosynthetic pathway has five steps (EgtA-E catalysis) with two novel reactions: a mononuclear nonheme iron enzyme (EgtB) catalyzed oxidative C-S bond formation and a PLP-mediated C-S lyase (EgtE) reaction. Our bioinformatic and biochemical analyses indicate that the fungus Neurospora crassa has a more concise ergothioneine biosynthetic pathway because its nonheme iron enzyme, Egt1, makes use of cysteine instead of γ-Glu-Cys as the substrate. Such a change of substrate preference eliminates the competition between ergothioneine and glutathione biosyntheses. In addition, we have identified the N. crassa C-S lyase (NCU11365) and reconstituted its activity in vitro, which makes the future ergothioneine production through metabolic engineering feasible.
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Affiliation(s)
- Wen Hu
- State
Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou, P. R. China
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Heng Song
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ampon Sae Her
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Daniel W. Bak
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Nathchar Naowarojna
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Sean J. Elliott
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Li Qin
- State
Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou, P. R. China
| | - Xiaoping Chen
- State
Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine
and Health, Chinese Academy of Sciences, Guangzhou, P. R. China
| | - Pinghua Liu
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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26
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Ravikiran B, Mahalakshmi R. Unusual post-translational protein modifications: the benefits of sophistication. RSC Adv 2014. [DOI: 10.1039/c4ra04694c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This review summarizes the “seemingly bizarre”, yet naturally occurring, covalent non-disulphide cross-links in enzymatic and scaffolding proteins and their functions.
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Affiliation(s)
- Boddepalli Ravikiran
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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27
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Abstract
Methylamine dehydrogenase (MADH) requires the cofactor tryptophan tryptophylquinone (TTQ) for activity. TTQ is a posttranslational modification that results from an 8-electron oxidation of two specific tryptophans in the MADH β-subunit. The final 6-electron oxidation is catalyzed by an unusual c-type di-heme enzyme, MauG. The di-ferric enzyme can react with H(2)O(2), but atypically for c-type hemes the di-ferrous enzyme can react with O(2) as well. In both cases, an unprecedented bis-Fe(IV) redox state is formed, composed of a ferryl heme (Fe(IV)=O) with the second heme as Fe(IV) stabilized by His-Tyr axial ligation. Bis-Fe(IV) MauG acts as a potent 2-electron oxidant. Catalysis is long-range and requires a hole hopping electron transfer mechanism. This review highlights the current knowledge and focus of research into this fascinating system.
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Affiliation(s)
- Carrie M Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, Minnesota 55455, USA.
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28
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Timms N, Windle CL, Polyakova A, Ault JR, Trinh CH, Pearson AR, Nelson A, Berry A. Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy. Chembiochem 2013; 14:474-81. [PMID: 23418011 PMCID: PMC3792637 DOI: 10.1002/cbic.201200714] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Indexed: 11/29/2022]
Abstract
Chemical modification has been used to introduce the unnatural amino acid γ-thialysine in place of the catalytically important Lys165 in the enzyme N-acetylneuraminic acid lyase (NAL). The Staphylococcus aureus nanA gene, encoding NAL, was cloned and expressed in E. coli. The protein, purified in high yield, has all the properties expected of a class I NAL. The S. aureus NAL which contains no natural cysteine residues was subjected to site-directed mutagenesis to introduce a cysteine in place of Lys165 in the enzyme active site. Subsequently chemical mutagenesis completely converted the cysteine into γ-thialysine through dehydroalanine (Dha) as demonstrated by ESI-MS. Initial kinetic characterisation showed that the protein containing γ-thialysine regained 17 % of the wild-type activity. To understand the reason for this lower activity, we solved X-ray crystal structures of the wild-type S. aureus NAL, both in the absence of, and in complex with, pyruvate. We also report the structures of the K165C variant, and the K165-γ-thialysine enzyme in the presence, or absence, of pyruvate. These structures reveal that γ-thialysine in NAL is an excellent structural mimic of lysine. Measurement of the pH-activity profile of the thialysine modified enzyme revealed that its pH optimum is shifted from 7.4 to 6.8. At its optimum pH, the thialysine-containing enzyme showed almost 30 % of the activity of the wild-type enzyme at its pH optimum. The lowered activity and altered pH profile of the unnatural amino acid-containing enzyme can be rationalised by imbalances of the ionisation states of residues within the active site when the pK(a) of the residue at position 165 is perturbed by replacement with γ-thialysine. The results reveal the utility of chemical mutagenesis for the modification of enzyme active sites and the exquisite sensitivity of catalysis to the local structural and electrostatic environment in NAL.
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Affiliation(s)
- Nicole Timms
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Claire L Windle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Anna Polyakova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Arwen R Pearson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Chemistry, University of LeedsLeeds, LS2 9JT (UK)
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
- School of Molecular and Cellular Biology, University of Leeds, Garstang BuildingLeeds, LS2 9JT (UK)
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29
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The role of protein crystallography in defining the mechanisms of biogenesis and catalysis in copper amine oxidase. Int J Mol Sci 2012; 13:5375-5405. [PMID: 22754303 PMCID: PMC3382800 DOI: 10.3390/ijms13055375] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 04/22/2012] [Accepted: 04/26/2012] [Indexed: 12/22/2022] Open
Abstract
Copper amine oxidases (CAOs) are a ubiquitous group of enzymes that catalyze the conversion of primary amines to aldehydes coupled to the reduction of O2 to H2O2. These enzymes utilize a wide range of substrates from methylamine to polypeptides. Changes in CAO activity are correlated with a variety of human diseases, including diabetes mellitus, Alzheimer’s disease, and inflammatory disorders. CAOs contain a cofactor, 2,4,5-trihydroxyphenylalanine quinone (TPQ), that is required for catalytic activity and synthesized through the post-translational modification of a tyrosine residue within the CAO polypeptide. TPQ generation is a self-processing event only requiring the addition of oxygen and Cu(II) to the apoCAO. Thus, the CAO active site supports two very different reactions: TPQ synthesis, and the two electron oxidation of primary amines. Crystal structures are available from bacterial through to human sources, and have given insight into substrate preference, stereospecificity, and structural changes during biogenesis and catalysis. In particular both these processes have been studied in crystallo through the addition of native substrates. These latter studies enable intermediates during physiological turnover to be directly visualized, and demonstrate the power of this relatively recent development in protein crystallography.
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30
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Wendlandt AE, Suess AM, Stahl SS. Kupferkatalysierte aerobe oxidative C-H-Funktionalisierungen: Trends und Erkenntnisse zum Mechanismus. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103945] [Citation(s) in RCA: 296] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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31
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Wendlandt AE, Suess AM, Stahl SS. Copper-catalyzed aerobic oxidative C-H functionalizations: trends and mechanistic insights. Angew Chem Int Ed Engl 2011; 50:11062-87. [PMID: 22034061 DOI: 10.1002/anie.201103945] [Citation(s) in RCA: 1103] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Indexed: 01/04/2023]
Abstract
The selective oxidation of C-H bonds and the use of O(2) as a stoichiometric oxidant represent two prominent challenges in organic chemistry. Copper(II) is a versatile oxidant, capable of promoting a wide range of oxidative coupling reactions initiated by single-electron transfer (SET) from electron-rich organic molecules. Many of these reactions can be rendered catalytic in Cu by employing molecular oxygen as a stoichiometric oxidant to regenerate the active copper(II) catalyst. Meanwhile, numerous other recently reported Cu-catalyzed C-H oxidation reactions feature substrates that are electron-deficient or appear unlikely to undergo single-electron transfer to copper(II). In some of these cases, evidence has been obtained for the involvement of organocopper(III) intermediates in the reaction mechanism. Organometallic C-H oxidation reactions of this type represent important new opportunities for the field of Cu-catalyzed aerobic oxidations.
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Affiliation(s)
- Alison E Wendlandt
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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32
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Tabuchi K, Ertem MZ, Sugimoto H, Kunishita A, Tano T, Fujieda N, Cramer CJ, Itoh S. Reactions of Copper(II)-Phenol Systems with O2: Models for TPQ Biosynthesis in Copper Amine Oxidases. Inorg Chem 2011; 50:1633-47. [DOI: 10.1021/ic101832c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kae Tabuchi
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Mehmed Z. Ertem
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Sugimoto
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Atsushi Kunishita
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tetsuro Tano
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Nobutaka Fujieda
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Shinobu Itoh
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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33
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Fujieda N, Ikeda T, Murata M, Yanagisawa S, Aono S, Ohkubo K, Nagao S, Ogura T, Hirota S, Fukuzumi S, Nakamura Y, Hata Y, Itoh S. Post-translational His-Cys cross-linkage formation in tyrosinase induced by copper(II)-peroxo species. J Am Chem Soc 2011; 133:1180-3. [PMID: 21218798 DOI: 10.1021/ja108280w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Autocatalytic formation of His-Cys cross-linkage in the enzyme active site of tyrosinase from Aspergillus oryzae has been demonstrated to proceed by the treatment of apoenzyme with Cu(II) under aerobic conditions, where a (μ-η(2):η(2)-peroxo)dicopper(II) species has been suggested to be involved as a key reactive intermediate.
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Affiliation(s)
- Nobutaka Fujieda
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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34
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Davidson VL. Generation of protein-derived redox cofactors by posttranslational modification. MOLECULAR BIOSYSTEMS 2010; 7:29-37. [PMID: 20936199 DOI: 10.1039/c005311b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Redox enzymes which catalyze the oxidation and reduction of substrates are ubiquitous in nature. These enzymes typically possess exogenous cofactors to allow them to perform catalytic functions which cannot be accomplished using only amino acid residues. It is now evident that nature also employs an alternative strategy of generating catalytic and redox-active sites in proteins by posttranslational modification of amino acid residues. This review describes the structures and functions of several of these protein-derived cofactors and the diverse mechanisms of posttranslational modification through which they are generated.
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Affiliation(s)
- Victor L Davidson
- Department of Biochemistry, University of Mississippi Medical Center, 2500 N. State St, Jackson, Mississippi 39216-4505, USA.
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Tabuchi K, Sugimoto H, Kunishita A, Fujieda N, Itoh S. Oxygenation Chemistry at a Mononuclear Copper(II) Hydroquinone System with O2. Inorg Chem 2010; 49:6820-2. [DOI: 10.1021/ic101037v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kae Tabuchi
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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36
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Wilmot CM, Davidson VL. Uncovering novel biochemistry in the mechanism of tryptophan tryptophylquinone cofactor biosynthesis. Curr Opin Chem Biol 2009; 13:469-74. [PMID: 19648051 DOI: 10.1016/j.cbpa.2009.06.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 06/26/2009] [Accepted: 06/30/2009] [Indexed: 11/15/2022]
Abstract
Catalytic quinone cofactors derived from post-translational modification of amino acid residues within the enzyme polypeptide have roles in a variety of biological processes ranging from metabolism in bacteria to inflammation and connective tissue maturation in humans. In recent years, studies of the biosynthesis of one of these cofactors, tryptophan tryptophylquinone (TTQ), have provided examples of novel chemistry that is required for the generation of these protein-derived cofactors. A novel c-type diheme enzyme, MauG, catalyzes a six-electron oxidation that completes TTQ biosynthesis in a 119-kDa protein substrate. The post-translational modification reactions proceed via an unprecedented Fe(V) equivalent catalytic intermediate comprising two hemes; one an Fe(IV)=O and the other a six-coordinate Fe(IV) with axial ligands provided by amino acid residues. This high-valent diheme species is an alternative to Compound I, an Fe(IV)=O heme with a porphyrin or amino acid cation radical, which is typically the reactive intermediate of heme-dependent oxygenases and peroxidases.
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Affiliation(s)
- Carrie M Wilmot
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA.
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37
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38
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Rogers MS, Hurtado-Guerrero R, Firbank SJ, Halcrow MA, Dooley DM, Phillips SEV, Knowles PF, McPherson MJ. Cross-link formation of the cysteine 228-tyrosine 272 catalytic cofactor of galactose oxidase does not require dioxygen. Biochemistry 2008; 47:10428-39. [PMID: 18771294 DOI: 10.1021/bi8010835] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Galactose oxidase (GO) belongs to a class of proteins that self-catalyze assembly of their redox-active cofactors from active site amino acids. Generation of enzymatically active GO appears to require at least four sequential post-translational modifications: cleavage of a secretion signal sequence, copper-dependent cleavage of an N-terminal pro sequence, copper-dependent formation of a C228-Y272 thioether bond, and generation of the Y272 radical. The last two processes were investigated using a truncated protein (termed premat-GO) lacking the pro sequence and purified under copper-free conditions. Reactions of premat-GO with Cu(II) were investigated using optical, EPR, and resonance Raman spectroscopy, SDS-PAGE, and X-ray crystallography. Premat-GO reacted anaerobically with excess Cu(II) to efficiently form the thioether bond but not the Y272 radical. A potential C228-copper coordinated intermediate (lambda max = 406 nm) in the processing reaction, which had not yet formed the C228-Y272 cross-link, was identified from the absorption spectrum. A copper-thiolate protein complex, with copper coordinated to C228, H496, and H581, was also observed in a 3 min anaerobic soak by X-ray crystallography, whereas a 24 h soak revealed the C228-Y272 thioether bond. In solution, addition of oxygenated buffer to premat-GO preincubated with excess Cu(II) generated the Y272 radical state. On the basis of these data, a mechanism for the formation of the C228-Y272 bond and tyrosyl radical generation is proposed. The 406 nm complex is demonstrated to be a catalytically competent processing intermediate under anaerobic conditions. We propose a potential mechanism which is in common with aerobic processing by Cu(II) until the step at which the second electron acceptor is required.
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Affiliation(s)
- Melanie S Rogers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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39
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Carlson BL, Ballister ER, Skordalakes E, King DS, Breidenbach MA, Gilmore SA, Berger JM, Bertozzi CR. Function and structure of a prokaryotic formylglycine-generating enzyme. J Biol Chem 2008; 283:20117-25. [PMID: 18390551 PMCID: PMC2459300 DOI: 10.1074/jbc.m800217200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Type I sulfatases require an unusual co- or post-translational modification for their activity in hydrolyzing sulfate esters. In eukaryotic sulfatases, an active site cysteine residue is oxidized to the aldehyde-containing Cα-formylglycine residue by the formylglycine-generating enzyme (FGE). The machinery responsible for sulfatase activation is poorly understood in prokaryotes. Here we describe the identification of a prokaryotic FGE from Mycobacterium tuberculosis. In addition, we solved the crystal structure of the Streptomyces coelicolor FGE homolog to 2.1Å resolution. The prokaryotic homolog exhibits remarkable structural similarity to human FGE, including the position of catalytic cysteine residues. Both biochemical and structural data indicate the presence of an oxidized cysteine modification in the active site that may be relevant to catalysis. In addition, we generated a mutant M. tuberculosis strain lacking FGE. Although global sulfatase activity was reduced in the mutant, a significant amount of residual sulfatase activity suggests the presence of FGE-independent sulfatases in this organism.
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Affiliation(s)
- Brian L Carlson
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
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40
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Dominy JE, Hwang J, Guo S, Hirschberger LL, Zhang S, Stipanuk MH. Synthesis of amino acid cofactor in cysteine dioxygenase is regulated by substrate and represents a novel post-translational regulation of activity. J Biol Chem 2008; 283:12188-201. [PMID: 18308719 DOI: 10.1074/jbc.m800044200] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cysteine dioxygenase (CDO) catalyzes the conversion of cysteine to cysteinesulfinic acid and is important in the regulation of intracellular cysteine levels in mammals and in the provision of oxidized cysteine metabolites such as sulfate and taurine. Several crystal structure studies of mammalian CDO have shown that there is a cross-linked cofactor present in the active site of the enzyme. The cofactor consists of a thioether bond between the gamma-sulfur of residue cysteine 93 and the aromatic side chain of residue tyrosine 157. The exact requirements for cofactor synthesis and the contribution of the cofactor to the catalytic activity of the enzyme have yet to be fully described. In this study, therefore, we explored the factors necessary for cofactor biogenesis in vitro and in vivo and examined what effect cofactor formation had on activity in vitro. Like other cross-linked cofactor-containing enzymes, formation of the Cys-Tyr cofactor in CDO required a transition metal cofactor (Fe(2+)) and O(2). Unlike other enzymes, however, biogenesis was also strictly dependent upon the presence of substrate. Cofactor formation was also appreciably slower than the rates reported for other enzymes and, indeed, took hundreds of catalytic turnover cycles to occur. In the absence of the Cys-Tyr cofactor, CDO possessed appreciable catalytic activity, suggesting that the cofactor was not essential for catalysis. Nevertheless, at physiologically relevant cysteine concentrations, cofactor formation increased CDO catalytic efficiency by approximately 10-fold. Overall, the regulation of Cys-Tyr cofactor formation in CDO by ambient cysteine levels represents an unusual form of substrate-mediated feed-forward activation of enzyme activity with important physiological consequences.
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Affiliation(s)
- John E Dominy
- Department of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
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41
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Williams JB, Roberts SP, Elekonich MM. Age and natural metabolically-intensive behavior affect oxidative stress and antioxidant mechanisms. Exp Gerontol 2008; 43:538-49. [PMID: 18342467 DOI: 10.1016/j.exger.2008.02.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 02/01/2008] [Accepted: 02/05/2008] [Indexed: 11/15/2022]
Abstract
Flying honey bees have among the highest mass-specific metabolic rates ever measured, suggesting that their flight muscles may experience high levels of oxidative stress during normal daily activities. We measured parameters of oxidative stress and antioxidant capacity in highly metabolic flight muscle and less active head tissue in cohorts of age-matched nurse bees, which rarely fly, and foragers, which fly several hours per a day. Naturally occurring foraging flight elicited an increase in flight muscle Hsp70 content in both young and old foragers; however catalase and total antioxidant capacity increased only in young flight muscle. Surprisingly, young nurse bees also showed a modest daily increase in Hsp70, catalase levels and antioxidant capacity, and these effects were likely due to collecting the young nurses soon after orientation flights. There were no differences in flight muscle carbonyl content over the course of daily activity and few differences in Hsp70, catalase, total antioxidant capacity and protein carbonyl levels in head tissue regardless of age or activity. In summary, honey bee flight likely produces high levels of reactive oxygen species in flight muscle that, when coupled with age-related decreases in antioxidant activity may be responsible for behavioral senescence and reduced longevity.
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Affiliation(s)
- Jason B Williams
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA.
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42
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Naylor R, Hill AF, Barnham KJ. Neurotoxicity in Alzheimer’s disease: is covalently crosslinked Aβ responsible? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 37:265-8. [DOI: 10.1007/s00249-007-0243-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 11/18/2007] [Accepted: 11/20/2007] [Indexed: 11/28/2022]
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43
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Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED. Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation. J Am Chem Soc 2007; 128:4685-93. [PMID: 16594705 DOI: 10.1021/ja056635l] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The green fluorescent protein (GFP) creates a fluorophore out of three sequential amino acids by promoting spontaneous posttranslational modifications. Here, we use high-resolution crystallography to characterize GFP variants that not only undergo peptide backbone cyclization but additional denaturation-induced peptide backbone fragmentation, native peptide hydrolysis, and decarboxylation reactions. Our analyses indicate that architectural features that favor GFP peptide cyclization also drive peptide hydrolysis. These results are relevant for the maturation pathways of GFP homologues, such as the kindling fluorescent protein and the Kaede protein, which use backbone cleavage to red-shift the spectral properties of their chromophores. We further propose a photochemical mechanism for the decarboxylation reaction, supporting a role for the GFP protein environment in facilitating radical formation and one-electron chemistry, which may be important in activating oxygen for the oxidation step of chromophore biosynthesis. Together, our results characterize GFP posttranslational modification chemistry with implications for the energetic landscape of backbone cyclization and subsequent reactions, and for the rational design of predetermined spontaneous backbone cyclization and cleavage reactions.
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Affiliation(s)
- David P Barondeau
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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44
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Pearson AR, Marimanikkuppam S, Li X, Davidson VL, Wilmot CM. Isotope labeling studies reveal the order of oxygen incorporation into the tryptophan tryptophylquinone cofactor of methylamine dehydrogenase. J Am Chem Soc 2007; 128:12416-7. [PMID: 16984182 PMCID: PMC2517855 DOI: 10.1021/ja064466e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial enzyme methylamine dehydrogenase (MADH) contains the protein-derived cofactor tryptophan tryptophylquinone (TTQ). TTQ is generated by the posttranslational modification of two endogenous MADH tryptophans, betaW57 and betaW108. Two oxygens are inserted sequentially into betaW57 to generate the quinone moiety, after which it is cross-linked to betaW108. We have previously shown that the second oxygenation and cross-link formation are catalyzed by the novel di-heme cytochrome MauG. Here we show, using isotopically labeled oxygen and water, that the first addition of oxygen occurs specifically at the C7 position of betaW57 and that MauG then inserts the second oxygen at position C6.
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Affiliation(s)
- Arwen R Pearson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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45
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Trisler K, Looger LL, Sharma V, Baker M, Benson DE, Trauger S, Schultz PG, Smider VV. A Metalloantibody That Irreversibly Binds a Protein Antigen. J Biol Chem 2007; 282:26344-53. [PMID: 17617633 DOI: 10.1074/jbc.m704675200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibody affinity is critically important in therapeutic applications, as well as steady state diagnostic assays. Picomolar affinity antibodies, approaching the association limit of protein-protein interactions, have been discovered for highly potent antigens, but even such high-affinity binders have off-rates sufficient to negate therapeutic efficacy. To cross this affinity threshold, antibodies that tether their targets in a manner other than reversible non-covalent interaction will be required. Here we report the design and construction of an antibody that forms an irreversible complex with a protein antigen in a metal-dependent reaction. The complex resists thermal and chemical denaturation, as well as attempts to remove the coordinating metal ion. Such irreversibly binding antibodies could facilitate the development of next generation "reactive antibody" therapeutics and diagnostics.
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46
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Maiti D, Lucas HR, Sarjeant AAN, Karlin KD. Aryl Hydroxylation from a Mononuclear Copper-Hydroperoxo Species. J Am Chem Soc 2007; 129:6998-9. [PMID: 17497785 DOI: 10.1021/ja071704c] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debabrata Maiti
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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47
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Rogers MS, Tyler EM, Akyumani N, Kurtis CR, Spooner RK, Deacon SE, Tamber S, Firbank SJ, Mahmoud K, Knowles PF, Phillips SEV, McPherson MJ, Dooley DM. The stacking tryptophan of galactose oxidase: a second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis. Biochemistry 2007; 46:4606-18. [PMID: 17385891 PMCID: PMC2532978 DOI: 10.1021/bi062139d] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The function of the stacking tryptophan, W290, a second-coordination sphere residue in galactose oxidase, has been investigated via steady-state kinetics measurements, absorption, CD and EPR spectroscopy, and X-ray crystallography of the W290F, W290G, and W290H variants. Enzymatic turnover is significantly slower in the W290 variants. The Km for D-galactose for W290H is similar to that of the wild type, whereas the Km is greatly elevated in W290G and W290F, suggesting a role for W290 in substrate binding and/or positioning via the NH group of the indole ring. Hydrogen bonding between W290 and azide in the wild type-azide crystal structure are consistent with this function. W290 modulates the properties and reactivity of the redox-active tyrosine radical; the Y272 tyrosyl radicals in both the W290G and W290H variants have elevated redox potentials and are highly unstable compared to the radical in W290F, which has properties similar to those of the wild-type tyrosyl radical. W290 restricts the accessibility of the Y272 radical site to solvent. Crystal structures show that Y272 is significantly more solvent exposed in the W290G variant but that W290F limits solvent access comparable to the wild-type indole side chain. Spectroscopic studies indicate that the Cu(II) ground states in the semireduced W290 variants are very similar to that of the wild-type protein. In addition, the electronic structures of W290X-azide complexes are also closely similar to the wild-type electronic structure. Azide binding and azide-mediated proton uptake by Y495 are perturbed in the variants, indicating that tryptophan also modulates the function of the catalytic base (Y495) in the wild-type enzyme. Thus, W290 plays multiple critical roles in enzyme catalysis, affecting substrate binding, the tyrosyl radical redox potential and stability, and the axial tyrosine function.
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Affiliation(s)
- Melanie S. Rogers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Ejan M. Tyler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Nana Akyumani
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Christian R. Kurtis
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - R. Kate Spooner
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah E. Deacon
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sunita Tamber
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Susan J. Firbank
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Khaled Mahmoud
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter F. Knowles
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon E. V. Phillips
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology & Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David M. Dooley
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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Murakami Y, Yoshimoto N, Fujieda N, Ohkubo K, Hasegawa T, Kano K, Fukuzumi S, Itoh S. Model Studies of 6,7-Indolequinone Cofactors of Quinoprotein Amine Dehydrogenases. J Org Chem 2007; 72:3369-80. [PMID: 17388633 DOI: 10.1021/jo0700272] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electronic effects of the C-4 substituent on the physicochemical properties and reactivity of the 6,7-inodolequinone cofactors (CTQ and TTQ) have extensively been investigated with use of a series of C-4 substituted 6,7-inodolequinone derivatives (1-4). The one-electron reduction potentials of the 6,7-inodolequinone derivatives decrease with increasing the electron donating ability of the C-4 substituent (with the following order of E degrees': 4>1>2>3). The reaction of indolequinones 1-3 with benzylamine proceeds stepwise through the iminoquinone and the product-imine intermediates to give aminophenol as the final product as the case of TTQ model compound 4. The rate constants of each step have been determined by the detailed kinetic analysis, and the kinetic deuterium isotope effects have also been examined to confirm the rate-determining step. The reactivity of CTQ model compound 1 toward the amines is by one order of magnitude lower than that of TTQ model compound 4. The reactivity of indolequinones 2 and 3 is further decreased due to their stronger electron-donating substituents at C-4. A more important difference between CTQ model compound 1 and TTQ model compound 4 is the reactivity of the iminoquinone intermediate: the reaction of the CTQ model compound with amines stops at the iminoquinone formation stage at room temperature, whereas the reaction of the TTQ model compound with amines proceeds up to the aminophenol formation. Thus, the energy barrier for the rearrangement of the iminoquinone to the product-imine is higher in the CTQ model system than in the TTQ model system.
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Affiliation(s)
- Yoko Murakami
- Department of Chemistry, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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49
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Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res 2007; 6:1917-32. [PMID: 17391016 PMCID: PMC2588348 DOI: 10.1021/pr060394e] [Citation(s) in RCA: 298] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, the understanding of the relationships between function, amino acid sequence, and protein structure continues to represent one of the major challenges of the modern protein science. As many as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bionformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200 000 proteins from the Swiss-Prot database, each annotated with at least one of the 875 functional keywords, was described in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V.N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Using this tool, we have found that out of the 710 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (see above). The second paper of the series was devoted to the presentation of 87 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions (Vucetic, S.; Xie, H.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome Res. 2007, 5, 1899-1916). Protein structure and functionality can be modulated by various post-translational modifications or/and as a result of binding of specific ligands. Numerous human diseases are associated with protein misfolding/misassembly/misfunctioning. This work concludes the series of papers dedicated to the functional anthology of intrinsic disorder and describes approximately 80 Swiss-Prot functional keywords that are related to ligands, post-translational modifications, and diseases possessing strong positive or negative correlation with the predicted long disordered regions in proteins.
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Affiliation(s)
- Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Lilia M. Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Correspondence should be addressed to: Vladimir N. Uversky, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS#4021, Indianapolis, IN 46202, USA; Phone: 317-278-9194; Fax: 317-274-4686; E-mail:
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50
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Barondeau DP, Kassmann CJ, Tainer JA, Getzoff ED. The Case of the Missing Ring: Radical Cleavage of a Carbon−Carbon Bond and Implications for GFP Chromophore Biosynthesis. J Am Chem Soc 2007; 129:3118-26. [PMID: 17326633 DOI: 10.1021/ja063983u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The green fluorescent protein (GFP) creates its fluorophore by promoting spontaneous peptide backbone cyclization and amino acid oxidation chemistry on its own Ser65, Tyr66, Gly67 tripeptide sequence. Here we use high-resolution crystallography and mutational analyses to characterize GFP variants that undergo backbone cyclization followed by either anticipated chromophore synthesis via Y66F Calpha-Cbeta double-bond formation or unprecedented loss of a Y66F benzyl moiety via Calpha-Cbeta bond cleavage. We discovered a Y66F cleavage variant that subsequently incorporates an oxygen atom, likely from molecular oxygen, at the Y66 Calpha position. The post-translational products identified from these Y66F GFP structures support a common intermediate that partitions between Calpha-Cbeta oxidation and homolytic cleavage pathways. Our data indicate that Glu222 is the branchpoint control for this partitioning step and also influences subsequent oxygen incorporation reactions. From these results, we propose mechanisms for Y66F Calpha-Cbeta cleavage, oxygen incorporation, and chromophore biosynthesis with shared features that include radical chemistry. By revealing how GFP and RFP protein environments steer chemistry to favor fluorophore biosynthesis and disfavor alternative reactivity, we identify strategies for protein design. The proposed, common, one-electron oxidized, radical intermediate for post-translation modifications in the GFP family has general implications for how proteins drive and control spontaneous post-translational chemical modifications in the absence of metal ions.
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Affiliation(s)
- David P Barondeau
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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