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Feng W, Chittò M, Xie W, Ren Q, Liu F, Kang X, Zhao D, Li G, Moriarty TF, Wang X. Poly(d-amino acid) Nanoparticles Target Staphylococcal Growth and Biofilm Disassembly by Interfering with Peptidoglycan Synthesis. ACS Nano 2024; 18:8017-8028. [PMID: 38456817 DOI: 10.1021/acsnano.3c10983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
d-Amino acids are signals for biofilm disassembly. However, unexpected metabolic pathways severely attenuate the utilization of d-amino acids in biofilm disassembly, resulting in unsatisfactory efficiency. Herein, three-dimensional poly(d-amino acid) nanoparticles (NPs), which possess the ability to block intracellular metabolism, are constructed with the aim of disassembling the biofilms. The obtained poly(α-N-acryloyl-d-phenylalanine)-block-poly(β-N-acryloyl-d-aminoalanine NPs (denoted as FA NPs) present α-amino groups and α-carboxyl groups of d-aminoalanine on their surface, which guarantees that FA NPs can effectively insert into bacterial peptidoglycan (PG) via the mediation of PG binding protein 4 (PBP4). Subsequently, the FA NPs trigger the detachment of amyloid-like fibers that connect to the PG and reduce the number of polysaccharides and proteins in extracellular polymeric substances (EPS). Finally, FA NPs damage the structural stability of EPS and lead to the disassembly of the biofilm. Based on this feature, FA NPs significantly enhance the killing efficacy of encapsulated sitafloxacin sesquihydrate (Sita) by facilitating the penetration of Sita within the biofilm, achieving complete elimination of Staphylococcal biofilm in mice. Therefore, this study strongly demonstrates that FA NPs can effectively improve biofilm disassembly efficacy and provide great potential for bacterial biofilm infection treatment.
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Affiliation(s)
- Wenli Feng
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
- AO Research Institute Davos, Davos 7270, Switzerland
- China-Japan Friendship Hospital, Beijing 100029, People's Republic of China
| | - Marco Chittò
- AO Research Institute Davos, Davos 7270, Switzerland
| | - Wensheng Xie
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Qun Ren
- The Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, EMPA, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Fang Liu
- China-Japan Friendship Hospital, Beijing 100029, People's Republic of China
| | - Xiaoxu Kang
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Dongdong Zhao
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Guofeng Li
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | | | - Xing Wang
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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Ambade SS, Gupta VK, Bhole RP, Khedekar PB, Chikhale RV. A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant Staphylococcus aureus (MRSA). Molecules 2023; 28:7008. [PMID: 37894491 PMCID: PMC10609489 DOI: 10.3390/molecules28207008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen. Methicillin-resistant Staphylococcus aureus (MRSA) infections pose significant and challenging therapeutic difficulties. MRSA often acquires the non-native gene PBP2a, which results in reduced susceptibility to β-lactam antibiotics, thus conferring resistance. PBP2a has a lower affinity for methicillin, allowing bacteria to maintain peptidoglycan biosynthesis, a core component of the bacterial cell wall. Consequently, even in the presence of methicillin or other antibiotics, bacteria can develop resistance. Due to genes responsible for resistance, S. aureus becomes MRSA. The fundamental premise of this resistance mechanism is well-understood. Given the therapeutic concerns posed by resistant microorganisms, there is a legitimate demand for novel antibiotics. This review primarily focuses on PBP2a scaffolds and the various screening approaches used to identify PBP2a inhibitors. The following classes of compounds and their biological activities are discussed: Penicillin, Cephalosporins, Pyrazole-Benzimidazole-based derivatives, Oxadiazole-containing derivatives, non-β-lactam allosteric inhibitors, 4-(3H)-Quinazolinones, Pyrrolylated chalcone, Bis-2-Oxoazetidinyl macrocycles (β-lactam antibiotics with 1,3-Bridges), Macrocycle-embedded β-lactams as novel inhibitors, Pyridine-Coupled Pyrimidinones, novel Naphthalimide corbelled aminothiazoximes, non-covalent inhibitors, Investigational-β-lactam antibiotics, Carbapenem, novel Benzoxazole derivatives, Pyrazolylpyridine analogues, and other miscellaneous classes of scaffolds for PBP2a. Additionally, we discuss the penicillin-binding protein, a crucial target in the MRSA cell wall. Various aspects of PBP2a, bacterial cell walls, peptidoglycans, different crystal structures of PBP2a, synthetic routes for PBP2a inhibitors, and future perspectives on MRSA inhibitors are also explored.
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Affiliation(s)
- Shraddha S. Ambade
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra 282004, UP, India
| | - Ritesh P. Bhole
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, MH, India
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune 411018, MH, India
| | - Pramod B. Khedekar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440033, MH, India (P.B.K.)
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3
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He W, Huang X, Kelimu A, Li W, Cui C. Streamlined Efficient Synthesis and Antioxidant Activity of γ-[Glutamyl] (n≥1)-tryptophan Peptides by Glutaminase from Bacillus amyloliquefaciens. Molecules 2023; 28:4944. [PMID: 37446606 DOI: 10.3390/molecules28134944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
As a group of naturally occurring peptides in various foods, γ-glutamyl peptides possess a unique Kokumi taste and health benefits. However, few studies have focused on the functionality of γ-glutamyl peptides. In this study, the γ-[glutamyl] (n=1, 2, 3)-tryptophan peptides were synthesized from a solution of glutamine (Gln) and tryptophan (Trp) employing L-glutaminase from Bacillus amyloliquefaciens. Four different γ-glutamyl peptides were identified from the reaction mixture by UPLC-Q-TOF-MS/MS. Under optimal conditions of pH 10, 37 °C, 3 h, 0.1 mol/L Gln: 0.1 mol/L Trp = 1:3, and glutaminase at 0.1% (m/v), the yields of γ-l-glutamyl-l-tryptophan (γ-EW), γ-l-glutamyl-γ-l-glutamyl-l-tryptophan (γ-EEW) and γ-l-glutamyl-γ-l-glutamyl-γ-l-glutamyl-l-tryptophan (γ-EEEW) were 51.02%, 26.12% and 1.91% respectively. The antioxidant properties of the reaction mixture and the two peptides (γ-EW, γ-EEW) identified from the reaction media were further compared. Results showed that γ-EW exhibited the highest DPPH•, ABTS•+ and O2•--scavenging activity (EC50 = 0.2999 mg/mL, 67.6597 μg/mL and 5.99 mg/mL, respectively) and reducing power (EC50 = 4.61 mg/mL), while γ-EEW demonstrated the highest iron-chelating activity (76.22%). Thus, the synthesized mixture may be used as a potential source of antioxidant peptides for food and nutraceutical applications.
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Affiliation(s)
- Wenjiang He
- Infinitus (China) Co., Ltd., Guangzhou 510640, China
| | - Xiaoling Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Abulimiti Kelimu
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Nongda East Road 311, Urumqi 830052, China
| | - Wenzhi Li
- Infinitus (China) Co., Ltd., Guangzhou 510640, China
| | - Chun Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
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4
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Abstract
γ-Glutamylvalylglycine is known as a potent "kokumi" substance that increases the thickness, continuity, and mouthfulness of the taste of food. In this study, γ-glutamylvalylglycine was enzymatically synthesized from glutamine and valylglycine through the transpeptidation reaction of bacterial γ-glutamyltranspeptidase. The reaction conditions decided for the production of γ-glutamylvalylglycine are 20 mM glutamine, 100 mM valylglycine, 30 mU/mL γ-glutamyltranspeptidase, and 0.856 M (5%) NaCl at pH 8 and 37 °C, and 18.6 mM γ-glutamylvalylglycine was synthesized. Metal cations, Na+ and Mg2+, improved the transpeptidation reaction of γ-glutamyltranspeptidase, and the production of γ-glutamylvalylglycine increased. Moreover, by feeding a suitable amount of glutamine every 5 h, the maximum production of γ-glutamylvalylglycine increased 1.7 times after 20 h of incubation.
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Affiliation(s)
- Tatsuo Fukao
- Division of Applied Biology, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hideyuki Suzuki
- Division of Applied Biology, Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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Abstract
The T cell antigens driving autoimmune Type 1 Diabetes (T1D) have been pursued for more than three decades. When diabetogenic CD4 T cell clones and their relevant MHCII antigen presenting alleles were first identified in rodents and humans, the path to discovering the peptide epitopes within pancreatic beta cell proteins seemed straightforward. However, as experimental results accumulated, definitive data were often absent or controversial. Work within the last decade has helped to clear up some of the controversy by demonstrating that a number of the important MHCII presented epitopes are not encoded in the natural beta cell proteins, but in fact are fusions between peptide fragments derived from the same or different proteins. Recently, the mechanism for generating these MHCII diabetogenic chimeric epitopes has been attributed to a form of reverse proteolysis, called transpeptidation, a process that has been well-documented in the production of MHCI presented epitopes. In this mini-review we summarize these data and their implications for T1D and other autoimmune responses.
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Affiliation(s)
- Brendan K Reed
- Research Division, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, United States.,Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, United States.,Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States
| | - John W Kappler
- Research Division, Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, United States.,Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, United States.,Department of Immunology and Microbiology, University of Colorado, Aurora, CO, United States.,Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, United States
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6
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Dall E, Zauner FB, Soh WT, Demir F, Dahms SO, Cabrele C, Huesgen PF, Brandstetter H. Structural and functional studies of Arabidopsis thaliana legumain beta reveal isoform specific mechanisms of activation and substrate recognition. J Biol Chem 2020; 295:13047-13064. [PMID: 32719006 PMCID: PMC7489914 DOI: 10.1074/jbc.ra120.014478] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/14/2020] [Indexed: 01/19/2023] Open
Abstract
The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest, e.g. for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mechanisms behind their dual protease and ligase activities are still poorly understood, limiting their applications. Here, we present the crystal structure of Arabidopsis thaliana legumain isoform β (AtLEGβ) in its zymogen state. Combining structural and biochemical experiments, we show for the first time that plant legumains encode distinct, isoform-specific activation mechanisms. Whereas the autocatalytic activation of isoform γ (AtLEGγ) is controlled by the latency-conferring dimer state, the activation of the monomeric AtLEGβ is concentration independent. Additionally, in AtLEGβ the plant-characteristic two-chain intermediate state is stabilized by hydrophobic rather than ionic interactions, as in AtLEGγ, resulting in significantly different pH stability profiles. The crystal structure of AtLEGβ revealed unrestricted nonprime substrate binding pockets, consistent with the broad substrate specificity, as determined by degradomic assays. Further to its protease activity, we show that AtLEGβ exhibits a true peptide ligase activity. Whereas cleavage-dependent transpeptidase activity has been reported for other plant legumains, AtLEGβ is the first example of a plant legumain capable of linking free termini. The discovery of these isoform-specific differences will allow us to identify and rationally design efficient ligases with application in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
| | - Florian B Zauner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Sven O Dahms
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
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7
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Ramirez NA, Das A, Ton-That H. New Paradigms of Pilus Assembly Mechanisms in Gram-Positive Actinobacteria. Trends Microbiol 2020; 28:999-1009. [PMID: 32499101 DOI: 10.1016/j.tim.2020.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023]
Abstract
Adhesive pili in Gram-positive bacteria represent a variety of extracellular multiprotein polymers that mediate bacterial colonization of specific host tissues and associated pathogenesis. Pili are assembled in two distinct but coupled steps, an orderly crosslinking of pilin monomers and subsequent anchoring of the polymer to peptidoglycan, catalyzed by two transpeptidase enzymes - the pilus-specific sortase and the housekeeping sortase. Here, we review this biphasic assembly mechanism based on studies of two prototypical models, the heterotrimeric pili in Corynebacterium diphtheriae and the heterodimeric pili in Actinomyces oris, highlighting some newly emerged basic paradigms. The disparate mechanisms of protein ligation mediated by the pilus-specific sortase and the spatial positioning of adhesive pili on the cell surface modulated by the housekeeping sortase are among the notable highlights.
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Affiliation(s)
- Nicholas A Ramirez
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Asis Das
- Department of Medicine, Neag Comprehensive Cancer Center, University of Connecticut Health Center, Farmington, CT, USA
| | - Hung Ton-That
- Molecular Biology Institute, University of California, Los Angeles, CA, USA; Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, CA, USA.
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8
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Abstract
Ribosomes are ribonucleoprotein nanoparticles synthesizing all proteins in living cells. The function of the ribosome is to translate the genetic information encoded in a nucleotide sequence of mRNA into the amino acid sequence of a protein. Each translation step (occurring after the codon-dependent binding of the aminoacyl-tRNA with the ribosome and mRNA) includes (i) the transpeptidation reaction and (ii) the translocation that unidirectionally drives the mRNA chain and mRNA-bound tRNA molecules through the ribosomal intersubunit space; the latter process is driven by the free energy of the chemical reaction of transpeptidation. Thus, the translating ribosome can be considered a conveying protein-synthesizing molecular machine. In this review we analyze the role of ribosomal intersubunit mobility in the process of translocation.
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Affiliation(s)
- A V Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.,Biological Faculty, Moscow State University, Moscow, 119192 Russia
| | - S V Razin
- Biological Faculty, Moscow State University, Moscow, 119192 Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A S Spirin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.,Biological Faculty, Moscow State University, Moscow, 119192 Russia.,
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9
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Di Girolamo S, Puorger C, Castiglione M, Vogel M, Gébleux R, Briendl M, Hell T, Beerli RR, Grawunder U, Lipps G. Characterization of the housekeeping sortase from the human pathogen Propionibacterium acnes: first investigation of a class F sortase. Biochem J 2019; 476:665-82. [PMID: 30670573 DOI: 10.1042/BCJ20180885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/17/2022]
Abstract
Sortase enzymes play an important role in Gram-positive bacteria. They are responsible for the covalent attachment of proteins to the surface of the bacteria and perform this task via a highly sequence-specific transpeptidation reaction. Since these immobilized proteins are often involved in pathogenicity of Gram-positive bacteria, characterization of this type of enzyme is also of medical relevance. Different classes of sortases (A-F) have been found, which recognize characteristic recognition sequences present in substrate proteins. Up to date, sortase A from Staphylococcus aureus, a housekeeping class A sortase, is the most thoroughly studied representative of the sortase family of enzymes. Here we report the in-depth characterization of the class F sortase from Propionibacterium acnes, a class of sortases that has not been investigated before. As Sortase F is the only transpeptidase found in the P. acnes genome, it is the housekeeping sortase of this organism. Sortase F from P. acnes shows a behavior similar to sortases from class A in terms of pH dependence, recognition sequence and catalytic activity; furthermore, its activity is independent of bivalent ions, which contrasts to sortase A from S. aureus We demonstrate that sortase F is useful for protein engineering applications, by producing a site-specifically conjugated homogenous antibody-drug conjugate with a potency similar to that of a conjugate prepared with sortase A. Thus, the detailed characterization presented here will not only enable the development of anti-virulence agents targeting P. acnes but also provides a powerful alternative to sortase A for protein engineering applications.
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10
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Gonzalez-Duque S, Azoury ME, Colli ML, Afonso G, Turatsinze JV, Nigi L, Lalanne AI, Sebastiani G, Carré A, Pinto S, Culina S, Corcos N, Bugliani M, Marchetti P, Armanet M, Diedisheim M, Kyewski B, Steinmetz LM, Buus S, You S, Dubois-Laforgue D, Larger E, Beressi JP, Bruno G, Dotta F, Scharfmann R, Eizirik DL, Verdier Y, Vinh J, Mallone R. Conventional and Neo-antigenic Peptides Presented by β Cells Are Targeted by Circulating Naïve CD8+ T Cells in Type 1 Diabetic and Healthy Donors. Cell Metab 2018; 28:946-960.e6. [PMID: 30078552 DOI: 10.1016/j.cmet.2018.07.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/20/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022]
Abstract
Although CD8+ T-cell-mediated autoimmune β cell destruction occurs in type 1 diabetes (T1D), the target epitopes processed and presented by β cells are unknown. To identify them, we combined peptidomics and transcriptomics strategies. Inflammatory cytokines increased peptide presentation in vitro, paralleling upregulation of human leukocyte antigen (HLA) class I expression. Peptide sources featured several insulin granule proteins and all known β cell antigens, barring islet-specific glucose-6-phosphatase catalytic subunit-related protein. Preproinsulin yielded HLA-A2-restricted epitopes previously described. Secretogranin V and its mRNA splice isoform SCG5-009, proconvertase-2, urocortin-3, the insulin gene enhancer protein ISL-1, and an islet amyloid polypeptide transpeptidation product emerged as antigens processed into HLA-A2-restricted epitopes, which, as those already described, were recognized by circulating naive CD8+ T cells in T1D and healthy donors and by pancreas-infiltrating cells in T1D donors. This peptidome opens new avenues to understand antigen processing by β cells and for the development of T cell biomarkers and tolerogenic vaccination strategies.
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Affiliation(s)
- Sergio Gonzalez-Duque
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, 75005 Paris, France
| | - Marie Eliane Azoury
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Maikel L Colli
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Georgia Afonso
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Jean-Valery Turatsinze
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Laura Nigi
- University of Siena, Department of Medicine, Surgery and Neuroscience, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, 53100 Siena, Italy
| | - Ana Ines Lalanne
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Guido Sebastiani
- University of Siena, Department of Medicine, Surgery and Neuroscience, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, 53100 Siena, Italy
| | - Alexia Carré
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Sheena Pinto
- DKFZ, Division of Developmental Immunology, 69120 Heidelberg, Germany
| | - Slobodan Culina
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Noémie Corcos
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Marco Bugliani
- University of Pisa, Department of Clinical and Experimental Medicine, 56124 Pisa, Italy
| | - Piero Marchetti
- University of Pisa, Department of Clinical and Experimental Medicine, 56124 Pisa, Italy
| | - Mathieu Armanet
- Assistance Publique Hôpitaux de Paris, Cell Therapy Unit, Saint Louis Hospital, 75010 Paris, France
| | - Marc Diedisheim
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France
| | - Bruno Kyewski
- DKFZ, Division of Developmental Immunology, 69120 Heidelberg, Germany
| | - Lars M Steinmetz
- Stanford University, School of Medicine, Department of Genetics and Stanford Genome Technology Center, Stanford, CA 94305, USA; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Søren Buus
- Panum Institute, Department of International Health, Immunology and Microbiology, 2200 Copenhagen, Denmark
| | - Sylvaine You
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Daniele Dubois-Laforgue
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France
| | - Etienne Larger
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France
| | - Jean-Paul Beressi
- Centre Hospitalier de Versailles André Mignot, Service de Diabétologie, 78150 Le Chesnay, France
| | - Graziella Bruno
- University of Turin, Department of Medical Sciences, 10126 Turin, Italy
| | - Francesco Dotta
- University of Siena, Department of Medicine, Surgery and Neuroscience, Diabetes Unit and Fondazione Umberto di Mario ONLUS, Toscana Life Sciences, 53100 Siena, Italy
| | - Raphael Scharfmann
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France
| | - Decio L Eizirik
- Université Libre de Bruxelles Center for Diabetes Research and Welbio, Medical Faculty, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Yann Verdier
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, 75005 Paris, France
| | - Joelle Vinh
- ESPCI Paris, PSL University, Spectrométrie de Masse Biologique et Protéomique, CNRS USR3149, 75005 Paris, France
| | - Roberto Mallone
- INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France.
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11
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Abstract
Proteases have evolved to mediate the hydrolysis of peptide bonds but may perform transpeptidation in the presence of a proper nucleophilic molecule that can effectively compete with water to react with the acyl-enzyme intermediate. There have been several examples of protease-mediated transpeptidation, but they are generally inefficient, and little effort has been made to systematically control the transpeptidation activity of other proteases with good nucleophiles. Here, we developed an on-bead screening approach to find a probe that functions efficiently as a nucleophile in the protease-mediated transpeptidation reaction, and we identified good probes for a model protease DegP. These probes were covalently linked to the C-termini of the cleaved peptides in a mild condition and made the selective enrichment of ligated peptides possible. We suggest that good nucleophilic probes can be found for many other proteases that act via acyl-enzyme intermediates, and these probes will help characterize their substrates.
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Affiliation(s)
- Ga-Eul Eom
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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12
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Zhang L, Veith PD, Huq NL, Chen YY, Seers CA, Cross KJ, Gorasia DG, Reynolds EC. Porphyromonas gingivalis Gingipains Display Transpeptidation Activity. J Proteome Res 2018; 17:2803-2818. [PMID: 29984580 DOI: 10.1021/acs.jproteome.8b00286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Porphyromonas gingivalis is a keystone periodontal pathogen that has been associated with autoimmune disorders. The cell surface proteases Lys-gingipain (Kgp) and Arg-gingipains (RgpA and RgpB) are major virulence factors, and their proteolytic activity is enhanced by small peptides such as glycylglycine (GlyGly). The reaction kinetics suggested that GlyGly may function as an acceptor molecule for gingipain-catalyzed transpeptidation. Purified gingipains and P. gingivalis whole cells were used to digest selected substrates including human hemoglobin in the presence or absence of peptide acceptors. Mass spectrometric analysis of the substrates digested with gingipains in the presence of GlyGly showed that transpeptidation outcompeted hydrolysis, whereas the trypsin-digested controls exhibited predominantly hydrolysis activity. The transpeptidation levels increased with increasing concentration of GlyGly. Purified gingipains and whole cells exhibited extensive transpeptidation activities on human hemoglobin. All hemoglobin cleavage sites were found to be suitable for GlyGly transpeptidation, and this transpeptidation enhanced hemoglobin digestion. The transpeptidation products were often more abundant than the corresponding hydrolysis products. In the absence of GlyGly, hemoglobin peptides produced during digestion were utilized as acceptors leading to the detection of up to 116 different transpeptidation products in a single reaction. P. gingivalis cells were able to digest hemoglobin faster when acceptor peptides derived from human serum albumin were included in the reaction, suggesting that gingipain-catalyzed transpeptidation may be relevant for substrates encountered in vivo. The transpeptidation of host proteins in vivo may potentially lead to the breakdown of immunological tolerance, culminating in autoimmune reactions.
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Affiliation(s)
- Lianyi Zhang
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Paul D Veith
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - N Laila Huq
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Yu-Yen Chen
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Christine A Seers
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Keith J Cross
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Dhana G Gorasia
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, Bio21 Institute , The University of Melbourne , Melbourne , Victoria , Australia
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13
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Chang C, Amer BR, Osipiuk J, McConnell SA, Huang IH, Hsieh V, Fu J, Nguyen HH, Muroski J, Flores E, Ogorzalek Loo RR, Loo JA, Putkey JA, Joachimiak A, Das A, Clubb RT, Ton-That H. In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linking. Proc Natl Acad Sci U S A 2018; 115:E5477-E5486. [PMID: 29844180 PMCID: PMC6004493 DOI: 10.1073/pnas.1800954115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Covalently cross-linked pilus polymers displayed on the cell surface of Gram-positive bacteria are assembled by class C sortase enzymes. These pilus-specific transpeptidases located on the bacterial membrane catalyze a two-step protein ligation reaction, first cleaving the LPXTG motif of one pilin protomer to form an acyl-enzyme intermediate and then joining the terminal Thr to the nucleophilic Lys residue residing within the pilin motif of another pilin protomer. To date, the determinants of class C enzymes that uniquely enable them to construct pili remain unknown. Here, informed by high-resolution crystal structures of corynebacterial pilus-specific sortase (SrtA) and utilizing a structural variant of the enzyme (SrtA2M), whose catalytic pocket has been unmasked by activating mutations, we successfully reconstituted in vitro polymerization of the cognate major pilin (SpaA). Mass spectrometry, electron microscopy, and biochemical experiments authenticated that SrtA2M synthesizes pilus fibers with correct Lys-Thr isopeptide bonds linking individual pilins via a thioacyl intermediate. Structural modeling of the SpaA-SrtA-SpaA polymerization intermediate depicts SrtA2M sandwiched between the N- and C-terminal domains of SpaA harboring the reactive pilin and LPXTG motifs, respectively. Remarkably, the model uncovered a conserved TP(Y/L)XIN(S/T)H signature sequence following the catalytic Cys, in which the alanine substitutions abrogated cross-linking activity but not cleavage of LPXTG. These insights and our evidence that SrtA2M can terminate pilus polymerization by joining the terminal pilin SpaB to SpaA and catalyze ligation of isolated SpaA domains in vitro provide a facile and versatile platform for protein engineering and bio-conjugation that has major implications for biotechnology.
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Affiliation(s)
- Chungyu Chang
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030
| | - Brendan R Amer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Jerzy Osipiuk
- Center for Structural Genomics of Infectious Diseases, Argonne National Laboratory, Argonne, IL 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Scott A McConnell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - I-Hsiu Huang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Van Hsieh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Janine Fu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Hong H Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - John Muroski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Erika Flores
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - John A Putkey
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Argonne National Laboratory, Argonne, IL 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Asis Das
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
- University of California, Los Angeles-US Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095
| | - Hung Ton-That
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030;
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14
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Abstract
Contents Summary 923 I. Introduction 923 II. Plant AEPs with macrocyclizing ability 924 III. Mechanism of macrocyclization by AEPs 925 IV. Conclusions 927 Acknowledgements 927 References 927 SUMMARY: Plant asparaginyl endopeptidases (AEPs) are important for the post-translational processing of seed storage proteins via cleavage of precursor proteins. Some AEPs also function as peptide bond-makers during the biosynthesis of several unrelated classes of cyclic peptides, namely the kalata-type cyclic peptides, PawS-Derived Peptides and cyclic knottins. These three families of gene-encoded peptides have different evolutionary origins, but all have recruited AEPs for their maturation. In the last few years, the field has advanced rapidly, with the biochemical characterization of three plant AEPs capable of peptide macrocyclization, and insights have been gained from the first AEP crystal structures, albeit mammalian ones. Although the biochemical studies have improved our understanding of the mechanism of action, the focus now is to understand what changes in AEP sequence and structure enable some plant AEPs to perform macrocyclization reactions.
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Affiliation(s)
- Amy M James
- School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
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15
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Zauner FB, Elsässer B, Dall E, Cabrele C, Brandstetter H. Structural analyses of Arabidopsis thaliana legumain γ reveal differential recognition and processing of proteolysis and ligation substrates. J Biol Chem 2018; 293:8934-8946. [PMID: 29628443 PMCID: PMC5995516 DOI: 10.1074/jbc.m117.817031] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 02/18/2018] [Indexed: 11/06/2022] Open
Abstract
Legumain is a dual-function protease-peptide ligase whose activities are of great interest to researchers studying plant physiology and to biotechnological applications. However, the molecular mechanisms determining the specificities for proteolysis and ligation are unclear because structural information on the substrate recognition by a fully activated plant legumain is unavailable. Here, we present the X-ray structure of Arabidopsis thaliana legumain isoform γ (AtLEGγ) in complex with the covalent peptidic Ac-YVAD chloromethyl ketone (CMK) inhibitor targeting the catalytic cysteine. Mapping of the specificity pockets preceding the substrate-cleavage site explained the known substrate preference. The comparison of inhibited and free AtLEGγ structures disclosed a substrate-induced disorder-order transition with synergistic rearrangements in the substrate-recognition sites. Docking and in vitro studies with an AtLEGγ ligase substrate, sunflower trypsin inhibitor (SFTI), revealed a canonical, protease substrate-like binding to the active site-binding pockets preceding and following the cleavage site. We found the interaction of the second residue after the scissile bond, P2'-S2', to be critical for deciding on proteolysis versus cyclization. cis-trans-Isomerization of the cyclic peptide product triggered its release from the AtLEGγ active site and prevented inadvertent cleavage. The presented integrative mechanisms of proteolysis and ligation (transpeptidation) explain the interdependence of legumain and its preferred substrates and provide a rational framework for engineering optimized proteases, ligases, and substrates.
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Affiliation(s)
- Florian B Zauner
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Brigitta Elsässer
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Elfriede Dall
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Chiara Cabrele
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
| | - Hans Brandstetter
- From the Department of Biosciences, University of Salzburg, Salzburg 5020, Austria
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16
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Haywood J, Schmidberger JW, James AM, Nonis SG, Sukhoverkov KV, Elias M, Bond CS, Mylne JS. Structural basis of ribosomal peptide macrocyclization in plants. eLife 2018; 7:32955. [PMID: 29384475 PMCID: PMC5834244 DOI: 10.7554/elife.32955] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions use the substrates amino terminus instead of water to deacylate, so a peptide bond is formed. How solvent-exposed plant AEPs macrocyclize is poorly understood. Here we present the crystal structure of an active plant AEP from the common sunflower, Helianthus annuus. The active site contained electron density for a tetrahedral intermediate with partial occupancy that predicted a binding mode for peptide macrocyclization. By substituting catalytic residues we could alter the ratio of cyclic to acyclic products. Moreover, we showed AEPs from other species lacking cyclic peptides can perform macrocyclization under favorable pH conditions. This structural characterization of AEP presents a logical framework for engineering superior enzymes that generate macrocyclic peptide drug leads. Most proteins are long, chain-like molecules that have two ends respectively called the N-terminus and C-terminus. However, certain proteins can close on themselves to become circular. This requires a chemical reaction between the N- and C-termini, which creates a strong bond between the two extremities. To go through this ‘cyclization’ process, a straight protein attaches to a certain type of protease, a class of enzyme that usually cuts proteins into smaller pieces. In plants that are distantly related, the same group of enzymes – called AEPs – has been selected to perform cyclization. Here, Haywood et al. study an AEP enzyme from sunflowers: they identify what about this enzyme’s structure is important to drive the complex chemical reaction that results in the protein being cyclized rather than simply cut. Using a technique called X-ray crystallography to see the positions of individual atoms in the enzyme, Haywood et al. caught a snapshot of the enzyme. Its structure explained how the enzyme’s shape can guide cyclization. In particular, the part of the enzyme that binds to the proteins, the active site, was relatively flat and open, but also flexible: this helped the N and C-termini react with each other and close the protein. Further experiments artificially mutated specific areas of the enzyme, which helped determine exactly which elements guide this succession of chemical reactions. The activity of AEPs is influenced by their local environment, such as acidity. In fact, Haywood et al. showed that certain AEPs, which do not normally carry out cyclization, can start performing this role when exposed to a different level of acidity. The pharmaceutical industry is increasingly interested in circular proteins, as these are stable, easily used by the body, and can be genetically customized to act only on specific targets. If the cyclization process is better understood, and then harnessed, new drug compounds could be produced.
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Affiliation(s)
- Joel Haywood
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Jason W Schmidberger
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Amy M James
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Samuel G Nonis
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Kirill V Sukhoverkov
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
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17
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Mannering SI, So M, Elso CM, Kay TWH. Shuffling peptides to create T-cell epitopes: does the immune system play cards? Immunol Cell Biol 2017; 96:34-40. [PMID: 29359347 DOI: 10.1111/imcb.1015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/17/2017] [Accepted: 09/18/2017] [Indexed: 11/27/2022]
Abstract
For a long time, immunologists have believed that classical CD4+ and CD8+ T cells recognize peptides (referred to as epitopes), derived from protein antigens presented by MHC/HLA class I or II. Over the past 10-15 years, it has become clear that epitopes recognized by CD8+, and more recently CD4+ T cells, can be formed by protein splicing. Here, we review the discovery of spliced epitopes recognized by tumor-specific human CD8+ T cells. We discuss how these epitopes are formed and some of the unusual variants that have been reported. Now, over a decade since the first report, evidence is emerging that spliced CD8+ T-cell epitopes are much more common, and potentially much more important, than previously imagined. Recent work has shown that epitopes recognized by CD4+ T cells can also be formed by protein splicing. We discuss the recent discovery of spliced CD4+ T-cell epitopes and their potential role as targets of autoimmune T-cell responses. Finally, we highlight some of the new questions raised from our growing appreciation of T-cell epitopes formed by peptide splicing.
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Affiliation(s)
- Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| | - Michelle So
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| | - Colleen M Elso
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
| | - Thomas W H Kay
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, Vic., Australia
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18
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Antos JM, Ingram J, Fang T, Pishesha N, Truttmann MC, Ploegh HL. Site-Specific Protein Labeling via Sortase-Mediated Transpeptidation. Curr Protoc Protein Sci 2017; 89:15.3.1-15.3.19. [PMID: 28762490 PMCID: PMC5810355 DOI: 10.1002/cpps.38] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Strategies for site-specific protein modification are highly desirable for the construction of conjugates containing non-genetically-encoded functional groups. Ideally, these strategies should proceed under mild conditions, and be compatible with a wide range of protein targets and non-natural moieties. The transpeptidation reaction catalyzed by bacterial sortases is a prominent strategy for protein derivatization that possesses these features. Naturally occurring or engineered variants of sortase A from Staphylococcus aureus catalyze a ligation reaction between a five-amino-acid substrate motif (LPXTG) and oligoglycine nucleophiles. By pairing proteins and synthetic peptides that possess these ligation handles, it is possible to install modifications onto the protein N- or C-terminus in site-specific fashion. As described in this unit, the successful implementation of sortase-mediated labeling involves straightforward solid-phase synthesis and molecular biology techniques, and this method is compatible with proteins in solution or on the surface of live cells. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- John M Antos
- Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Jessica Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Tao Fang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthias C Truttmann
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
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19
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Kim SJ, Singh M, Sharif S, Schaefer J. Desleucyl-Oritavancin with a Damaged d-Ala-d-Ala Binding Site Inhibits the Transpeptidation Step of Cell-Wall Biosynthesis in Whole Cells of Staphylococcus aureus. Biochemistry 2017; 56:1529-1535. [PMID: 28221772 PMCID: PMC5508972 DOI: 10.1021/acs.biochem.6b01125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used solid-state nuclear magnetic resonance to characterize the exact nature of the dual mode of action of oritavancin in preventing cell-wall assembly in Staphylococcus aureus. Measurements performed on whole cells labeled selectively in vivo have established that des-N-methylleucyl-N-4-(4-fluorophenyl)benzyl-chloroeremomycin, an Edman degradation product of [19F]oritavancin, which has a damaged d-Ala-d-Ala binding aglycon, is a potent inhibitor of the transpeptidase activity of cell-wall biosynthesis. The desleucyl drug binds to partially cross-linked peptidoglycan by a cleft formed between the drug aglycon and its biphenyl hydrophobic side chain. This type of binding site is present in other oritavancin-like glycopeptides, which suggests that for these drugs a similar transpeptidase inhibition occurs.
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Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, 101 Bagby Ave., Waco, TX 76798
| | - Manmilan Singh
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Shasad Sharif
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
| | - Jacob Schaefer
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130
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20
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King DT, Wasney GA, Nosella M, Fong A, Strynadka NCJ. Structural Insights into Inhibition of Escherichia coli Penicillin-binding Protein 1B. J Biol Chem 2016; 292:979-993. [PMID: 27899450 DOI: 10.1074/jbc.m116.718403] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the peptidoglycan cell wall is synthesized by bifunctional penicillin-binding proteins such as PBP1b that have both transpeptidase and transglycosylase activities. The PBP1b transpeptidase domain is a major target of β-lactams, and therefore it is important to attain a detailed understanding of its inhibition. The peptidoglycan glycosyltransferase domain of PBP1b is also considered an excellent antibiotic target yet is not exploited by any clinically approved antibacterials. Herein, we adapt a pyrophosphate sensor assay to monitor PBP1b-catalyzed glycosyltransfer and present an improved crystallographic model for inhibition of the PBP1b glycosyltransferase domain by the potent substrate analog moenomycin. We elucidate the structure of a previously disordered region in the glycosyltransferase active site and discuss its implications with regards to peptidoglycan polymerization. Furthermore, we solve the crystal structures of E. coli PBP1b bound to multiple different β-lactams in the transpeptidase active site and complement these data with gel-based competition assays to provide a detailed structural understanding of its inhibition. Taken together, these biochemical and structural data allow us to propose new insights into inhibition of both enzymatic domains in PBP1b.
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Affiliation(s)
- Dustin T King
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Gregory A Wasney
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Michael Nosella
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Anita Fong
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Natalie C J Strynadka
- From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
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21
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Jin N, Wang Y, Crawford F, White J, Marrack P, Dai S, Kappler JW. N-terminal additions to the WE14 peptide of chromogranin A create strong autoantigen agonists in type 1 diabetes. Proc Natl Acad Sci U S A. 2015;112:13318-13323. [PMID: 26453556 DOI: 10.1073/pnas.1517862112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chromogranin A (ChgA) is an autoantigen for CD4(+) T cells in the nonobese diabetic (NOD) mouse model of type 1 diabetes (T1D). The natural ChgA-processed peptide, WE14, is a weak agonist for the prototypical T cell, BDC-2.5, and other ChgA-specific T-cell clones. Mimotope peptides with much higher activity share a C-terminal motif, WXRM(D/E), that is predicted to lie in the p5 to p9 position in the mouse MHC class II, IA(g7) binding groove. This motif is also present in WE14 (WSRMD), but at its N terminus. Therefore, to place the WE14 motif into the same position as seen in the mimotopes, we added the amino acids RLGL to its N terminus. Like the other mimotopes, RLGL-WE14, is much more potent than WE14 in T-cell stimulation and activates a diverse population of CD4(+) T cells, which also respond to WE14 as well as islets from WT, but not ChgA(-/-) mice. The crystal structure of the IA(g7)-RLGL-WE14 complex confirmed the predicted placement of the peptide within the IA(g7) groove. Fluorescent IA(g7)-RLGL-WE14 tetramers bind to ChgA-specific T-cell clones and easily detect ChgA-specific T cells in the pancreas and pancreatic lymph nodes of NOD mice. The prediction that many different N-terminal amino acid extensions to the WXRM(D/E) motif are sufficient to greatly improve T-cell stimulation leads us to propose that such a posttranslational modification may occur uniquely in the pancreas or pancreatic lymph nodes, perhaps via the mechanism of transpeptidation. This modification could account for the escape of these T cells from thymic negative selection.
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Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des 2014; 82:418-28. [PMID: 23701677 DOI: 10.1111/cbdd.12167] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/06/2013] [Accepted: 05/19/2013] [Indexed: 01/15/2023]
Abstract
Staphylococcus aureus is the leading cause of hospital-acquired infections in the United States. The emergence of multidrug-resistant strains of S. aureus has created an urgent need for new antibiotics. Staphylococcus aureus uses the sortase A enzyme to display surface virulence factors suggesting that compounds that inhibit its activity will function as potent anti-infective agents. Here, we report the identification of several inhibitors of sortase A using virtual screening methods that employ the relaxed complex scheme, an advanced computer-docking methodology that accounts for protein receptor flexibility. Experimental testing validates that several compounds identified in the screen inhibit the activity of sortase A. A lead compound based on the 2-phenyl-2,3-dihydro-1H-perimidine scaffold is particularly promising, and its binding mechanism was further investigated using molecular dynamics simulations and conducting preliminary structure-activity relationship studies.
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Affiliation(s)
- Albert H Chan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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23
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Liu H, Zhou X, Tian S, Hao X, You J, Zhang Y. Two-step transpeptidation of the insulin precursor expressed in Pichia pastoris to insulin ester via trypsin-catalyzed cleavage and coupling. Biotechnol Appl Biochem 2013; 61:408-17. [PMID: 24325254 DOI: 10.1002/bab.1186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/05/2013] [Indexed: 11/07/2022]
Abstract
Insulin precursor fusion protein expressed in Pichia pastoris is a single-chain protein with a spacer peptide (EEAEAEAEPK) localized at its N-terminal. Currently, the one-step transpeptidation reaction with low yield and high cost is generally employed to convert the insulin precursor fusion protein into human insulin ester. In this study, a two-step transpeptidation reaction was proposed separating the cleavage step from the coupling step so that each reaction was performed under its optimal conditions. Using this method, the total efficiency doubled and the reaction time was shortened compared with the one-step method. In addition, the amount of O-t-butyl-l-threonine t-butyl ester and trypsin dosages were reduced by 50% and 75%, respectively. This two-step transpeptidation strategy was simple and efficient and could be used for the pharmaceutical production of human insulin.
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Affiliation(s)
- Haifeng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China.,Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China.,Shandong Ehua Biopharmaceutical Co., Ltd., Shandong, People's Republic of China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Shousheng Tian
- Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China
| | - Xianghui Hao
- Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China
| | - Jinhua You
- Shandong Dong-e E-Jiao Co., Ltd., Shandong, People's Republic of China.,Shandong Ehua Biopharmaceutical Co., Ltd., Shandong, People's Republic of China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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24
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Kornberger P, Skerra A. Sortase-catalyzed in vitro functionalization of a HER2-specific recombinant Fab for tumor targeting of the plant cytotoxin gelonin. MAbs 2013; 6:354-66. [PMID: 24492291 DOI: 10.4161/mabs.27444] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We report on the preparation of a new type of immunotoxin via in vitro ligation of the αHer2 antigen binding fragment (Fab) of the clinically-validated antibody trastuzumab to the plant toxin gelonin, employing catalysis by the bacterial enzyme sortase A (SrtA). The αHer2 Fab was fused with the extended SrtA recognition motif LPET↓GLEH 6 at the C-terminus of its heavy chain, thereby preventing interference with antigen binding, while the toxin was equipped with a Gly 2 sequence at its N-terminus, distant to the catalytically active site in the C-terminal region. Site-specific in vitro transpeptidation led to a novel antibody-toxin conjugate wherein gelonin had effectively replaced the Fc region of a conventional (monomerized) immunoglobulin. After optimization of reaction conditions and incubation time, the resulting Fab-Gelonin ligation product was purified to homogeneity in a two-step procedure by means of Strep-Tactin affinity chromatography--utilizing the Strep-tag II appended to gelonin--and size exclusion chromatography. Binding activity of the immunotoxin for the Her2 ectodomain was indistinguishable from the unligated Fab as measured by real-time surface plasmon resonance spectroscopy. Specific cytotoxic potency of Fab-Gelonin was demonstrated against two Her2-positive cell lines, resulting in EC 50 values of ~1 nM or lower, indicating a 1000-fold enhanced cell-killing activity compared with gelonin itself. Thus, our strategy provides a convenient route to the modular construction of functional immunotoxins from Fabs of established tumor-specific antibodies with gelonin or related proteotoxins, also avoiding the elevated biosafety levels that would be mandatory for the direct biotechnological preparation of corresponding fusion proteins.
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Affiliation(s)
- Petra Kornberger
- Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie; Technische Universität München; Freising-Weihenstephan, Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie; Technische Universität München; Freising-Weihenstephan, Germany
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25
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Cozzi R, Zerbini F, Assfalg M, D'Onofrio M, Biagini M, Martinelli M, Nuccitelli A, Norais N, Telford JL, Maione D, Rinaudo CD. Group B Streptococcus pilus sortase regulation: a single mutation in the lid region induces pilin protein polymerization in vitro. FASEB J 2013; 27:3144-54. [PMID: 23631841 DOI: 10.1096/fj.13-227793] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Gram-positive bacteria build pili on their cell surface via a class C sortase-catalyzed transpeptidation mechanism from pilin protein substrates. Despite the availability of several crystal structures, pilus-related C sortases remain poorly characterized to date, and their mechanisms of transpeptidation and regulation need to be further investigated. The available 3-dimensional structures of these enzymes reveal a typical sortase fold, except for the presence of a unique feature represented by an N-terminal highly flexible loop known as the "lid." This region interacts with the residues composing the catalytic triad and covers the active site, thus maintaining the enzyme in an autoinhibited state and preventing the accessibility to the substrate. It is believed that enzyme activation may occur only after lid displacement from the catalytic domain. In this work, we provide the first direct evidence of the regulatory role of the lid, demonstrating that it is possible to obtain in vitro an efficient polymerization of pilin subunits using an active C sortase lid mutant carrying a single residue mutation in the lid region. Moreover, biochemical analyses of this recombinant mutant reveal that the lid confers thermodynamic and proteolytic stability to the enzyme.
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Affiliation(s)
- Roberta Cozzi
- Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100 Siena, Italy
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26
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Antos JM, Ingram J, Fang T, Pishesha N, Truttmann MC, Ploegh HL. Site-specific protein labeling via sortase-mediated transpeptidation. Curr Protoc Protein Sci 2009; Chapter 15:15.3.1-15.3.9. [PMID: 19365788 PMCID: PMC5551486 DOI: 10.1002/0471140864.ps1503s56] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Creation of functional protein bioconjugates demands methods for attaching a diverse array of probes to target proteins with high specificity, under mild conditions. The sortase A transpeptidase enzyme from Staphylococcus aureus catalyzes the cleavage of a short 5-aa recognition sequence (LPXTG) with the concomitant formation of an amide linkage between an oligoglycine peptide and the target protein. By functionalizing the oligoglycine peptide, it is possible to incorporate reporters into target proteins in a site-specific fashion. This reaction is applicable to proteins in solution and on the living cell surface. The method described in this unit only requires incubation of the target protein, which has been engineered to contain a sortase recognition site either at the C terminus or within solvent-accessible loops, with a purified sortase enzyme and a suitably functionalized oligoglycine peptide.
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Affiliation(s)
- John M. Antos
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - Jessica Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, MA 02215
| | - Tao Fang
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Matthias C. Truttmann
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
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27
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Erskine PT, Coates L, Mall S, Gill RS, Wood SP, Myles DAA, Cooper JB. Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides. Protein Sci 2003; 12:1741-9. [PMID: 12876323 PMCID: PMC2323960 DOI: 10.1110/ps.0305203] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The X-ray structures of native endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 A resolution demonstrates that there is a short peptide (probably Ser-Thr) bound noncovalently in the active site cleft. The N-terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N-terminal Ser-Thr sequence of the enzyme during crystallization.
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Affiliation(s)
- Peter T Erskine
- Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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28
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Abstract
Peptide bond synthesis was studied with native polyribosomes of E. coli. With the use of this system for transpeptidation, it was possible to show that a single K(+) activates the ribosome monomers of polyribosomes; that protonation of a single group (probably imidazole or an N-terminal amino group) with a pK(a) equal to about 7.2 inactivates the transpeptidase complex; that Mn(++) can substitute for Mg(++), but that Ca(++), spermidine, and putrescine do so only very poorly; and that the K(m) for puromycin in this system is about 2.4 x 10(-6) M.
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