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Elgazzaz M, Filipeanu C, Lazartigues E. The 2023 Lewis K. Dahl Memorial Lecture: Angiotensin-Converting Enzyme 2 Posttranslational Modifications-Implications for Hypertension and SARS-CoV-2 Infection. Hypertension 2024. [PMID: 38567498 DOI: 10.1161/hypertensionaha.124.22067] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
ACE2 (angiotensin-converting enzyme 2), a multifunctional transmembrane protein, is well recognized as an important member of the (RAS) renin-angiotensin system with important roles in the regulation of cardiovascular function by opposing the harmful effects of Ang-II (angiotensin II) and AT1R (Ang-II type 1 receptor) activation. More recently, ACE2 was found to be the entry point for the SARS-CoV-2 virus into cells, causing COVID-19. This finding has led to an exponential rise in the number of publications focused on ACE2, albeit these studies often have opposite objectives to the preservation of ACE2 in cardiovascular regulation. However, notwithstanding accumulating data of the role of ACE2 in the generation of angiotensin-(1-7) and SARS-CoV-2 internalization, numerous other putative roles of this enzyme remain less investigated and not yet characterized. Currently, no drug modulating ACE2 function or expression is available in the clinic, and the development of new pharmacological tools should attempt targeting each step of the lifespan of the protein from synthesis to degradation. The present review expands on our presentation during the 2023 Lewis K. Dahl Memorial Lecture Sponsored by the American Heart Association Council on Hypertension. We provide a critical summary of the current knowledge of the mechanisms controlling ACE2 internalization and intracellular trafficking, the mutual regulation with GPCRs (G-protein-coupled receptors) and other proteins, and posttranslational modifications. A major focus is on ubiquitination which has become a critical step in the modulation of ACE2 cellular levels.
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Affiliation(s)
- Mona Elgazzaz
- Department of Physiology, Augusta University, Medical College of Georgia, Augusta, GA (M.E.)
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt (M.E.)
| | - Catalin Filipeanu
- Department of Pharmacology, Howard University, Washington, DC (C.F.)
| | - Eric Lazartigues
- Cardiovascular Center of Excellence, Louisiana State University Health Sciences Center, New Orleans (E.L.)
- Southeast Louisiana Veterans Health Care System, New Orleans (E.L.)
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Datta S, Nabeel Asim M, Dengel A, Ahmed S. NTpred: a robust and precise machine learning framework for in silico identification of Tyrosine nitration sites in protein sequences. Brief Funct Genomics 2024; 23:163-179. [PMID: 37248673 DOI: 10.1093/bfgp/elad018] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/12/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Post-translational modifications (PTMs) either enhance a protein's activity in various sub-cellular processes, or degrade their activity which leads toward failure of intracellular processes. Tyrosine nitration (NT) modification degrades protein's activity that initiates and propagates various diseases including neurodegenerative, cardiovascular, autoimmune diseases and carcinogenesis. Identification of NT modification supports development of novel therapies and drug discoveries for associated diseases. Identification of NT modification in biochemical labs is expensive, time consuming and error-prone. To supplement this process, several computational approaches have been proposed. However these approaches fail to precisely identify NT modification, due to the extraction of irrelevant, redundant and less discriminative features from protein sequences. This paper presents the NTpred framework that is competent in extracting comprehensive features from raw protein sequences using four different sequence encoders. To reap the benefits of different encoders, it generates four additional feature spaces by fusing different combinations of individual encodings. Furthermore, it eradicates irrelevant and redundant features from eight different feature spaces through a Recursive Feature Elimination process. Selected features of four individual encodings and four feature fusion vectors are used to train eight different Gradient Boosted Tree classifiers. The probability scores from the trained classifiers are utilized to generate a new probabilistic feature space, which is used to train a Logistic Regression classifier. On the BD1 benchmark dataset, the proposed framework outperforms the existing best-performing predictor in 5-fold cross validation and independent test evaluation with combined improvement of 13.7% in MCC and 20.1% in AUC. Similarly, on the BD2 benchmark dataset, the proposed framework outperforms the existing best-performing predictor with combined improvement of 5.3% in MCC and 1.0% in AUC. NTpred is publicly available for further experimentation and predictive use at: https://sds_genetic_analysis.opendfki.de/PredNTS/.
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Affiliation(s)
- Sourajyoti Datta
- Department of Computer Science, Rheinland Pfälzische Technische Universität, Kaiserslautern, 67663, Germany
| | - Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence, Kaiserslautern, 67663, Germany
| | - Andreas Dengel
- Department of Computer Science, Rheinland Pfälzische Technische Universität, Kaiserslautern, 67663, Germany
- German Research Center for Artificial Intelligence, Kaiserslautern, 67663, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence, Kaiserslautern, 67663, Germany
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Toscano G, Höfurthner T, Nagl B, Beier A, Mayer M, Geist L, McConnell DB, Weinstabl H, Konrat R, Lichtenecker RJ. 13 Cβ-Valine and 13 Cγ-Leucine Methine Labeling To Probe Protein Ligand Interaction. Chembiochem 2024; 25:e202300762. [PMID: 38294275 DOI: 10.1002/cbic.202300762] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/01/2024]
Abstract
Precise information regarding the interaction between proteins and ligands at molecular resolution is crucial for effectively guiding the optimization process from initial hits to lead compounds in early stages of drug development. In this study, we introduce a novel aliphatic side chain isotope-labeling scheme to directly probe interactions between ligands and aliphatic sidechains using NMR techniques. To demonstrate the applicability of this method, we selected a set of Brd4-BD1 binders and analyzed 1 H chemical shift perturbation resulting from CH-π interaction of Hβ -Val and Hγ -Leu as CH donors with corresponding ligand aromatic moieties as π acceptors.
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Affiliation(s)
- Giorgia Toscano
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
- Vienna Doctoral School of Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Theresa Höfurthner
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Vienna Doctoral School of Chemistry, University of Vienna, Währingerstr. 38, 1090, Vienna, Austria
| | - Benjamin Nagl
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
| | - Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Harald Weinstabl
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer, Gasse 5-Wien, 11, 1121, Vienna
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Max Perutz Laboratories, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- MAG-LAB, Karl-Farkas Gasse 22, 1030, Vienna
| | - Roman J Lichtenecker
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090, Vienna, Austria
- MAG-LAB, Karl-Farkas Gasse 22, 1030, Vienna
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Nyenhuis DA, Watanabe S, Bernstein R, Swenson RE, Raju N, Sabbasani VR, Mushti C, Lee DY, Carter C, Tjandra N. Structural Relationships to Efficacy for Prazole-Derived Antivirals. Adv Sci (Weinh) 2024:e2308312. [PMID: 38447164 DOI: 10.1002/advs.202308312] [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] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/25/2024] [Indexed: 03/08/2024]
Abstract
Here, an in vitro characterization of a family of prazole derivatives that covalently bind to the C73 site on Tsg101 and assay their ability to inhibit viral particle production is presented. Structurally, increased steric bulk on the 4-pyridyl of the prazole expands the prazole site on the UEV domain toward the β-hairpin in the Ub-binding site and is coupled to increased inhibition of virus-like particle production in HIV-1. Increased bulk also increased toxicity, which is alleviated by increasing flexibility. Further, the formation of a novel secondary Tsg101 adduct for several of the tested compounds and the commercial drug lansoprazole. The secondary adduct involved the loss of the 4-pyridyl substituent to form an irreversible species, with implications for increasing the half-life of the active species or its specificity toward Tsg101 UEV. It is also determined that sulfide derivatives display effective viral inhibition, presumably through cellular sulfoxidation, allowing for delayed conversion within the cellular environment, and identify SARS-COV-2 as a target of prazole inhibition. These results open multiple avenues for the design of prazole derivatives for antiviral applications.
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Affiliation(s)
- David A Nyenhuis
- Biochemistry and Biophysics Center, NHLBI, NIH, 50 South Drive, Bld 50, Rm 3503, Bethesda, MD, 20892, USA
| | - Susan Watanabe
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stonybrook University, Life Sciences Bldg, Rm 248, Stonybrook, NY, 11790, USA
| | - Rebecca Bernstein
- Biochemistry and Biophysics Center, NHLBI, NIH, 50 South Drive, Bld 50, Rm 3503, Bethesda, MD, 20892, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, NHLBI, NIH, 9800 Medical Center Drive, Bldg B, #2034, Rockville, MD, 20850, USA
| | - Natarajan Raju
- Chemistry and Synthesis Center, NHLBI, NIH, 9800 Medical Center Drive, Bldg B, #2034, Rockville, MD, 20850, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, NHLBI, NIH, 9800 Medical Center Drive, Bldg B, #2034, Rockville, MD, 20850, USA
| | - Chandrasekhar Mushti
- Chemistry and Synthesis Center, NHLBI, NIH, 9800 Medical Center Drive, Bldg B, #2034, Rockville, MD, 20850, USA
| | - Duck-Yeon Lee
- Biochemistry Core Facility, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Carol Carter
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stonybrook University, Life Sciences Bldg, Rm 248, Stonybrook, NY, 11790, USA
| | - Nico Tjandra
- Biochemistry and Biophysics Center, NHLBI, NIH, 50 South Drive, Bld 50, Rm 3503, Bethesda, MD, 20892, USA
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Kokollari A, Werner M, Lindner C, Pham TL, Thomas F. Rapid On-Resin N-Formylation of Peptides as One-Pot Reaction. Chembiochem 2023; 24:e202300571. [PMID: 37695727 DOI: 10.1002/cbic.202300571] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
N-formylation is a common pre- and post-translational modification of the N-terminus or the lysine side chain of peptides and proteins that plays a role in the initiation of immune responses, gene expression, or epigenetics. Despite its high biological relevance, protocols for the chemical N-formylation of synthetic peptides are scarce. The few available methods are elaborate in their execution and the yields are highly sequence-dependent. We present a rapid, easy-to-use one-pot procedure that runs at room temperature and can be used to formylate protected peptides at both the N-terminus and the lysine side chain on the resin in near-quantitative yields. Only insensitive, storage-stable standard chemicals - formic acid, acetic anhydride, pyridine and DMF - are used. Formylation works for both short and long peptides of up to 34 amino acids and over the spectrum of canonical amino acids.
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Affiliation(s)
- Agon Kokollari
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Marius Werner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Department of Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Department of Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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6
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Yates NDJ, Hatton NE, Fascione MA, Parkin A. Site-Selective Aryl Diazonium Installation onto Protein Surfaces at Neutral pH using a Maleimide-Functionalized Triazabutadiene. Chembiochem 2023; 24:e202300313. [PMID: 37311168 DOI: 10.1002/cbic.202300313] [Citation(s) in RCA: 1] [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] [Received: 04/20/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
Aryl diazonium cations are versatile bioconjugation reagents due to their reactivity towards electron-rich aryl residues and secondary amines, but historically their usage has been hampered by both their short lifespan in aqueous solution and the harsh conditions required to generate them in situ. Triazabutadienes address many of these issues as they are stable enough to endure multiple-step chemical syntheses and can persist for several hours in aqueous solution, yet upon UV-exposure rapidly release aryl diazonium cations under biologically-relevant conditions. This paper describes the synthesis of a novel maleimide-functionalized triazabutadiene suitable for site-selectively installing aryl diazonium cations into proteins at neutral pH; we show reaction with this molecule and a surface-cysteine of a thiol disulfide oxidoreductase. Through photoactivation of the site-selectively installed triazabutadiene motifs, we generate aryl diazonium functionality, which we further derivatize via azo-bond formation to electron-rich aryl species, showcasing the potential utility of this strategy for the generation of photoswitches or protein-drug conjugates.
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Affiliation(s)
- Nicholas D J Yates
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
| | - Natasha E Hatton
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
| | - Martin A Fascione
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
| | - Alison Parkin
- Department of Chemistry, University of York Heslington, York, YO10 5DD, UK
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7
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Yamashita M, Kawakami N, Miyamoto K. Hydrophobization of a TIP60 Protein Nanocage for the Encapsulation of Hydrophobic Compounds. Chempluschem 2023; 88:e202200392. [PMID: 36775805 DOI: 10.1002/cplu.202200392] [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: 11/07/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 02/14/2023]
Abstract
Encapsulation of hydrophobic molecules in protein-based nanocages is a promising approach for dispersing these molecules in water. Here, we report a chemical modification approach to produce a protein nanocage with a hydrophobic interior surface based on our previously developed nanocage, TIP60. The large pores of TIP60 act as tunnels for small molecules, allowing modification of the interior surface by hydrophobic compounds without nanocage disassembly. We used four different hydrophobic compounds for modification. The largest modification group tested, pyrene, resulted in a modified TIP60 that could encapsulate aromatic photosensitizer zinc phthalocyanine (ZnPC) more efficiently than the other modification compounds. The encapsulated ZnPC generated singlet oxygen upon light activation in the aqueous phase, whereas ZnPC alone formed inert aggregates under the same experimental conditions. Given that chemical modification allows a wider diversity of modifications than mutagenesis, this approach could be used to develop more suitable nanocages for encapsulating hydrophobic molecules of interest.
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Affiliation(s)
- Maika Yamashita
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223- 8522, Japan
| | - Norifumi Kawakami
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223- 8522, Japan
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223- 8522, Japan
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Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [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: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
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Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
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Gathercole JL, Nguyen HTH, Harris P, Weeks M, Reis MG. Protein modifications due to homogenisation and heat treatment of cow milk. J DAIRY RES 2023; 90:1-8. [PMID: 36815389 DOI: 10.1017/s0022029923000122] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
This research paper aimed to locate protein modifications caused by treatment of milk and determine if the modification locations were consistent. The majority of milk for consumption is homogenised using pressure and heat, and this causes changes in the location of proteins in the milk as well as protein modifications. To investigate these proteomic changes, raw milk was pasteurised (72°C, 15 s), then, to separate the treatment for homogenisation, heated at these different pressures and temperatures: 45°C without no pressure applied, 45°C with 35 MPa, 80°C without pressure applied and 80°C, with 35 MPa. Proteomic analysis was done after separating the milk into three fractions: whey, casein and cream. Protein modifications in each fraction were examined and we found Maillard products as well as oxidation to be of interest. The proteins were also further identified and characterised to compare protein modification sites and differences in proteins present in the cream resulting from homogenisation and/or pasteurisation. This experiment showed that both heat and pressure during homogenisation can cause increases in protein modifications as a result of oxidation or the Maillard reaction. Total cysteine oxidation and total proline oxidation differed between treatments although this was only significantly different for cysteine. It was observed that protein modifications occurred in the same location in the protein sequence rather than in random locations which we highlighted by examining α-S1-casein, lactadherin and β-lactoglobulin.
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Affiliation(s)
| | - Hanh T H Nguyen
- AgResearch Ltd, Te Ohu Rangahau Kai, Massey University, Palmerston North, 4474, New Zealand
| | - Paul Harris
- AgResearch Ltd, Te Ohu Rangahau Kai, Massey University, Palmerston North, 4474, New Zealand
| | - Mike Weeks
- AgResearch Ltd, Te Ohu Rangahau Kai, Massey University, Palmerston North, 4474, New Zealand
| | - Mariza G Reis
- AgResearch Ltd, Te Ohu Rangahau Kai, Massey University, Palmerston North, 4474, New Zealand
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Walker MG, Mendez CG, Ho PS. Non-classical Non-covalent σ-Hole Interactions in Protein Structure and Function: Concepts for Potential Protein Engineering Applications. Chem Asian J 2023; 18:e202300026. [PMID: 36764929 DOI: 10.1002/asia.202300026] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/12/2023]
Abstract
The structures and associated functions of biological molecules are driven by noncovalent interactions, which have classically been dominated by the hydrogen bond (H-bond). Introduction of the σ-hole concept to describe the anisotropic distribution of electrostatic potential of covalently bonded elements from across the periodic table has opened a broad range of nonclassical noncovalent (ncNC) interactions for applications in chemistry and biochemistry. Here, we review how halogen bonds, chalcogen bonds and tetrel bonds, as they are found naturally or introduced synthetically, affect the structures, assemblies, and potential functions of peptides and proteins. This review intentionally focuses on examples that introduce or support principles of stability, assembly and catalysis that can potentially guide the design of new functional proteins. These three types of ncNC interactions have energies that are comparable to the H-bond and, therefore, are now significant concepts in molecular recognition and design. However, the recently described H-bond enhanced X-bond shows how synergism among ncNC interactions can be exploited as potential means to broaden the range of their applications to affect protein structures and functions.
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Affiliation(s)
- Margaret G Walker
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - C Gustavo Mendez
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO, 80523-1870, USA
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11
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Gong Y, Li Y, Liu D, Jiang L, Liang H, Wu Y, Wang F, Yang J. Analysis of lysine acetylation in tomato spot wilt virus infection in Nicotiana benthamiana. Front Microbiol 2023; 14:1046163. [PMID: 36819054 PMCID: PMC9935083 DOI: 10.3389/fmicb.2023.1046163] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Kac is a model for all acylation modification studies. Kac plays a critical role in eukaryotes and prokaryotes. It is mainly involved in six major biological functions: gene expression, signal transduction, cell development, protein conversion, metabolism, and metabolite transport. Method We investigated and compared the acetylation modification of proteins in healthy and tomato spot wilt virus (TSWV)-infected Nicotiana benthamiana leaves. Result We identified 3,418 acetylated lysine sites on 1962 proteins acetylation of proteins in the TSWV-infected and control groups were compared; it was observed that 408 sites on 294 proteins were upregulated and 284 sites on 219 proteins (involved in pentose phosphate, photosynthesis, and carbon fixation in photosynthesis) were downregulated after the infection. Overall, 35 conserved motifs were identified, of which xxxkxxxxx_K_ Rxxxxxxxxx represented 1,334 (31.63%) enrichment motifs and was the most common combination. Bioinformatic analysis revealed that most of the proteins with Kac sites were located in the chloroplast and cytoplasm. They were involved in biological processes, such as cellular and metabolic processes. Discussion In conclusion, our results revealed that Kac may participate in the regulation of TSWV infection in N. benthamiana.
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Affiliation(s)
- Yanwei Gong
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dongyang Liu
- Liangshan State Company of Sichuan Province Tobacco Company, Mile, China
| | - Lianqiang Jiang
- Liangshan State Company of Sichuan Province Tobacco Company, Mile, China
| | - Hui Liang
- Liangshan State Company of Sichuan Province Tobacco Company, Mile, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China,*Correspondence: Fenglong Wang, ✉
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China,Jinguang Yang, ✉
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12
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Ray DM, Flood JR, David Y. Harnessing Split-Inteins as a Tool for the Selective Modification of Surface Receptors in Live Cells. Chembiochem 2023; 24:e202200487. [PMID: 36178424 PMCID: PMC9977608 DOI: 10.1002/cbic.202200487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Received: 08/22/2022] [Revised: 09/29/2022] [Indexed: 02/04/2023]
Abstract
Biochemical studies of integral membrane proteins are often hampered by low purification yields and technical limitations such as aggregation causing in vitro manipulations to be challenging. The ability of controlling proteins in live cells bypasses these limitations while broadening the scope of accessible questions owing to the proteins being in their native environment. Here we take advantage of the intein biorthogonality to mammalian systems, site specificity, fast kinetics, and auto-processing nature as an attractive option for modifying surface proteins. Using EGFR as a model, we demonstrate that the split-intein pair AvaN /NpuC can be used to efficiently and specifically modify target membrane proteins with a synthetic adduct for downstream live cell application.
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Affiliation(s)
- Devin M Ray
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Julia R Flood
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA
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13
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Abstract
Proteins are intriguing biomacromolecules for all living systems, not only as essential building blocks of organisms, but also as participants in almost every aspect of cellular activity such as metabolism and gene transcription/expression. Developing chemical biology tools that are capable of labeling/modifying proteins is a powerful method for decoding their detailed structures and functions. However, most current approaches heavily rely on the installation of permanent tags or genetic engineering of unnatural amino acids. There has been slow development in reversible chemical labeling using small organic probes and bioorthogonal transformations to construct site-selectively modified proteins and conditionally restore their activities or structures. This review summarizes recent advances in the field of chemical regulation of proteins with reversible transformations towards distinct motifs, including amino acid residues, amide backbones and native post-translational lysine. Finally, current challenges and future perspectives are discussed.
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Affiliation(s)
- Chuan-Shuo Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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14
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Makarov D, Kielkowski P. Chemical Proteomics Reveals Protein Tyrosination Extends Beyond the Alpha-Tubulins in Human Cells. Chembiochem 2022; 23:e202200414. [PMID: 36218090 PMCID: PMC10099736 DOI: 10.1002/cbic.202200414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/21/2022] [Revised: 10/10/2022] [Indexed: 01/25/2023]
Abstract
Tubulin detyrosination-tyrosination cycle regulates the stability of microtubules. With respect to α-tubulins, the tyrosination level is maintained by a single tubulin-tyrosine ligase (TTL). However, the precise dynamics and tubulin isoforms which undergo (de)tyrosination in neurons are unknown. Here, we exploit the substrate promiscuity of the TTL to introduce an O-propargyl-l-tyrosine to neuroblastoma cells and neurons. Mass spectrometry-based chemical proteomics in neuroblastoma cells using the O-propargyl-l-tyrosine probe revealed previously discussed tyrosination of TUBA4A, MAPRE1, and other non-tubulin proteins. This finding was further corroborated in differentiating neurons. Together we present the method for tubulin tyrosination profiling in living cells. Our results show that detyrosination-tyrosination is not restricted to α-tubulins with coded C-terminal tyrosine and is thus involved in fine-tuning of the tubulin and non-tubulin proteins during neuronal differentiation.
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Affiliation(s)
- Dmytro Makarov
- LMU München, Department of Chemistry, Institute for Chemical Epigenetics - Munich (ICEM), Würmtalstrasse 201, 81375, Munich, Germany
| | - Pavel Kielkowski
- LMU München, Department of Chemistry, Institute for Chemical Epigenetics - Munich (ICEM), Würmtalstrasse 201, 81375, Munich, Germany
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15
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Abstract
Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.
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Affiliation(s)
- Nanna L. Kjærsgaard
- Center for Multifunctional Biomolecular Drug Design Interdisciplinary Nanoscience CenterAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade 1408000Aarhus CDenmark
| | | | - Kurt V. Gothelf
- Center for Multifunctional Biomolecular Drug Design Interdisciplinary Nanoscience CenterAarhus UniversityGustav Wieds Vej 148000Aarhus CDenmark
- Department of ChemistryAarhus UniversityLangelandsgade 1408000Aarhus CDenmark
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16
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Hoppe IJ, Prommegger B, Uhl A, Lohrig U, Huber CG, Brandstetter H. The Fluorescent Enzyme Cascade Detects Low Abundance Protein Modifications Suitable for the Assembly of Functionally Annotated Modificatome Databases. Chembiochem 2022; 23:e202200399. [PMID: 35920326 DOI: 10.1002/cbic.202200399] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/27/2022] [Indexed: 01/07/2023]
Abstract
Pathophysiological functions of proteins critically depend on both their chemical composition, including post-translational modifications, and their three-dimensional structure, commonly referred to as structure-activity relationship. Current analytical methods, like capillary electrophoresis or mass spectrometry, suffer from limitations, such as the detection of unexpected modifications at low abundance and their insensitivity to conformational changes. Building on previous enzyme-based analytical methods, we here introduce a fluorescence-based enzyme cascade (fEC), which can detect diverse chemical and conformational variations in protein samples and assemble them into digital databases. Together with complementary analytical methods an automated fEC analysis established unique modification-function relationships, which can be expanded to a proteome-wide scale, i. e. a functionally annotated modificatome. The fEC offers diverse applications, including hypersensitive biomarker detection in complex samples.
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Affiliation(s)
- Isabel J Hoppe
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Bernhard Prommegger
- Department of Artificial Intelligence and Human Interfaces, University of Salzburg, Jakob Haringer Str. 2, A-5020, Salzburg, Austria
| | - Andreas Uhl
- Department of Artificial Intelligence and Human Interfaces, University of Salzburg, Jakob Haringer Str. 2, A-5020, Salzburg, Austria
| | - Urs Lohrig
- Technical Development Biosimilars, Global Drug Development, Novartis, Sandoz GmbH, Biochemiestr. 10, A-6250, Kundl, Austria
| | - Christian G Huber
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology and Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
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17
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Huppelschoten Y, Elhebieshy AF, Hameed DS, Sapmaz A, Buchardt J, Nielsen TE, Ovaa H, van der Heden van Noort GJ. Total Chemical Synthesis of a Functionalized GFP Nanobody. Chembiochem 2022; 23:e202200304. [PMID: 35920208 PMCID: PMC9804225 DOI: 10.1002/cbic.202200304] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 01/05/2023]
Abstract
Chemical protein synthesis has proven to be a powerful tool to access homogenously modified proteins. The chemical synthesis of nanobodies (Nb) would create possibilities to design tailored Nbs with a range of chemical modifications such as tags, linkers, reporter groups, and subsequently, Nb-drug conjugates. Herein, we describe the total chemical synthesis of a 123 amino-acid Nb against GFP. A native chemical ligation- desulfurization strategy was successfully applied for the synthesis of this GFP Nb, modified with a propargyl (PA) moiety for on-demand functionalization. Biophysical characterization indicated that the synthetic GFP Nb-PA was correctly folded after internal disulfide bond formation. The synthetic Nb-PA was functionalized with a biotin or a sulfo-cyanine5 dye by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), resulting in two distinct probes used for functional in vitro validation in pull-down and confocal microscopy settings.
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Affiliation(s)
- Yara Huppelschoten
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands,Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Angela F. Elhebieshy
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Dharjath S. Hameed
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Aysegul Sapmaz
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
| | - Jens Buchardt
- Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Thomas E. Nielsen
- Global Research Technologies, Novo NordiskNovo Nordisk Park2760MåløvDenmark
| | - Huib Ovaa
- Oncode Institute and Dept. Cell and Chemical BiologyLeiden University Medical CentreEinthovenweg 22333 ZCLeidenThe Netherlands
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18
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Adak AK, Huang KT, Liao CY, Lee YJ, Kuo WH, Huo YR, Li PJ, Chen YJ, Chen BS, Chen YJ, Chu Hwang K, Wayne Chang WS, Lin CC. Investigating a Boronate-Affinity-Guided Acylation Reaction for Labelling Native Antibodies. Chemistry 2022; 28:e202104178. [PMID: 35143090 DOI: 10.1002/chem.202104178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Indexed: 12/12/2022]
Abstract
The excellent molecular recognition capabilities of monoclonal antibodies (mAbs) have opened up exciting opportunities for biotherapeutic discovery. Taking advantage of the full potential of this tool necessitates affinity ligands capable of conjugating directly with small molecules to a defined degree of biorthogonality, especially when modifying natural Abs. Herein, a bioorthogonal boronate-affinity-based Ab ligand featuring a 4-(dimethylamino)pyridine and an S-aryl thioester to label full-length Abs is reported. The photoactivatable linker in the acyl donor facilitated purification of azide-labelled Ab (N3 -Ab) was quantitatively cleaved upon brief exposure to UV light while retaining the original Ab activity. Click reactions enabled the precise addition of biotin, a fluorophore, and a pharmacological agent to the purified N3 -Abs. The resulting immunoconjugate showed selectivity against targeted cells. Bioorthogonal traceless design and reagentless purification allow this strategy to be a powerful tool to engineer native antibodies amenable to therapeutic intervention.
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Affiliation(s)
- Avijit K Adak
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Kuan-Ting Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chien-Yu Liao
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, 350, Taiwan
| | - Yuan-Jung Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wen-Hua Kuo
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yi-Ren Huo
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Pei-Jhen Li
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Bo-Shiun Chen
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kuo Chu Hwang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wun-Shang Wayne Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, 350, Taiwan
| | - Chun-Cheng Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
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19
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Ma B, Chen JL, Cui CY, Yang F, Gong YJ, Su XC. Rigid, Highly Reactive and Stable DOTA-like Tags Containing a Thiol-Specific Phenylsulfonyl Pyridine Moiety for Protein Modification and NMR Analysis*. Chemistry 2021; 27:16145-16152. [PMID: 34595784 DOI: 10.1002/chem.202102495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/09/2021] [Indexed: 11/06/2022]
Abstract
Site specific installation of a paramagnetic ion with magnetic anisotropy in a biomolecule generates valuable structural restraints, such as pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs). These paramagnetic effects can be used to characterize the structures, interactions and dynamics of biological macromolecules and their complexes. Two single-armed DOTA-like tags, BrPSPy-DO3M(S)A-Ln and BrPSPy-6M-DO3M(S)A-Ln, each containing a thiol-specific reacting group, that is, a phenylsulfonyl pyridine moiety, are demonstrated as rigid, reactive and stable paramagnetic tags for protein modification by formation of a reducing resistant thioether bond between the protein and the tag. The two tags present high reactivity with the solvent exposed thiol group in aqueous solution at room temperature. The introduction of Br at the meta-position in pyridine enhances the reactivity of 4-phenylsulfonyl pyridine towards the solvent exposed thiol group in a protein, whereas the ortho-methyl group in pyridine increases the rigidity of the tag in the protein conjugates. The high performance of these two tags has been demonstrated in different cysteine mutants of ubiquitin and GB1. The high reactivity and rigidity of these two tags can be added in the toolbox of paramagnetic tags suitable for the high-resolution NMR measurements of biological macromolecules and their complexes.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
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20
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Nasri Z, Memari S, Wenske S, Clemen R, Martens U, Delcea M, Bekeschus S, Weltmann K, von Woedtke T, Wende K. Singlet-Oxygen-Induced Phospholipase A 2 Inhibition: A Major Role for Interfacial Tryptophan Dioxidation. Chemistry 2021; 27:14702-14710. [PMID: 34375468 PMCID: PMC8596696 DOI: 10.1002/chem.202102306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Indexed: 11/16/2022]
Abstract
Several studies have revealed that various diseases such as cancer have been associated with elevated phospholipase A2 (PLA2 ) activity. Therefore, the regulation of PLA2 catalytic activity is undoubtedly vital. In this study, effective inactivation of PLA2 due to reactive species produced from cold physical plasma as a source to model oxidative stress is reported. We found singlet oxygen to be the most relevant active agent in PLA2 inhibition. A more detailed analysis of the plasma-treated PLA2 identified tryptophan 128 as a hot spot, rich in double oxidation. The significant dioxidation of this interfacial tryptophan resulted in an N-formylkynurenine product via the oxidative opening of the tryptophan indole ring. Molecular dynamics simulation indicated that the efficient interactions between the tryptophan residue and phospholipids are eliminated following tryptophan dioxidation. As interfacial tryptophan residues are predominantly involved in the attaching of membrane enzymes to the bilayers, tryptophan dioxidation and indole ring opening leads to the loss of essential interactions for enzyme binding and, consequently, enzyme inactivation.
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Affiliation(s)
- Zahra Nasri
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Seyedali Memari
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
- Institute of Anatomy and Cell BiologyUniversity Medicine GreifswaldFriedrich-Loeffler-Straße 23cGreifswald17487Germany
| | - Sebastian Wenske
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Ramona Clemen
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Ulrike Martens
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Straße 4Greifswald17489Germany
- Center for Innovation Competence (ZIK) HIKE (Humoral Immune Reactions in Cardiovascular Diseases)University of GreifswaldGreifswaldFleischmannstraße 4217489Germany
| | - Mihaela Delcea
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Straße 4Greifswald17489Germany
- Center for Innovation Competence (ZIK) HIKE (Humoral Immune Reactions in Cardiovascular Diseases)University of GreifswaldGreifswaldFleischmannstraße 4217489Germany
| | - Sander Bekeschus
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Klaus‐Dieter Weltmann
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
| | - Thomas von Woedtke
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
- Institute for Hygiene and Environmental MedicineUniversity Medicine GreifswaldGreifswaldWalther-Rathenau-Straße 49 A17489Germany
| | - Kristian Wende
- Center for Innovation Competence (ZIK) plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix-Hausdorff-Straße 217489GreifswaldGermany
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21
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Brune KD, Liekniņa I, Sutov G, Morris AR, Jovicevic D, Kalniņš G, Kazāks A, Kluga R, Kastaljana S, Zajakina A, Jansons J, Skrastiņa D, Spunde K, Cohen AA, Bjorkman PJ, Morris HR, Suna E, Tārs K. N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone. Chembiochem 2021; 22:3199-3207. [PMID: 34520613 DOI: 10.1002/cbic.202100381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/30/2021] [Revised: 09/13/2021] [Indexed: 01/07/2023]
Abstract
Site-specific protein modifications are vital for biopharmaceutical drug development. Gluconoylation is a non-enzymatic, post-translational modification of N-terminal HisTags. We report high-yield, site-selective in vitro α-aminoacylation of peptides, glycoproteins, antibodies, and virus-like particles (VLPs) with azidogluconolactone at pH 7.5 in 1 h. Conjugates slowly hydrolyse, but diol-masking with borate esters inhibits reversibility. In an example, we multimerise azidogluconoylated SARS-CoV-2 receptor-binding domain (RBD) onto VLPs via click-chemistry, to give a COVID-19 vaccine. Compared to yeast antigen, HEK-derived RBD was immunologically superior, likely due to observed differences in glycosylation. We show the benefits of ordered over randomly oriented multimeric antigen display, by demonstrating single-shot seroconversion and best virus-neutralizing antibodies. Azidogluconoylation is simple, fast and robust chemistry, and should accelerate research and development.
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Affiliation(s)
- Karl D Brune
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Ilva Liekniņa
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Grigorij Sutov
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Lab Group LT, UAB, Vilnius, Lithuania
| | - Alexander R Morris
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom.,Lab Group LT, UAB, Vilnius, Lithuania.,BioPharmaSpec Ltd., Suite 3.1, Lido Medical Centre, St. Saviour, JE2 7LA, UK
| | - Dejana Jovicevic
- Genie Biotech Ltd., Lido Medical Centre, St. Saviour, JE2 7LA, United Kingdom
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Andris Kazāks
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Rihards Kluga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Sabine Kastaljana
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Anna Zajakina
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Dace Skrastiņa
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Karīna Spunde
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Howard R Morris
- BioPharmaSpec Ltd., Suite 3.1, Lido Medical Centre, St. Saviour, JE2 7LA, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Ratsupites 1, 1067, Riga, Latvia.,University of Latvia, Jelgavas 1, 1004, Riga, Latvia
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22
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Ahmed F, Kleffmann T, Husain M. Acetylation, Methylation and Allysine Modification Profile of Viral and Host Proteins during Influenza A Virus Infection. Viruses 2021; 13:1415. [PMID: 34372620 DOI: 10.3390/v13071415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/08/2021] [Accepted: 07/18/2021] [Indexed: 12/18/2022] Open
Abstract
Protein modifications dynamically occur and regulate biological processes in all organisms. Towards understanding the significance of protein modifications in influenza virus infection, we performed a global mass spectrometry screen followed by bioinformatics analyses of acetylation, methylation and allysine modification in human lung epithelial cells in response to influenza A virus infection. We discovered 8 out of 10 major viral proteins and 245 out of 2280 host proteins detected to be differentially modified by three modifications in infected cells. Some of the identified proteins were modified on multiple amino acids residues and by more than one modification; the latter occurred either on different or same residues. Most of the modified residues in viral proteins were conserved across >40 subtypes of influenza A virus, and influenza B or C viruses and located on the protein surface. Importantly, many of those residues have already been determined to be critical for the influenza A virus. Similarly, many modified residues in host proteins were conserved across influenza A virus hosts like humans, birds, and pigs. Finally, host proteins undergoing the three modifications clustered in common functional networks of metabolic, cytoskeletal, and RNA processes, all of which are known to be exploited by the influenza A virus.
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23
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Suto N, Kamoshita S, Hosoya S, Sakurai K. Exploration of the Reactivity of Multivalent Electrophiles for Affinity Labeling: Sulfonyl Fluoride as a Highly Efficient and Selective Label. Angew Chem Int Ed Engl 2021; 60:17080-17087. [PMID: 34060195 DOI: 10.1002/anie.202104347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/29/2021] [Revised: 05/16/2021] [Indexed: 12/23/2022]
Abstract
Here we explored the reactivity of a set of multivalent electrophiles cofunctionalized with a carbohydrate ligand on gold nanoparticles to achieve efficient affinity labeling for target protein analysis. Evaluation of the reactivity and selectivity of the electrophiles against three different cognate binding proteins identified arylsulfonyl fluoride as the most efficient protein-reactive group in this study. We demonstrated that multivalent arylsulfonyl fluoride probe 4 at 50 nm concentration achieved selective affinity labeling and enrichment of a model protein PNA in cell lysate, which was more effective than photoaffinity probe 1 with arylazide group. Labeling site analysis by LC-MS/MS revealed that the nanoparticle-immobilized arylsulfonyl fluoride group can target multiple amino acid residues around the ligand binding site of the target proteins. Our study highlights the utility of arylsulfonyl fluoride as a highly effective multivalent affinity label suitable for covalently capturing unknown target proteins.
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Affiliation(s)
- Nanako Suto
- Department of Bioengineering and Life Science, Tokyo University of Agriculture and Technology, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Shione Kamoshita
- Department of Bioengineering and Life Science, Tokyo University of Agriculture and Technology, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Shoichi Hosoya
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kaori Sakurai
- Department of Bioengineering and Life Science, Tokyo University of Agriculture and Technology, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
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24
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Kurhade SE, Weiner JD, Gao FP, Farrell MP. Functionalized High Mannose-Specific Lectins for the Discovery of Type I Mannosidase Inhibitors. Angew Chem Int Ed Engl 2021; 60:12313-12318. [PMID: 33728787 PMCID: PMC8131250 DOI: 10.1002/anie.202101249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Received: 01/26/2021] [Revised: 02/27/2021] [Indexed: 01/01/2023]
Abstract
An engineered cyanovirin-N homologue that exhibits specificity for high mannose N-glycans has been constructed to aid type I α 1,2-mannosidase inhibitor discovery and development. Engineering the lectins C-terminus permitted facile functionalization with fluorophores via a sortase and click strategy. The resulting lectin constructs exhibit specificity for cells presenting high mannose N-glycans. Importantly, these lectin constructs can also be applied to specifically assess changes in cell surface glycosylation induced by type I mannosidase inhibitors. Testing the utility of these lectin constructs led to the discovery of type I mannosidase inhibitors with nanomolar potency. Cumulatively, these findings reveal the specificity and utility of the functionalized cyanovirin-N homologue constructs, and highlight their potential in analytical contexts that require high mannose-specific lectins.
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Affiliation(s)
- Suresh E Kurhade
- Department of Medicinal Chemistry, The University of Kansas, 2034 Becker Drive, Lawrence, KS, 66047, USA
| | - Jack D Weiner
- Department of Medicinal Chemistry, The University of Kansas, 2034 Becker Drive, Lawrence, KS, 66047, USA
| | - Fei Philip Gao
- Protein Production Group, The University of Kansas, 2034 Becker Drive, Lawrence, KS, 66047, USA
| | - Mark P Farrell
- Department of Medicinal Chemistry, The University of Kansas, 2034 Becker Drive, Lawrence, KS, 66047, USA
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25
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Baccile JA, Voorhees PJ, Chillo AJ, Berry M, Morgenstern R, Schwertfeger TJ, Rossi FM, Nelson CDS. Site-Specific Small Molecule Labeling of an Internal Loop in JC Polyomavirus Pentamers Using the π-Clamp-Mediated Cysteine Conjugation. Chembiochem 2021; 22:3037-3041. [PMID: 34018291 DOI: 10.1002/cbic.202100188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/19/2021] [Indexed: 12/21/2022]
Abstract
The major capsid protein VP1 of JC Polyomavirus assembles into pentamers that serve as a model for studying viral entry of this potentially severe human pathogen. Previously, labeling of viral proteins utilized large fusion proteins or non-specific amine- or cysteine-functionalization with fluorescent dyes. Imaging of these sterically hindered fusion proteins or heterogeneously labeled virions limits reproducibility and could prevent the detection of subtle trafficking phenomena. Here we advance the π-clamp-mediated cysteine conjugation for site-selective fluorescent labeling of VP1-pentamers. We demonstrate a one-step synthesis of a probe consisting of a bio-orthogonal click chemistry handle bridged to a perfluoro-biphenyl π-clamp reactive electrophile by a polyethylene glycol linker. We expand the scope of the π-clamp conjugation by demonstrating selective labeling of an internal, surface exposed loop in VP1. Thus, the π-clamp conjugation offers a general method to selectively bioconjugate tags-of-interest to viral proteins without impeding their ability to bind and enter cells.
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Affiliation(s)
- Joshua A Baccile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Peter J Voorhees
- Department of Biological Sciences, SUNY Cortland, Cortland, NY, 13045, USA
| | - Anthony J Chillo
- Department of Biological Sciences, SUNY Cortland, Cortland, NY, 13045, USA
| | - Madeline Berry
- Department of Chemistry, SUNY Cortland, Cortland, NY, 13045, USA
| | | | | | - Francis M Rossi
- Department of Chemistry, SUNY Cortland, Cortland, NY, 13045, USA
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26
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Meng LH, Chen YX. Lipid accumulation and protein modifications of Bruch's membrane in age-related macular degeneration. Int J Ophthalmol 2021; 14:766-773. [PMID: 34012894 DOI: 10.18240/ijo.2021.05.19] [Citation(s) in RCA: 2] [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: 04/23/2020] [Accepted: 02/26/2021] [Indexed: 12/26/2022] Open
Abstract
Age-related macular degeneration (AMD) is a progressive retinal disease, which is the leading cause of blindness in western countries. There is an urgency to establish new therapeutic strategies that could prevent or delay the progression of AMD more efficiently. Until now, the pathogenesis of AMD has remained unclear, limiting the development of the novel therapy. Bruch's membrane (BM) goes through remarkable changes in AMD, playing a significant role during the disease course. The main aim of this review is to present the crucial processes that occur at the level of BM, with special consideration of the lipid accumulation and protein modifications. Besides, some therapies targeted at these molecules and the construction of BM in tissue engineering of retinal pigment epithelium (RPE) cells transplantation were listed. Hopefully, this review may provide a reference for researchers engaged in pathogenesis or management on AMD.
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Affiliation(s)
- Li-Hui Meng
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - You-Xin Chen
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China.,Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
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27
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Rehm FBH, Tyler TJ, Xie J, Yap K, Durek T, Craik DJ. Asparaginyl Ligases: New Enzymes for the Protein Engineer's Toolbox. Chembiochem 2021; 22:2079-2086. [PMID: 33687132 DOI: 10.1002/cbic.202100071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/08/2021] [Indexed: 01/11/2023]
Abstract
Enzyme-catalysed site-specific protein modifications enable the precision manufacture of conjugates for the study of protein function and/or for therapeutic or diagnostic applications. Asparaginyl ligases are a class of highly efficient transpeptidases with the capacity to modify proteins bearing only a tripeptide recognition motif. Herein, we review the types of protein modification that are accessible using these enzymes, including N- and C-terminal protein labelling, head-to-tail cyclisation, and protein-protein conjugation. We describe the progress that has been made to engineer highly efficient ligases as well as efforts to chemically manipulate the enzyme reaction to favour product formation. These enzymes are powerful additions to the protein engineer's toolbox.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jing Xie
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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28
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Keenan EK, Zachman DK, Hirschey MD. Discovering the landscape of protein modifications. Mol Cell 2021; 81:1868-1878. [PMID: 33798408 DOI: 10.1016/j.molcel.2021.03.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/21/2021] [Accepted: 03/10/2021] [Indexed: 02/08/2023]
Abstract
Protein modifications modulate nearly every aspect of cell biology in organisms, ranging from Archaea to Eukaryotes. The earliest evidence of covalent protein modifications was found in the early 20th century by studying the amino acid composition of proteins by chemical hydrolysis. These discoveries challenged what defined a canonical amino acid. The advent and rapid adoption of mass-spectrometry-based proteomics in the latter part of the 20th century enabled a veritable explosion in the number of known protein modifications, with more than 500 discrete modifications counted today. Now, new computational tools in data science, machine learning, and artificial intelligence are poised to allow researchers to make significant progress in discovering new protein modifications and determining their function. In this review, we take an opportunity to revisit the historical discovery of key post-translational modifications, quantify the current landscape of covalent protein adducts, and assess the role that new computational tools will play in the future of this field.
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Affiliation(s)
- E Keith Keenan
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Derek K Zachman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Division of Endocrinology, Metabolism, & Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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29
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Spöttel J, Brockelt J, Badekow S, Rohn S. Immunological Analysis of Isothiocyanate-Modified α-Lactalbumin Using High-Performance Thin Layer Chromatography. Molecules 2021; 26:molecules26071842. [PMID: 33805932 PMCID: PMC8036266 DOI: 10.3390/molecules26071842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Undirected modifications between food proteins and secondary plant metabolites can occur during food processing. The results of covalent interactions can alter the functional and biological properties of the proteins. The present work studied the extent of which covalent conjugation of the bioactive metabolite benzyl isothiocyanate (BITC; a glucosinolate breakdown product) to the whey protein α-lactalbumin affects the protein’s allergenicity. Additional to the immunological analysis of native untreated and BITC-modified α-lactalbumin, the analysis of antigenic properties of proteolytically digested protein derivatives was also performed by high performance thin layer chromatography and immunostaining. As a result of the chemical modifications, structural changes in the protein molecule affected the allergenic properties. In this process, epitopes are destroyed or inactivated, but at the same time, buried epitopes can be exposed or newly formed, so that the net effect was an increase in allergenicity, in this case. Results from the tryptic hydrolysis suggest that BITC conjugation sterically hindered the cleavage sites for the enzyme, resulting in reduced digestibility and allergenicity. Residual antigenicity can be still present as short peptide fragments that provide epitopes. The desire to make food safer for allergy sufferers and to protect sensitized individuals from an allergenic reaction makes it clear that the detection of food antigens is mandatory; especially by considering protein interactions.
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Affiliation(s)
- Jenny Spöttel
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; (J.S.); (J.B.); (S.B.)
| | - Johannes Brockelt
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; (J.S.); (J.B.); (S.B.)
| | - Svenja Badekow
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; (J.S.); (J.B.); (S.B.)
| | - Sascha Rohn
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; (J.S.); (J.B.); (S.B.)
- Department of Food Chemistry and Analysis, Institute of Food Technology and Food Chemistry, Technische Universität Berlin, TIB 4/3-1, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
- Correspondence: ; Tel.: +49-30-314-72583
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30
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Nwajiobi O, Mahesh S, Streety X, Raj M. Selective Triazenation Reaction (STaR) of Secondary Amines for Tagging Monomethyl Lysine Post-Translational Modifications. Angew Chem Int Ed Engl 2021; 60:7344-7352. [PMID: 33354813 DOI: 10.1002/anie.202013997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/18/2020] [Revised: 11/29/2020] [Indexed: 11/09/2022]
Abstract
Lysine monomethylation (Kme) is an impactful post-translational modification (PTM) responsible for regulating biological processes and implicated in diseases, thus there is great interest in identifying these methylation marks globally. However, the progress in this area has been challenging because the addition of a small methyl group on lysine leads to negligible change in the bulk, charge, and hydrophobicity. Herein, we report an empowering chemical technology selective triazenation reaction, which we term "STaR", of secondary amines using arene diazonium salts to achieve highly selective, rapid, and robust tagging of Kme peptides from a complex mixture under biocompatible conditions. Although the resulting triazene-linkage with Kme is stable, we highlight the efficient decoupling of the triazene-conjugate to afford unmodified starting components under mild conditions when desired. Our work establishes a unique chemoselective, traceless bioconjugation strategy for the selective enrichment of Kme PTMs.
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Affiliation(s)
- Ogonna Nwajiobi
- Present address: Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Sriram Mahesh
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA
| | - Xavier Streety
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA
| | - Monika Raj
- Present address: Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
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31
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Mannerstedt K, Mishra NK, Engholm E, Lundh M, Madsen CS, Pedersen PJ, Le-Huu P, Pedersen SL, Buch-Månson N, Borgström B, Brimert T, Fink LN, Fosgerau K, Vrang N, Jensen KJ. An Aldehyde Responsive, Cleavable Linker for Glucose Responsive Insulins. Chemistry 2021; 27:3166-3176. [PMID: 33169429 DOI: 10.1002/chem.202004878] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/08/2020] [Indexed: 12/30/2022]
Abstract
A glucose responsive insulin (GRI) that responds to changes in blood glucose concentrations has remained an elusive goal. Here we describe the development of glucose cleavable linkers based on hydrazone and thiazolidine structures. We developed linkers with low levels of spontaneous hydrolysis but increased level of hydrolysis with rising concentrations of glucose, which demonstrated their glucose responsiveness in vitro. Lipidated hydrazones and thiazolidines were conjugated to the LysB29 side-chain of HI by pH-controlled acylations providing GRIs with glucose responsiveness confirmed in vitro for thiazolidines. Clamp studies showed increased glucose infusion at hyperglycemic conditions for one GRI indicative of a true glucose response. The glucose responsive cleavable linker in these GRIs allow changes in glucose levels to drive the release of active insulin from a circulating depot. We have demonstrated an unprecedented, chemically responsive linker concept for biopharmaceuticals.
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Affiliation(s)
| | - Narendra Kumar Mishra
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark.,Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Ebbe Engholm
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark.,Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Morten Lundh
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark
| | | | | | - Priska Le-Huu
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark
| | | | | | - Björn Borgström
- Red Glead Discovery AB, Scheelevägen 17, 22363, Lund, Sweden
| | - Thomas Brimert
- Red Glead Discovery AB, Scheelevägen 17, 22363, Lund, Sweden
| | - Lisbeth N Fink
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark
| | - Keld Fosgerau
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark
| | - Niels Vrang
- Gubra ApS, Hørsholm Kongevej, 11B, 2970, Hørsholm, Denmark
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
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32
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Hadar D, Gelkop S, Vaserman L, Amiram M. Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria. Chembiochem 2021; 22:1379-1384. [PMID: 33350556 DOI: 10.1002/cbic.202000663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/22/2020] [Indexed: 11/09/2022]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment - typically at a single site or at a few sites per protein - of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l-phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production - using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain - of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.
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Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Sigal Gelkop
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
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33
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van Lier RCW, de Bruijn AD, Roelfes G. A Water-Soluble Iridium Photocatalyst for Chemical Modification of Dehydroalanines in Peptides and Proteins. Chemistry 2020; 27:1430-1437. [PMID: 32896943 PMCID: PMC7898865 DOI: 10.1002/chem.202002599] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 05/27/2020] [Revised: 09/04/2020] [Indexed: 12/27/2022]
Abstract
Dehydroalanine (Dha) residues are attractive noncanonical amino acids that occur naturally in ribosomally synthesised and post-translationally modified peptides (RiPPs). Dha residues are attractive targets for selective late-stage modification of these complex biomolecules. In this work, we show the selective photocatalytic modification of dehydroalanine residues in the antimicrobial peptide nisin and in the proteins small ubiquitin-like modifier (SUMO) and superfolder green fluorescent protein (sfGFP). For this purpose, a new water-soluble iridium(III) photoredox catalyst was used. The design and synthesis of this new photocatalyst, [Ir(dF(CF3 )ppy)2 (dNMe3 bpy)]Cl3 , is presented. In contrast to commonly used iridium photocatalysts, this complex is highly water soluble and allows peptides and proteins to be modified in water and aqueous solvents under physiologically relevant conditions, with short reaction times and with low reagent and catalyst loadings. This work suggests that photoredox catalysis using this newly designed catalyst is a promising strategy to modify dehydroalanine-containing natural products and thus could have great potential for novel bioconjugation strategies.
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Affiliation(s)
- Roos C W van Lier
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - A Dowine de Bruijn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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34
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Zhao Q, Guo G, Zhu W, Zhu L, Da Y, Han Y, Xu H, Wu S, Cheng Y, Zhou Y, Cai X, Jiang X. Suzuki Cross-Coupling Reaction with Genetically Encoded Fluorosulfates for Fluorogenic Protein Labeling. Chemistry 2020; 26:15938-15943. [PMID: 32776653 DOI: 10.1002/chem.202002037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/24/2020] [Indexed: 11/09/2022]
Abstract
A palladium-catalyzed cross-coupling reaction with aryl halide functionalities has recently emerged as a valuable tool for protein modification. Herein, a new fluorogenic modification methodology for proteins, with genetically encoded fluorosulfate-l-tyrosine, which exhibits high efficiency and biocompatibility in bacterial cells as well as in aqueous medium, is described. Furthermore, the cross-coupling of 4-cyanophenylboronic acid on green fluorescent protein was shown to possess a unique fluorogenic property, which could open up the possibility of a responsive "off/on" switch with great potential to enable spectroscopic imaging of proteins with minimal background noise. Taken together, a convenient and efficient catalytic system has been developed that may provide broad utilities in protein visualization and live-cell imaging.
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Affiliation(s)
- Qian Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Guoying Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Weiwei Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Liping Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P.R. China
| | - Yifan Da
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Ying Han
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Hongjiao Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Shuohan Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yaping Cheng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yani Zhou
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, P.R. China
| | - Xiaoqing Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Xianxing Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
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35
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Abstract
By providing long-term protection against infectious diseases, vaccinations have significantly reduced death and morbidity worldwide. In the 21st century, (bio)technological advances have paved the way for developing prophylactic vaccines that are safer and more effective as well as enabling the use of vaccines as therapeutics to treat human diseases. Here, we provide a focused review of the utility of genetic code expansion as an emerging tool for the development of vaccines. Specifically, we discuss how the incorporation of immunogenic noncanonical amino acids can aid in eliciting immune responses against adverse self-proteins and highlight the potential of an expanded genetic code for the construction of replication-incompetent viruses. We close the review by discussing the future prospects and remaining challenges for the application of these approaches in the development of both prophylactic and therapeutic vaccines in the near future.
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Affiliation(s)
- Jelle A. Fok
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474 AGGroningen (TheNetherlands
| | - Clemens Mayer
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49474 AGGroningen (TheNetherlands
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36
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Wölk M, Schröter T, Hoffmann R, Milkovska-Stamenova S. Profiling of Low-Molecular-Weight Carbonyls and Protein Modifications in Flavored Milk. Antioxidants (Basel) 2020; 9:antiox9111169. [PMID: 33238606 PMCID: PMC7700654 DOI: 10.3390/antiox9111169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 10/12/2020] [Accepted: 11/14/2020] [Indexed: 12/05/2022] Open
Abstract
Thermal treatments of dairy products favor oxidations, Maillard reactions, and the formation of sugar or lipid oxidation products. Additives including flavorings might enhance these reactions or even induce further reactions. Here we aimed to characterize protein modifications in four flavored milk drinks using samples along the production chain—raw milk, pasteurization, mixing with flavorings, heat treatment, and the commercial product. Therefore, milk samples were analyzed using a bottom up proteomics approach and a combination of data-independent (MSE) and data-dependent acquisition methods (DDA). Twenty-one small carbonylated lipids were identified by shotgun lipidomics triggering 13 protein modifications. Additionally, two Amadori products, 12 advanced glycation end products (AGEs), and 12 oxidation-related modifications were targeted at the protein level. The most common modifications were lactosylation, formylation, and carboxymethylation. The numbers and distribution of modification sites present in raw milk remained stable after pasteurization and mixing with flavorings, while the final heat treatment significantly increased lactosylation and hexosylation in qualitative and quantitative terms. The processing steps did not significantly affect the numbers of AGE-modified, oxidized/carbonylated, and lipid-carbonylated sites in proteins.
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Affiliation(s)
- Michele Wölk
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | | | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
| | - Sanja Milkovska-Stamenova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04103 Leipzig, Germany
- Correspondence:
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Abstract
Oral squamous cell carcinoma (OSCC) is the most common head and neck cancer characterized by aggressive local invasion and metastasis. The pathogenesis of OSCC is mainly due to the accumulation of genetic alterations in epithelial cells, but the underlying mechanism for its development remains unclear. Here, we found that the expression level of regulator of G protein signaling 12 (RGS12) was significantly reduced in human OSCC. To understand the role and mechanism of RGS12 in OSCC, we generated a novel RGS12 global knockout (CMVCre/+; RGS12fl/fl) mouse model by crossing RGS12fl/fl mice with CMV-Cre transgenic mice and then further induced the mice to develop OSCC by using 4-nitroquinoline 1-oxide (4NQO). Deletion of RGS12 exhibited aggressive OSCC in the tongue compared with the control RGS12fl/fl mice. Knockdown of RGS12 in OSCC cells significantly increased cell proliferation and migration. Mechanistically, we found that RGS12 associated with phosphatase and tension homolog (PTEN) via the PDZ domain to upregulate the phosphorylation and SUMOylation of PTEN and then correspondingly inactivated the AKT/mTOR signaling pathway. To test the potential therapeutic effect of RGS12 on OSCC, we overexpressed RGS12 in OSCC cells and found a significant inhibition of cancer cell proliferation and migration. Moreover, subcutaneous inoculation of RGS12-overexpressed OSCC cells in NOD scid mice showed a significant reduction in tumor formation. Our findings reveal that RGS12 is an essential tumor suppressor and highlights RGS12 as a potential therapeutic target and prognostic biomarker of OSCC.
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Affiliation(s)
- C Fu
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Orthodontics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Orthodontics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - G Yuan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S T Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - D Zhang
- Department of Orthodontics, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Orthodontics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - S Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center for Innovation and Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.,The Penn Center for Musculoskeletal Disorders, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Götting I, Jendrossek V, Matschke J. A New Twist in Protein Kinase B/Akt Signaling: Role of Altered Cancer Cell Metabolism in Akt-Mediated Therapy Resistance. Int J Mol Sci 2020; 21:ijms21228563. [PMID: 33202866 PMCID: PMC7697684 DOI: 10.3390/ijms21228563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer resistance to chemotherapy, radiotherapy and molecular-targeted agents is a major obstacle to successful cancer therapy. Herein, aberrant activation of the phosphatidyl-inositol-3-kinase (PI3K)/protein kinase B (Akt) pathway is one of the most frequently deregulated pathways in cancer cells and has been associated with multiple aspects of therapy resistance. These include, for example, survival under stress conditions, apoptosis resistance, activation of the cellular response to DNA damage and repair of radiation-induced or chemotherapy-induced DNA damage, particularly DNA double strand breaks (DSB). One further important, yet not much investigated aspect of Akt-dependent signaling is the regulation of cell metabolism. In fact, many Akt target proteins are part of or involved in the regulation of metabolic pathways. Furthermore, recent studies revealed the importance of certain metabolites for protection against therapy-induced cell stress and the repair of therapy-induced DNA damage. Thus far, the likely interaction between deregulated activation of Akt, altered cancer metabolism and therapy resistance is not yet well understood. The present review describes the documented interactions between Akt, its target proteins and cancer cell metabolism, focusing on antioxidant defense and DSB repair. Furthermore, the review highlights potential connections between deregulated Akt, cancer cell metabolism and therapy resistance of cancer cells through altered DSB repair and discusses potential resulting therapeutic implications.
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39
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Wójcik P, Gęgotek A, Wroński A, Jastrząb A, Żebrowska A, Skrzydlewska E. Effect of redox imbalance on protein modifications in lymphocytes of psoriatic patients. J Biochem 2020; 167:323-331. [PMID: 31710683 DOI: 10.1093/jb/mvz096] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022] Open
Abstract
Lymphocytes are one of the most important cells involved in the pathophysiology of psoriasis; therefore, the aim of this study was to assess the redox imbalance and protein modifications in the lymphocytes of patients with psoriasis vulgaris (PsV) or psoriatic arthritis (PsA). The results show a stronger shift in redox status to pro-oxidative conditions (observed as an increased reactive oxygen species level, a decrease in catalase activity and lower levels of glutathione peroxidase and vitamin E compared with healthy controls) in the lymphocytes of PsA than PsV patients. It is also favoured by the enhanced level of activators of the Nrf2 transcription factor in lymphocytes of PsV compared with decreased of these proteins level in PsA. Moreover, the differential modifications of proteins by lipid peroxidation products 4-oxononenal (mainly binding proteins) and malondialdehyde (mainly catalytic proteins with redox activity), promoted a pro-apoptotic pathway in lymphocytes of PsV, which was manifested by enhanced expression of pro-apoptotic caspases, particularly caspase 3. Taken together, differences in Nrf2 pathway activation may be responsible for the differential level of redox imbalance in lymphocytes of patients with PsV and PsA. This finding may enable identification of a targeted therapy to modify the metabolic pathways disturbed in psoriasis.
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Affiliation(s)
- Piotr Wójcik
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2D, 15-222 Białystok, Poland
| | - Agnieszka Gęgotek
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2D, 15-222 Białystok, Poland
| | - Adam Wroński
- Dermatological Specialized Center "DERMAL" NZOZ in Białystok, Nowy Świat 17/5, 15-453 Białystok, Poland
| | - Anna Jastrząb
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2D, 15-222 Białystok, Poland
| | - Agnieszka Żebrowska
- Regional Center for Blood Donation and Blood Treatment, M. Skłodowskiej - Curie 23, 15-950 Białystok, Poland
| | - Elżbieta Skrzydlewska
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2D, 15-222 Białystok, Poland
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40
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Morgan GL, Li B. In Vitro Reconstitution Reveals a Central Role for the N-Oxygenase PvfB in (Dihydro)pyrazine-N-oxide and Valdiazen Biosynthesis. Angew Chem Int Ed Engl 2020; 59:21387-21391. [PMID: 32662921 DOI: 10.1002/anie.202005554] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 04/16/2020] [Revised: 06/18/2020] [Indexed: 12/22/2022]
Abstract
The Pseudomonas virulence factor (pvf) operon is essential for the biosynthesis of two very different natural product scaffolds: the (dihydro)pyrazine-N-oxides and the diazeniumdiolate, valdiazen. PvfB is a member of the non-heme diiron N-oxygenase enzyme family that commonly convert anilines to their nitroaromatic counterparts. In contrast, we show that PvfB catalyzes N-oxygenation of the α-amine of valine, first to the hydroxylamine and then the nitroso, while linked to the carrier protein of PvfC. PvfB modification of PvfC-tethered valine was observed directly by protein NMR spectroscopy, establishing the intermediacy of the hydroxylamine. This work reveals a central role for PvfB in the biosynthesis of (dihydro)pyrazine-N-oxides and valdiazen.
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Affiliation(s)
- Gina L Morgan
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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41
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Piscopo M, Notariale R, Tortora F, Lettieri G, Palumbo G, Manna C. Novel Insights into Mercury Effects on Hemoglobin and Membrane Proteins in Human Erythrocytes. Molecules 2020; 25:molecules25143278. [PMID: 32707650 PMCID: PMC7397049 DOI: 10.3390/molecules25143278] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 12/20/2022] Open
Abstract
Mercury (Hg) is a global environmental pollutant that affects human and ecosystem health. With the aim of exploring the Hg-induced protein modifications, intact human erythrocytes were exposed to HgCl2 (1-60 µM) and cytosolic and membrane proteins were analyzed by SDS-PAGE and AU-PAGE. A spectrofluorimetric assay for quantification of Reactive Oxygen Species (ROS) generation was also performed. Hg2+ exposure induces alterations in the electrophoretic profile of cytosolic proteins with a significant decrease in the intensity of the hemoglobin monomer, associated with the appearance of a 64 kDa band, identified as a mercurized tetrameric form. This protein decreases with increasing HgCl2 concentrations and Hg-induced ROS formation. Moreover, it appears resistant to urea denaturation and it is only partially dissociated by exposure to dithiothreitol, likely due to additional protein-Hg interactions involved in aggregate formation. In addition, specific membrane proteins, including band 3 and cytoskeletal proteins 4.1 and 4.2, are affected by Hg2+-treatment. The findings reported provide new insights into the Hg-induced possible detrimental effects on erythrocyte physiology, mainly related to alterations in the oxygen binding capacity of hemoglobin as well as decreases in band 3-mediated anion exchange. Finally, modifications of cytoskeletal proteins 4.1 and 4.2 could contribute to the previously reported alteration in cell morphology.
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Affiliation(s)
- Marina Piscopo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy;
- Correspondence: (M.P.); (C.M.)
| | - Rosaria Notariale
- Department of Precision Medicine, School of Medicine, University of Campania “Luigi Vanvitelli”, via Luigi de Crecchio, 80138 Naples, Italy; (R.N.); (F.T.)
| | - Fabiana Tortora
- Department of Precision Medicine, School of Medicine, University of Campania “Luigi Vanvitelli”, via Luigi de Crecchio, 80138 Naples, Italy; (R.N.); (F.T.)
| | - Gennaro Lettieri
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy;
| | - Giancarlo Palumbo
- Department of Economics, Management, Institutions, University of Naples Federico II, via Cupa Nuova Cinthia, 80126 Naples, Italy;
| | - Caterina Manna
- Department of Precision Medicine, School of Medicine, University of Campania “Luigi Vanvitelli”, via Luigi de Crecchio, 80138 Naples, Italy; (R.N.); (F.T.)
- Correspondence: (M.P.); (C.M.)
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42
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Abstract
Spider web proteins are unique materials created by nature that, considering the combination of their properties, do not have analogues among natural or human-created materials. Obtaining significant amounts of these proteins from natural sources is not feasible. Biotechnological manufacturing in heterological systems is complicated by the very high molecular weight of spidroins and their specific amino acid composition. Obtaining recombinant analogues of spidroins in heterological systems, mainly in bacteria and yeast, has become a compromise solution. Because they can self-assemble, these proteins can form various materials, such as fibers, films, 3D-foams, hydrogels, tubes, and microcapsules. The effectiveness of spidroin hydrogels in deep wound healing, as 3D scaffolds for bone tissue regeneration and as oriented fibers for axon growth and nerve tissue regeneration, was demonstrated in animal models. The possibility to use spidroin micro- and nanoparticles for drug delivery was demonstrated, including the use of modified spidroins for virus-free DNA delivery into animal cell nuclei. In the past few years, significant interest has arisen concerning the use of these materials as biocompatible and biodegradable soft optics to construct photonic crystal super lenses and fiber optics and as soft electronics to use in triboelectric nanogenerators. This review summarizes the latest achievements in the field of spidroin production, the creation of materials based on them, the study of these materials as a scaffold for the growth, proliferation, and differentiation of various types of cells, and the prospects for using these materials for medical applications (e.g., tissue engineering, drug delivery, coating medical devices), soft optics, and electronics. Accumulated data suggest the use of recombinant spidroins in medical practice in the near future.
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Affiliation(s)
- Vladimir G Debabov
- State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute" (NRC "Kurchatov Institute"-GOSNIIGENETIKA), Moscow 117545, Russia
| | - Vladimir G Bogush
- State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute" (NRC "Kurchatov Institute"-GOSNIIGENETIKA), Moscow 117545, Russia
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43
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Roller RF, Malik A, Carillo MA, Garg M, Rella A, Raulf MK, Lepenies B, Seeberger PH, Varón Silva D. Semisynthesis of Functional Glycosylphosphatidylinositol-Anchored Proteins. Angew Chem Int Ed Engl 2020; 59:12035-12040. [PMID: 32307806 PMCID: PMC7383966 DOI: 10.1002/anie.202002479] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 02/17/2020] [Revised: 03/30/2020] [Indexed: 12/23/2022]
Abstract
Glypiation is a common posttranslational modification of eukaryotic proteins involving the attachment of a glycosylphosphatidylinositol (GPI) glycolipid. GPIs contain a conserved phosphoglycan that is modified in a cell‐ and tissue‐specific manner. GPI complexity suggests roles in biological processes and effects on the attached protein, but the difficulties to get homogeneous material have hindered studies. We disclose a one‐pot intein‐mediated ligation (OPL) to obtain GPI‐anchored proteins. The strategy enables the glypiation of folded and denatured proteins with a natural linkage to the glycolipid. Using the strategy, glypiated eGFP, Thy1, and the Plasmodium berghei protein MSP119 were prepared. Glypiation did not alter the structure of eGFP and MSP119 proteins in solution, but it induced a strong pro‐inflammatory response in vitro. The strategy provides access to glypiated proteins to elucidate the activity of this modification and for use as vaccine candidates against parasitic infections.
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Affiliation(s)
- Renée F Roller
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Ankita Malik
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Maria A Carillo
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Monika Garg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Antonella Rella
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Marie-Kristin Raulf
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany.,Institute for Parasitology, Center for infection Medicine, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Bernd Lepenies
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniel Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
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44
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Murar CE, Ninomiya M, Shimura S, Karakus U, Boyman O, Bode JW. Chemical Synthesis of Interleukin-2 and Disulfide Stabilizing Analogues. Angew Chem Int Ed Engl 2020; 59:8425-8429. [PMID: 32032465 DOI: 10.1002/anie.201916053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/31/2020] [Indexed: 12/17/2022]
Abstract
Chemical protein synthesis allows the construction of well-defined structural variations and facilitates the development of deeper understanding of protein structure-function relationships and new protein engineering strategies. Herein, we report the chemical synthesis of interleukin-2 (IL-2) variants on a multimilligram scale and the formation of non-natural disulfide mimetics that improve stability against reduction. The synthesis was accomplished by convergent KAHA ligations; the acidic conditions of KAHA ligation proved to be valuable for the solubilization of the hydrophobic segments of IL-2. The bioactivity of the synthetic IL-2 and its analogues were shown to be equipotent to recombinant IL-2 and exhibit improved stability against reducing agents.
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Affiliation(s)
- Claudia E Murar
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Mamiko Ninomiya
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Satomi Shimura
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Ufuk Karakus
- Department of Immunology, University Hospital Zurich, Gloriastrasse 23, 8091, Zürich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Gloriastrasse 23, 8091, Zürich, Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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45
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Haj‐Yahya M, Gopinath P, Rajasekhar K, Mirbaha H, Diamond MI, Lashuel HA. Site-Specific Hyperphosphorylation Inhibits, Rather than Promotes, Tau Fibrillization, Seeding Capacity, and Its Microtubule Binding. Angew Chem Int Ed Engl 2020; 59:4059-4067. [PMID: 31863676 PMCID: PMC7065254 DOI: 10.1002/anie.201913001] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/11/2019] [Indexed: 12/14/2022]
Abstract
The consistent observation of phosphorylated tau in the pathology of Alzheimer's disease has contributed to the emergence of a model where hyperphosphorylation triggers both tau disassociation from microtubules and its subsequent aggregation. Herein, we applied a total chemical synthetic approach to site-specifically phosphorylate the microtubule binding repeat domain of tau (K18) at single (pS356) or multiple (pS356/pS262 and pS356/pS262/pS258) residues. We show that hyperphosphorylation of K18 inhibits 1) its aggregation in vitro, 2) its seeding activity in cells, 3) its binding to microtubules, and 4) its ability to promote microtubule polymerization. The inhibition increased with increasing the number of phosphorylated sites, with phosphorylation at S262 having the strongest effect. Our results argue against the hyperphosphorylation hypothesis and underscore the importance of revisiting the role of site-specific hyperphosphorylation in regulating tau functions in health and disease.
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Affiliation(s)
- Mahmood Haj‐Yahya
- Laboratory of Molecular and Chemical Biology of NeurodegenerationBrain Mind InstituteFaculty of Life SciencesEcole Polytechnique Fédérale de Lausanne1015LausanneSwitzerland
| | - Pushparathinam Gopinath
- Laboratory of Molecular and Chemical Biology of NeurodegenerationBrain Mind InstituteFaculty of Life SciencesEcole Polytechnique Fédérale de Lausanne1015LausanneSwitzerland
- Current Address: Department of ChemistrySRM Institute of Science and TechnologyChennaiTamilNaduIndia
| | - Kolla Rajasekhar
- Laboratory of Molecular and Chemical Biology of NeurodegenerationBrain Mind InstituteFaculty of Life SciencesEcole Polytechnique Fédérale de Lausanne1015LausanneSwitzerland
| | - Hilda Mirbaha
- Center for Alzheimer's and Neurodegenerative DiseasesPeter O'Donnell Jr. Brain InstituteUniversity of Texas Southwestern Medical CenterDallasTX75390USA
| | - Marc I. Diamond
- Center for Alzheimer's and Neurodegenerative DiseasesPeter O'Donnell Jr. Brain InstituteUniversity of Texas Southwestern Medical CenterDallasTX75390USA
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of NeurodegenerationBrain Mind InstituteFaculty of Life SciencesEcole Polytechnique Fédérale de Lausanne1015LausanneSwitzerland
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Jakovčević A, Žarković K, Jakovčević D, Rakušić Z, Prgomet D, Waeg G, Šunjić SB, Žarković N. The Appearance of 4-Hydroxy-2-Nonenal (HNE) in Squamous Cell Carcinoma of the Oropharynx. Molecules 2020; 25:molecules25040868. [PMID: 32079077 PMCID: PMC7070326 DOI: 10.3390/molecules25040868] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/23/2022] Open
Abstract
Tumor growth is associated with oxidative stress, which causes lipid peroxidation. The most intensively studied product of lipid peroxidation is 4-hydroxy-2-nonenal (HNE), which is considered as a “second messenger of free radicals” that binds to proteins and acts as a growth-regulating signaling factor. The incidence of squamous cell carcinoma of the oropharynx is associated with smoking, alcohol and infection of human papilloma virus (HPV), with increasing incidence world-wide. The aim of this retrospective study involving 102 patients was to determine the immunohistochemical appearance of HNE-protein adducts as a potential biomarker of lipid peroxidation in squamous cell carcinoma of the oropharynx. The HNE-protein adducts were detected in almost all tumor samples and in the surrounding non-tumorous tissue, while we found that HNE is differentially distributed in squamous cell carcinomas in dependence of clinical stage and histological grading of these tumors. Namely, the level of HNE-immunopositivity was increased in comparison to the normal oropharyngeal epithelium in well- and in moderately-differentiated squamous cell carcinoma, while it was decreasing in poorly differentiated carcinomas and in advanced stages of cancer. However, more malignant and advanced cancer was associated with the increase of HNE in surrounding, normal tissue. This study confirmed the onset of lipid peroxidation, generating HNE-protein adducts that can be used as a valuable bioactive marker of carcinogenesis in squamous cell carcinoma of the oropharynx, as well as indicating involvement of HNE in pathophysiological changes of the non-malignant tissue in the vicinity of cancer.
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Affiliation(s)
- Antonia Jakovčević
- Clinical Hospital Centre Zagreb, Clinical Department of Pathology and Cytology, School of Medicine, University of Zagreb, Kispaticeva 12, 10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-123-880-89
| | - Kamelija Žarković
- Clinical Hospital Centre Zagreb, Clinical Department of Pathology and Cytology, School of Medicine, University of Zagreb, Kispaticeva 12, 10000 Zagreb, Croatia;
| | - Danica Jakovčević
- Department of Pathology, Clinical Hospital “Sv. Duh”, Ul. Sveti Duh 64, 10000 Zagreb, Croatia;
| | - Zoran Rakušić
- Department of Oncology, University Hospital Centre Zagreb, Kispaticeva 12, 10000 Zagreb, Croatia;
| | - Drago Prgomet
- Clinic for Ear, Nose and Throat Diseases and Head and Neck Surgeries, University Hospital Center Zagreb, Kispaticeva 12, 10000 Zagreb, Croatia;
| | - Georg Waeg
- Institute of Molecular Biosciences, Karl Franzens University, Humboldtstrasse 50, A-8010 Graz, Austria;
| | - Suzana Borović Šunjić
- Rudjer Boskovic Institute, Laboratory for Oxidative Stress, Bijenička cesta 54, 10000 Zagreb, Croatia; (S.B.Š.); (N.Ž.)
| | - Neven Žarković
- Rudjer Boskovic Institute, Laboratory for Oxidative Stress, Bijenička cesta 54, 10000 Zagreb, Croatia; (S.B.Š.); (N.Ž.)
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Liu J, Ekanayake O, Santoleri D, Walker K, Rozovsky S. Efficient Generation of Hydrazides in Proteins by RadA Split Intein. Chembiochem 2020; 21:346-352. [PMID: 31265209 DOI: 10.1002/cbic.201900160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 03/13/2019] [Revised: 06/30/2019] [Indexed: 12/27/2022]
Abstract
Protein C-terminal hydrazides are useful for bioconjugation and construction of proteins from multiple fragments through native chemical ligation. To generate C-terminal hydrazides in proteins, an efficient intein-based preparation method has been developed by using thiols and hydrazine to accelerate the formation of the transient thioester intermediate and subsequent hydrazinolysis. This approach not only increases the yield, but also improves biocompatibility. The scope of the method has been expanded by employing Pyrococcus horikoshii RadA split intein, which can accommodate a broad range of extein residues before the site of cleavage. The use of split RadA minimizes premature intein N cleavage in vivo and offers control over the initiation of the intein N cleavage reaction. It is expected that this versatile preparation method will expand the utilization of protein C-terminal hydrazides in protein preparation and modification.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, 555 Mission Bay Boulevard South, San Francisco, CA, 94158, USA
| | - Oshini Ekanayake
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Dominic Santoleri
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kelsi Walker
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
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48
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Meltretter J, Wüst J, Dittrich D, Lach J, Ludwig J, Eichler J, Pischetsrieder M. Untargeted Proteomics-Based Profiling for the Identification of Novel Processing-Induced Protein Modifications in Milk. J Proteome Res 2020; 19:805-818. [PMID: 31902209 DOI: 10.1021/acs.jproteome.9b00630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 02/06/2023]
Abstract
Nonenzymatic post-translational protein modifications (nePTMs) affect the nutritional, physiological, and technological properties of proteins in food and in vivo. In contrast to the usual targeted analyses, the present study determined nePTMs in processed milk in a truly untargeted proteomic approach. Thus, it was possible to determine to which extent known nePTM structures explain protein modifications in processed milk and to detect and identify novel products. The method combined ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry with bioinformatic data analysis by the software XCMS. The nePTMs detected by untargeted profiling of a β-lactoglobulin-lactose model were incorporated in a sensitive scheduled multiple reaction monitoring method to analyze these modifications in milk samples and to monitor their reaction kinetics during thermal treatment. Additionally, we identified the structures of unknown modifications. Lactosylation, carboxymethylation, formylation of lysine and N-terminus, glycation of arginine, oxidation of methionine, tryptophan, and cysteine, oxidative deamination of N-terminus, and deamidation of asparagine and glutamine were the most important reactions of β-lactoglobulin during milk processing. The isomerization of aspartic acid was observed for the first time in milk products, and N-terminal 4-imidazolidinone was identified as a novel nePTM.
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Affiliation(s)
- Jasmin Meltretter
- Department of Chemistry and Pharmacy, Food Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
| | - Johannes Wüst
- Department of Chemistry and Pharmacy, Food Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
| | - Daniel Dittrich
- Department of Chemistry and Pharmacy, Food Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
| | - Johannes Lach
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
| | - Jonas Ludwig
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
| | - Monika Pischetsrieder
- Department of Chemistry and Pharmacy, Food Chemistry, Emil Fischer Center , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Nikolaus-Fiebiger-Str. 10 , 91058 Erlangen , Germany
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Schiedel M, Daub H, Itzen A, Jung M. Validation of the Slow Off-Kinetics of Sirtuin-Rearranging Ligands (SirReals) by Means of Label-Free Electrically Switchable Nanolever Technology. Chembiochem 2020; 21:1161-1166. [PMID: 31692222 PMCID: PMC7217041 DOI: 10.1002/cbic.201900527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 08/23/2019] [Revised: 10/31/2019] [Indexed: 12/17/2022]
Abstract
We have discovered the sirtuin-rearranging ligands (SirReals) to be highly potent and selective inhibitors of the NAD+ -dependent lysine deacetylase Sirt2. Using a biotinylated SirReal in combination with biolayer interferometry, we previously observed a slow dissociation rate of the inhibitor-enzyme complex; this had been postulated to be the key to the high affinity and selectivity of SirReals. However, to attach biotin to the SirReal core, we introduced a triazole as a linking moiety; this was shown by X-ray co-crystallography to interact with Arg97 of the cofactor binding loop. Herein, we aim to elucidate whether the observed long residence time of the SirReals is induced mainly by triazole incorporation or is an inherent characteristic of the SirReal inhibitor core. We used the novel label-free switchSENSE® technology, which is based on electrically switchable DNA nanolevers, to prove that the long residence time of the SirReals is indeed caused by the core scaffold.
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Affiliation(s)
- Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
| | - Herwin Daub
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany.,Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
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Wesalo JS, Luo J, Morihiro K, Liu J, Deiters A. Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation. Chembiochem 2020; 21:141-148. [PMID: 31664790 PMCID: PMC6980333 DOI: 10.1002/cbic.201900464] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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] [Received: 07/25/2019] [Revised: 09/03/2019] [Indexed: 11/06/2022]
Abstract
The Staudinger reduction and its variants have exceptional compatibility with live cells but can be limited by slow kinetics. Herein we report new small-molecule triggers that turn on proteins through a Staudinger reduction/self-immolation cascade with substantially improved kinetics and yields. We achieved this through site-specific incorporation of a new set of azidobenzyloxycarbonyl lysine derivatives in mammalian cells. This approach allowed us to activate proteins by adding a nontoxic, bioorthogonal phosphine trigger. We applied this methodology to control a post-translational modification (SUMOylation) in live cells, using native modification machinery. This work significantly improves the rate, yield, and tunability of the Staudinger reduction-based activation, paving the way for its application in other proteins and organisms.
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Affiliation(s)
- Joshua S. Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Ji Luo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Kunihiko Morihiro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
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