1
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Gazzi T, Heinke M, Landolt F, Bode JW. Chemical Synthesis of Secretoglobin 3A2 Covalent Homodimer and Photocaged Monomeric Variants. Angew Chem Int Ed Engl 2024; 63:e202404992. [PMID: 38635000 DOI: 10.1002/anie.202404992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 04/19/2024]
Abstract
Secretoglobin (SCGB) 3A2 belongs to an intriguing family of small, secreted proteins present only in mammals. Although members of the SCGB protein family have distinct amino acid sequences, they share structural similarities. Of particularly interest is the not yet fully understood self-assembly ability of SCGBs, which arise from covalent disulfide dimerization and non-covalent oligomerization. Recently, SCGB3A2 has attracted attention for its singular expression profile in airways. However, the knowledge on SCGB3A2 (patho)physiology derives exclusively from in vivo and complex ex vivo mixtures, which hampers characterization of the mechanisms driving SCGB3A2 structural behavior. Herein, we document the chemical synthesis of SCGB3A2 in multi-milligram quantities. Key to access both monomeric and homodimeric SCGB3A2 analogues was the use of KAHA ligation and enabled masking of the cysteine residue. The synthetic proteins were used to investigate the SCGB3A2 self-assembly profile, confirming their high propensity to dimerization even in the absence of the key Cys residue.
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Affiliation(s)
- Thais Gazzi
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Maria Heinke
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Fabienne Landolt
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, 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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2
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Liao P, He C. Azole reagents enabled ligation of peptide acyl pyrazoles for chemical protein synthesis. Chem Sci 2024; 15:7965-7974. [PMID: 38817582 PMCID: PMC11134319 DOI: 10.1039/d3sc06697e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Native chemical ligation (NCL) has been playing an increasingly important role in chemical protein synthesis (CPS). More efficient ligation methods that circumvent the requirement of a peptidyl thioester and thiol additive-which allow the following desulfurization or refolding in one pot-are urgently needed for the synthesis of more complex protein targets and in large quantities. Herein, we discover that the weak acyl donor peptidyl N-acyl pyrazole can be activated by azole reagents like 3-methylpyrazole or imidazole to facilitate its ligation directly with an N-terminal cysteine peptide. As it requires no thioester or thiol additive, this ligation strategy can be conveniently combined with metal-free desulfurization (MFD) or oxidative protein folding to allow various one-pot protocols. The utility and generality of the strategy are showcased by the total synthesis of ubiquitin via an N-to-C sequential ligation-MFD strategy, the semi-synthesis of the copper protein azurin, and the efficient assembly of a sulfated hirudin variant and the cyclotide kalata B1, all in a one-pot fashion.
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Affiliation(s)
- Peisi Liao
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology Guangzhou 510640 China
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3
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Paul S, Verma S, Chen YC. Peptide Dendrimer-Based Antibacterial Agents: Synthesis and Applications. ACS Infect Dis 2024; 10:1034-1055. [PMID: 38428037 PMCID: PMC11019562 DOI: 10.1021/acsinfecdis.3c00624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
Pathogenic bacteria cause the deaths of millions of people every year. With the development of antibiotics, hundreds and thousands of people's lives have been saved. Nevertheless, bacteria can develop resistance to antibiotics, rendering them insensitive to antibiotics over time. Peptides containing specific amino acids can be used as antibacterial agents; however, they can be easily degraded by proteases in vivo. To address these issues, branched peptide dendrimers are now being considered as good antibacterial agents due to their high efficacy, resistance to protease degradation, and low cytotoxicity. The ease with which peptide dendrimers can be synthesized and modified makes them accessible for use in various biological and nonbiological fields. That is, peptide dendrimers hold a promising future as antibacterial agents with prolonged efficacy without bacterial resistance development. Their in vivo stability and multivalence allow them to effectively target multi-drug-resistant strains and prevent biofilm formation. Thus, it is interesting to have an overview of the development and applications of peptide dendrimers in antibacterial research, including the possibility of employing machine learning approaches for the design of AMPs and dendrimers. This review summarizes the synthesis and applications of peptide dendrimers as antibacterial agents. The challenges and perspectives of using peptide dendrimers as the antibacterial agents are also discussed.
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Affiliation(s)
- Suchita Paul
- Institute
of Semiconductor Technology, National Yang
Ming Chiao Tung University, Hsinchu 300, Taiwan
- Department
of Chemistry, Indian Institute of Technology
Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Sandeep Verma
- Department
of Chemistry, Indian Institute of Technology
Kanpur, Kanpur 208016, Uttar Pradesh, India
- Gangwal
School of Medical Sciences and Technology, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Yu-Chie Chen
- Institute
of Semiconductor Technology, National Yang
Ming Chiao Tung University, Hsinchu 300, Taiwan
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 300, Taiwan
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4
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Mahmoodi Y, Mehrnejad F, Khanmohammadi S, Shahriari M, Rahimi F, Vakili MR, Lavasanifar A. Molecular insights into the crystalline nanocellulose and human lysozyme interactions: An experimental and theoretical research. Int J Biol Macromol 2022; 213:83-95. [PMID: 35598725 DOI: 10.1016/j.ijbiomac.2022.05.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022]
Abstract
In the present research, we performed a combination of detailed computational and spectroscopic methods to determine the effect of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz). Fluorescence spectroscopy revealed static quenching as the major mechanism in forming a stable CNC-hLyz complex, and the binding was energetically favorable. The obtained values of the thermodynamic parameters (∆G, ∆H, and ∆S) proposed that the complex formation between the enzyme and cellulose nanocrystals is driven by electrostatic interactions, which were also confirmed by molecular dynamics (MD) simulation. Additionally, the MD simulation analysis displays that the enzyme's structural elements and tertiary structure were primarily maintained, and only loops regions were affected in the presence of cellulose nanocrystals. At the same time, circular dichroism (CD) outcomes highlighted that higher cellulose nanocrystals concentration caused a reduction in the secondary structure of hLyz. Our observations proved that low cellulose nanocrystals concentrations have no considerable effect on the human lysozyme structure. The current research results provide a valuable opportunity to elucidate the molecular interactions between protein and nanocelluloses, guiding further investigations of CNC-based material for biomedical, pharmaceutical, and food industry applications.
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Affiliation(s)
- Yasaman Mahmoodi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran.
| | - Somayeh Khanmohammadi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Masoud Shahriari
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Fereshteh Rahimi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton AB T6G 2E1, Canada
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5
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Rodríguez DF, Moglie Y, Ramírez-Sarmiento CA, Singh SK, Dua K, Zacconi FC. Bio-click chemistry: a bridge between biocatalysis and click chemistry. RSC Adv 2022; 12:1932-1949. [PMID: 35425264 PMCID: PMC8979012 DOI: 10.1039/d1ra08053a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/28/2021] [Indexed: 11/21/2022] Open
Abstract
The fields of click chemistry and biocatalysis have rapidly grown over the last two decades. The development of robust and active biocatalysts and the widespread use of straightforward click reactions led to significant interactions between these two fields. Therefore the name bio-click chemistry seems to be an accurate definition of chemoenzymatic reactions cooperating with click transformations. Bio-click chemistry can be understood as the approach towards molecules of high-value using a green and sustainable approach by exploiting the potential of biocatalytic enzyme activity combined with the reliable nature of click reactions. This review summarizes the principal bio-click chemistry reactions reported over the last two decades, with a special emphasis on small molecules. Contributions to the field of bio-click chemistry are manifold, but the synthesis of chiral molecules with applications in medicinal chemistry and sustainable syntheses will be especially highlighted.
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Affiliation(s)
- Diego F Rodríguez
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile Chile
| | - Yanina Moglie
- Departamento de Química, INQUISUR, Universidad Nacional del Sur (UNS)-CONICET Argentina
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile Santiago Chile.,ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio) Santiago Chile
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University Phagwara 144411 Punjab India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney NSW 2007 Australia.,Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney Ultimo Australia
| | - Flavia C Zacconi
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile Chile .,Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile Santiago Chile.,Centro de Investigaciones en Nanotecnología y Materiales Avanzados, CIEN-UC, Pontificia Universidad Católica de Chile Santiago Chile
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6
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Khalil TH, Zoabi A, Falah M, Nseir N, David DB, Laevsky I, Zussman E, Ronen O, Redenski I, Srouji S. Micro-Osteo Tubular Scaffolds: a Method for Induction of Bone Tissue Constructs. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2021. [DOI: 10.1007/s40883-021-00236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Wang K, Luo F, Wang L, Zhang B, Fan Y, Wang X, Xu D, Zhang X. Biomineralization from the Perspective of Ion Aggregation: Calcium Phosphate Nucleation in the Physiological Environment. ACS APPLIED MATERIALS & INTERFACES 2021; 13:49519-49534. [PMID: 34609125 DOI: 10.1021/acsami.1c15393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomineralization is an important process of bone tissue generation. Calcium (Ca) and phosphate (P) ions aggregate and nucleate under the regulation of biomolecules at the initial mineralization stage. Due to the complexity of the physiological environment, the movement behavior and mineralization mechanism of calcium and phosphate ions, as well as the effect of biomolecules on them, are not clear. In this study, computer simulations and experimental verification were applied to investigate the characteristics of the initial biomineralization from the view of ion aggregation and nucleation. The results prove that P ions play a more important role in mineralization than Ca ions. The guanidyl group and surrounding carboxyl terminal groups are a potential excellent nucleation domain on proteins. The interval distribution of acidic/basic residues on protein is more conductive to the formation of large Ca and P ions clusters. The involvement of protein could increase the probability of hydroxyapatite phase precipitation, especially in the presence of a helical conformation. The detailed information on Ca and P ions behavior provided by the computer simulations is helpful for further understanding the mechanism of biomineralization, which will promote the development of bone repair materials to the biomimetic mineralized materials.
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Affiliation(s)
- Kefeng Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
| | - Fengxiong Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Ling Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Boqing Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Yujiang Fan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
| | - Xin Wang
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dingguo Xu
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xingdong Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610064, China
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8
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Dhayalan B, Chatterjee D, Chen YS, Weiss MA. Structural Lessons From the Mutant Proinsulin Syndrome. Front Endocrinol (Lausanne) 2021; 12:754693. [PMID: 34659132 PMCID: PMC8514764 DOI: 10.3389/fendo.2021.754693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022] Open
Abstract
Insight into folding mechanisms of proinsulin has been provided by analysis of dominant diabetes-associated mutations in the human insulin gene (INS). Such mutations cause pancreatic β-cell dysfunction due to toxic misfolding of a mutant proinsulin and impairment in trans of wild-type insulin secretion. Anticipated by the "Akita" mouse (a classical model of monogenic diabetes mellitus; DM), this syndrome illustrates the paradigm endoreticulum (ER) stress leading to intracellular proteotoxicity. Diverse clinical mutations directly or indirectly perturb native disulfide pairing leading to protein misfolding and aberrant aggregation. Although most introduce or remove a cysteine (Cys; leading in either case to an unpaired thiol group), non-Cys-related mutations identify key determinants of folding efficiency. Studies of such mutations suggest that the hormone's evolution has been constrained not only by structure-function relationships, but also by the susceptibility of its single-chain precursor to impaired foldability. An intriguing hypothesis posits that INS overexpression in response to peripheral insulin resistance likewise leads to chronic ER stress and β-cell dysfunction in the natural history of non-syndromic Type 2 DM. Cryptic contributions of conserved residues to folding efficiency, as uncovered by rare genetic variants, define molecular links between biophysical principles and the emerging paradigm of Darwinian medicine: Biosynthesis of proinsulin at the edge of non-foldability provides a key determinant of "diabesity" as a pandemic disease of civilization.
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Affiliation(s)
| | | | | | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
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9
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Kamo N, Kujirai T, Kurumizaka H, Murakami H, Hayashi G, Okamoto A. Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factors. Chem Sci 2021; 12:5926-5937. [PMID: 35342540 PMCID: PMC8872386 DOI: 10.1039/d1sc00731a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/21/2021] [Indexed: 12/21/2022] Open
Abstract
The application of organometallic compounds for protein science has received attention. Recently, total chemical protein synthesis using transition metal complexes has been developed to produce various proteins bearing site-specific posttranslational modifications (PTMs). However, in general, significant amounts of metal complexes were required to achieve chemical reactions of proteins bearing a large number of nucleophilic functional groups. Moreover, syntheses of medium-size proteins (>20 kDa) were plagued by time-consuming procedures due to cumbersome purification and isolation steps, which prevented access to variously decorated proteins. Here, we report a one-pot multiple peptide ligation strategy assisted by an air-tolerant organoruthenium catalyst that showed more than 50-fold activity over previous palladium complexes, leading to rapid and quantitative deprotection on a protein with a catalytic amount (20 mol%) of the metal complex even in the presence of excess thiol moieties. Utilizing the organoruthenium catalyst, heterochromatin factors above 20 kDa, such as linker histone H1.2 and heterochromatin protein 1α (HP1α), bearing site-specific PTMs including phosphorylation, ubiquitination, citrullination, and acetylation have been synthesized. The biochemical assays using synthetic proteins revealed that the citrullination at R53 in H1.2 resulted in the reduced electrostatic interaction with DNA and the reduced binding affinity to nucleosomes. Furthermore, we identified a key phosphorylation region in HP1α to control its DNA-binding ability. The ruthenium chemistry developed here will facilitate the preparation of a variety of biologically and medically significant proteins containing PTMs and non-natural amino acids.
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Affiliation(s)
- Naoki Kamo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo Bunkyo-ku Tokyo 113-0032 Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo Bunkyo-ku Tokyo 113-0032 Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Nagoya 464-8603 Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Research Center for Advanced Science and Technology, The University of Tokyo Meguro-ku Tokyo 153-8904 Japan
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10
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Dhayalan B, Chatterjee D, Chen YS, Weiss MA. Diabetes mellitus due to toxic misfolding of proinsulin variants. Mol Metab 2021:101229. [PMID: 33823319 DOI: 10.1016/j.molmet.2021.101229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Dominant mutations in the human insulin gene (INS) lead to pancreatic β-cell dysfunction and diabetes mellitus (DM) due to toxic misfolding of a mutant proinsulin. Analogous to a classical mouse model of monogenic DM ("Akita"), this syndrome highlights the susceptibility of β-cells to endoreticulum (ER) stress due to protein misfolding and aberrant aggregation. SCOPE OF REVIEW Diverse clinical mutations directly or indirectly perturb native disulfide pairing. Whereas most introduce or remove a cysteine (Cys; leading in either case to an unpaired thiol group), non-Cys-related mutations identify key determinants of folding efficiency. Studies of such mutations suggest that the hormone's evolution has been constrained not only by structure-function relationships but also by the susceptibility of its single-chain precursor to impaired foldability. An intriguing hypothesis posits that INS overexpression in response to peripheral insulin resistance likewise leads to chronic ER stress and β-cell dysfunction in the natural history of nonsyndromic Type 2 DM. MAJOR CONCLUSIONS Cryptic contributions of conserved residues to folding efficiency, as uncovered by rare genetic variants, define molecular links between biophysical principles and the emerging paradigm of Darwinian medicine: Biosynthesis of proinsulin at the edge of nonfoldability provides a key determinant of "diabesity" as a pandemic disease of civilization.
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Affiliation(s)
- Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Deepak Chatterjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael A Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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11
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Biophysical Insight into the Interaction of Human Lysozyme with Anticancer Drug Anastrozole: A Multitechnique Approach. ScientificWorldJournal 2020; 2020:8363685. [PMID: 32908463 PMCID: PMC7468670 DOI: 10.1155/2020/8363685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
In the present study, we employ fluorescence spectroscopy, dynamic light scattering, and molecular docking methods. Binding of anticancer drug anastrozole with human lysozyme (HL) is studied. Binding of anastrozole to HL is moderate but spontaneous. There is anastrozole persuaded hydrodynamic change in HL, leading to molecular compaction. Binding of anastrozole to HL also decreased in vitro lytic activity of HL. Molecular docking results suggest the electrostatic interactions and van der Waals forces played key role in binding interaction of anastrozole near the catalytic site. Binding interaction of anastrozole to proteins other than major transport proteins in blood can significantly affect pharmacokinetics of this molecule. Hence, rationalizing drug dosage is important. This study also points to unrelated effects that small molecules bring in the body that are considerable and need thorough investigation.
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12
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Kar A, Mannuthodikayil J, Singh S, Biswas A, Dubey P, Das A, Mandal K. Efficient Chemical Protein Synthesis using Fmoc-Masked N-Terminal Cysteine in Peptide Thioester Segments. Angew Chem Int Ed Engl 2020; 59:14796-14801. [PMID: 32333711 PMCID: PMC7891605 DOI: 10.1002/anie.202000491] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Indexed: 01/23/2023]
Abstract
We report an operationally simple method to facilitate chemical protein synthesis by fully convergent and one-pot native chemical ligations utilizing the fluorenylmethyloxycarbonyl (Fmoc) moiety as an N-masking group of the N-terminal cysteine of the middle peptide thioester segment(s). The Fmoc group is stable to the harsh oxidative conditions frequently used to generate peptide thioesters from peptide hydrazide or o-aminoanilide. The ready availability of Fmoc-Cys(Trt)-OH, which is routinely used in Fmoc solid-phase peptide synthesis, where the Fmoc group is pre-installed on cysteine residue, minimizes additional steps required for the temporary protection of the N-terminal cysteinyl peptides. The Fmoc group is readily removed after ligation by short exposure (<7 min) to 20 % piperidine at pH 11 in aqueous conditions at room temperature. Subsequent native chemical ligation reactions can be performed in presence of piperidine in the same solution at pH 7.
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Affiliation(s)
- Abhisek Kar
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Jamsad Mannuthodikayil
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Sameer Singh
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Anamika Biswas
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Puneet Dubey
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
| | - Amit Das
- Protein Crystallography Section, Radiation Biology and Health Sciences DivisionBhabha Atomic Research CentreTrombayMumbai400085India
- Homi Bhabha National InstituteAnushaktinagarMumbai400094India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabad500046TelanganaIndia
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13
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Hartrampf N, Saebi A, Poskus M, Gates ZP, Callahan AJ, Cowfer AE, Hanna S, Antilla S, Schissel CK, Quartararo AJ, Ye X, Mijalis AJ, Simon MD, Loas A, Liu S, Jessen C, Nielsen TE, Pentelute BL. Synthesis of proteins by automated flow chemistry. Science 2020; 368:980-987. [PMID: 32467387 DOI: 10.1126/science.abb2491] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
Ribosomes can produce proteins in minutes and are largely constrained to proteinogenic amino acids. Here, we report highly efficient chemistry matched with an automated fast-flow instrument for the direct manufacturing of peptide chains up to 164 amino acids long over 327 consecutive reactions. The machine is rapid: Peptide chain elongation is complete in hours. We demonstrate the utility of this approach by the chemical synthesis of nine different protein chains that represent enzymes, structural units, and regulatory factors. After purification and folding, the synthetic materials display biophysical and enzymatic properties comparable to the biologically expressed proteins. High-fidelity automated flow chemistry is an alternative for producing single-domain proteins without the ribosome.
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Affiliation(s)
- N Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Saebi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - M Poskus
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Z P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A E Cowfer
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Antilla
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C K Schissel
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - X Ye
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - M D Simon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C Jessen
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - T E Nielsen
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - B L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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14
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Kar A, Mannuthodikayil J, Singh S, Biswas A, Dubey P, Das A, Mandal K. Efficient Chemical Protein Synthesis using Fmoc‐Masked N‐Terminal Cysteine in Peptide Thioester Segments. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Abhisek Kar
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Jamsad Mannuthodikayil
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Sameer Singh
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Anamika Biswas
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Puneet Dubey
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
| | - Amit Das
- Protein Crystallography Section, Radiation Biology and Health Sciences Division Bhabha Atomic Research Centre Trombay Mumbai 400085 India
- Homi Bhabha National Institute Anushaktinagar Mumbai 400094 India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana −500046 India
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15
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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. [DOI: 10.1002/ange.201916053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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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16
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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] [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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17
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Lee TK, Manandhar B, Kassees KJ, Ahn JM. Peptide Ligation via the Suzuki-Miyaura Cross-Coupling Reaction. J Org Chem 2020; 85:1376-1384. [PMID: 31773962 DOI: 10.1021/acs.joc.9b02313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chemoselective ligation of two 28-mer peptides has been accomplished using the Suzuki-Miyaura cross-coupling reaction at or near physiological temperature in an aqueous solution containing sodium dodecyl sulfate in 83% yield. The effects of Pd source, solvent, base, and temperature were investigated, and the optimized reaction conditions were studied for compatibility with naturally present and artificially introduced functional groups in peptides including S-protected thiol and azide. The peptide conjugations were carried out in high yield (90%) with their functional groups intact. This method also allowed for facile introduction of an affinity tag or fluorescent probe into 20-mer peptides in >80% yield. These results suggest that the Suzuki-Miyaura cross-coupling is useful for multiple conjugations of peptides in conjunction with conventional conjugation reactions performed in sequence.
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Affiliation(s)
- Tae-Kyung Lee
- Department of Chemistry and Biochemistry , University of Texas at Dallas , 800 West Campbell Road , Richardson , Texas 75080 , United States
| | - Bikash Manandhar
- Department of Chemistry and Biochemistry , University of Texas at Dallas , 800 West Campbell Road , Richardson , Texas 75080 , United States
| | - Kara J Kassees
- Department of Chemistry and Biochemistry , University of Texas at Dallas , 800 West Campbell Road , Richardson , Texas 75080 , United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry , University of Texas at Dallas , 800 West Campbell Road , Richardson , Texas 75080 , United States
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18
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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19
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Schwarz DH, Elgaher WAM, Hollemeyer K, Hirsch AKH, Wenz G. Reversible immobilization of a protein to a gold surface through multiple host–guest interactions. J Mater Chem B 2019; 7:6148-6155. [DOI: 10.1039/c9tb00560a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Monolayers were formed by specific interactions between adamantylated proteins (transferrin, lysozyme) and a β-cyclodextrin (β-CD) monolayer on a gold surface.
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Affiliation(s)
- Dennis H. Schwarz
- Organic Macromolecular Chemistry
- Saarland University
- Saarbrücken
- Germany
| | - Walid A. M. Elgaher
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI)
- Department of Drug Design and Optimization
- Saarbrücken
- Germany
| | | | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI)
- Department of Drug Design and Optimization
- Saarbrücken
- Germany
- Department of Pharmacy
| | - Gerhard Wenz
- Organic Macromolecular Chemistry
- Saarland University
- Saarbrücken
- Germany
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20
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Abstract
A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo. REVIEWERS This article was reviewed by Eugene Koonin and Frank Eisenhaber.
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21
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Li X, Xie B, Dong X, Sun Y. Bifunctionality of Iminodiacetic Acid-Modified Lysozyme on Inhibiting Zn 2+-Mediated Amyloid β-Protein Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5106-5115. [PMID: 29631401 DOI: 10.1021/acs.langmuir.8b00254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aggregation of amyloid β-proteins (Aβ) mediated by metal ions such as Zn2+ has been suggested to be implicated in the progression of Alzheimer's disease (AD). Hence, development of bifunctional agents capable of inhibiting Aβ aggregation and modulating metal-Aβ species is an effective strategy for the treatment of AD. In this work, we modified iminodiacetic acid (IDA) onto human lysozyme (hLys) surface to create an inhibitor of Zn2+-mediated Aβ aggregation and cytotoxicity. The IDA-modified hLys (IDA-hLys) retained the stability and biocompatibility of native hLys. Extensive biophysical and biological analyses indicated that IDA-hLys significantly attenuated Zn2+-mediated Aβ aggregation and cytotoxicity due to its strong binding affinity for Zn2+, whereas native hLys showed little effect. Stopped-flow fluorescence spectroscopy showed that IDA-hLys could protect Aβ from Zn2+-induced aggregation and rapidly depolymerize Zn2+-Aβ aggregates. The research indicates that IDA-hLys is a bifunctional agent capable of inhibiting Aβ fibrillization and modulating Zn2+-mediated Aβ aggregation and cytotoxicity as a strong Zn2+ chelator.
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Affiliation(s)
- Xi Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
| | - Baolong Xie
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
- Institute of Tianjin Seawater Desalination and Multipurpose Utilization , State Oceanic Administration (SOA) , Tianjin 300192 , China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology , Tianjin University , Tianjin 300354 , China
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22
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Giuffrida MC, Cigliana G, Spoto G. Ultrasensitive detection of lysozyme in droplet-based microfluidic devices. Biosens Bioelectron 2017; 104:8-14. [PMID: 29294408 DOI: 10.1016/j.bios.2017.12.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 12/27/2022]
Abstract
Lysozyme (LYS) is a bacteriolytic enzyme, available in secretions such as saliva, tears and human milk. LYS is an important defence molecule of the innate immune system, and its overexpression can be a consequence of diseases such as leukemia, kidney disease and sarcoidosis. This paper reports on a digital microfluidic-based approach that combines the gold nanoparticle-enhanced chemiluminescence with aptamer interaction to detect human lysozyme into droplets 20 nanoliters in volume. The described method allows identifying LYS with a 44.6 femtomolar limit of detection, using sample volume as low as 1μL and detection time in the range of 10min. We used luminol to generate the chemiluminescence and demonstrated that the compartmentalization of LYS in droplets also comprising gold nanoparticles provided enhanced luminescence. We functionalized the gold nanoparticles with a thiolated aptamer to achieve the required selectivity that allowed us to detect LYS in human serum.
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Affiliation(s)
- Maria Chiara Giuffrida
- Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, Catania, Italy
| | - Giovanni Cigliana
- Clinical Pathology Unit, Regina Elena National Cancer Institute, Via Chianesi, Roma, Italy
| | - Giuseppe Spoto
- Consorzio Interuniversitario "Istituto Nazionale Biostrutture e Biosistemi", c/o Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, Catania, Italy; Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy.
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23
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Mousa R, Notis Dardashti R, Metanis N. Selen und Selenocystein in der Proteinchemie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reem Mousa
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
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24
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Mousa R, Notis Dardashti R, Metanis N. Selenium and Selenocysteine in Protein Chemistry. Angew Chem Int Ed Engl 2017; 56:15818-15827. [PMID: 28857389 DOI: 10.1002/anie.201706876] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/22/2023]
Abstract
Selenocysteine, the selenium-containing analogue of cysteine, is the twenty-first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.
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Affiliation(s)
- Reem Mousa
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
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25
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Kent S. Chemical protein synthesis: Inventing synthetic methods to decipher how proteins work. Bioorg Med Chem 2017; 25:4926-4937. [DOI: 10.1016/j.bmc.2017.06.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/07/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022]
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26
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Abstract
Nucleation, the primary step in crystallization, dictates the number of crystals, the distribution of their sizes, the polymorph selection, and other crucial properties of the crystal population. We used time-resolved liquid-cell transmission electron microscopy (TEM) to perform an in situ examination of the nucleation of lysozyme crystals. Our TEM images revealed that mesoscopic clusters, which are similar to those previously assumed to consist of a dense liquid and serve as nucleation precursors, are actually amorphous solid particles (ASPs) and act only as heterogeneous nucleation sites. Crystalline phases never form inside them. We demonstrate that a crystal appears within a noncrystalline particle assembling lysozyme on an ASP or a container wall, highlighting the role of heterogeneous nucleation. These findings represent a significant departure from the existing formulation of the two-step nucleation mechanism while reaffirming the role of noncrystalline particles. The insights gained may have significant implications in areas that rely on the production of protein crystals, such as structural biology, pharmacy, and biophysics, and for the fundamental understanding of crystallization mechanisms.
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27
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Buhler S, Akkerdaas JH, A. Pertinhez T, Van Ree R, Dossena A, Sforza S, Tedeschi T. Development of a strategy for the total chemical synthesis of an allergenic protein: the peach LTP Pru p 3. J Pept Sci 2017; 23:282-293. [DOI: 10.1002/psc.2981] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Sofie Buhler
- Food and Drug Department; University of Parma; Viale delle Scienze 17/A 43124 Parma Italy
| | - Jaap H. Akkerdaas
- Department of Experimental Immunology, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Thelma A. Pertinhez
- Transfusion Medicine Unit; ASMN-IRCCS; Reggio Emilia Italy
- Department of Medicine and Surgery; Via Gramsci 14 43125 Parma
| | - Ronald Van Ree
- Department of Experimental Immunology, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Arnaldo Dossena
- Food and Drug Department; University of Parma; Viale delle Scienze 17/A 43124 Parma Italy
| | - Stefano Sforza
- Food and Drug Department; University of Parma; Viale delle Scienze 17/A 43124 Parma Italy
| | - Tullia Tedeschi
- Food and Drug Department; University of Parma; Viale delle Scienze 17/A 43124 Parma Italy
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28
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Thapa P, Cabalteja CC, Philips EE, Espiritu MJ, Peigneur S, Mille BG, Tytgat J, Cummins TR, Bingham JP. t-boc synthesis of huwentoxin-i through native chemical ligation incorporating a trifluoromethanesulfonic acid cleavage strategy. Biopolymers 2017; 106:737-45. [PMID: 27271997 DOI: 10.1002/bip.22887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 11/10/2022]
Abstract
Tert-butyloxycarbonyl (t-Boc)-based native chemical ligation (NCL) techniques commonly employ hydrogen fluoride (HF) to create the thioester fragment required for the ligation process. Our research aimed to assess the replacement of HF with Trifluoromethanesulfonic acid (TFMSA). Here we examined a 33 amino acid test peptide, Huwentoxin-I (HwTx-I) as a novel candidate for our TFMSA cleavage protocol. Structurally HwTx-I has an X-Cys(16) -Cys(17) -X sequence mid-region, which makes it an ideal candidate for NCL. Experiments determined that the best yields (16.8%) obtained for 50 mg of a thioester support resin were achieved with a TFMSA volume of 100 μL with a 0.5-h incubation on ice, followed by 2.0 h at room temperature. RP-HPLC/UV and mass spectra indicated the appropriate parent mass and retention of the cleaved HwTx-I N-terminal thioester fragment (Ala(1) -Cys(16) ), which was used in preparation for NCL. The resulting chemically ligated HwTx-I was oxidized/folded, purified, and then assessed for pharmacological target selectivity. Native-like HwTx-I produced by this method yielded an EC50 value of 340.5 ± 26.8 nM for Nav 1.2 and an EC50 value of 504.1 ± 81.3 nM for Nav 1.3, this being similar to previous literature results using native material. This article represents the first NCL based synthesis of this potent sodium channel blocker. Our illustrated approach removes potential restrictions in the advancement of NCL as a common peptide laboratory technique with minimal investment, and removes the hazards associated with HF usage. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 737-745, 2016.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Chino C Cabalteja
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Edwin E Philips
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Michael J Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Steve Peigneur
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, 3000, Belgium
| | - Bea G Mille
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, 3000, Belgium
| | - Jan Tytgat
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, 3000, Belgium
| | - Theodore R Cummins
- Department of Pharmacology and Toxicology, Indiana University, Indianapolis, IN.,Department of Pharmacology and Toxicology, Stark Neurosciences Research Institute, 320 West 25th Street, NB-414F, Indianapolis, IN, 46202-2266
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822.
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29
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Galm L, Amrhein S, Hubbuch J. Predictive approach for protein aggregation: Correlation of protein surface characteristics and conformational flexibility to protein aggregation propensity. Biotechnol Bioeng 2017; 114:1170-1183. [PMID: 26853436 DOI: 10.1002/bit.25949] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/11/2016] [Accepted: 02/03/2016] [Indexed: 11/11/2022]
Abstract
The aggregation of proteins became one of the major challenges in the development of biopharmaceu-ticals since the formation of aggregates can affect drug quality and immunogenicity. However, aggregation mechanisms are highly complex and the investigation requires cost, time, and material intensive experi-mental effort. In the present work, the predictive power of protein characteristics for the phase behavior of three different proteins which are very similar in size and structure was studied. In particular, the surface hydrophobicity, zeta potential, and conformational flexibility of human lysozyme, lysozyme from chicken egg white, and α-lactalbumin at pH 3, 5, 7, and 9 were assessed and examined for correlation with experimental stability studies focusing on protein phase behavior induced by sodium chloride and ammonium sulfate. The molecular dynamics (MD) simulation based study of the conformational flexibility without precipitants was able to identify highly flexible protein regions which could be associated to the less regular secondary structure elements and random coiled and terminal regions in particular. Conformational flex-ibility of the entire protein structure and protein surface hydrophobicity could be correlated to differing aggregation propensities among the studied proteins and could be identified to be applicable for predic-tion of protein phase behavior in aqueous solution without precipitants. For prediction of protein phase behavior and aggregation propensity in aqueous solution with precipitants, protein flexibility was further studied in dependency of salt concentration and species by means of human lysozyme. Even though the results of the salt dependent MD simulations could not be shown to be sufficient for prediction of salt depending phase behavior, this study revealed a more pronounced destabilizing effect of ammonium sulfate in comparison to sodium chloride and thus, was found to be in good agreement with theoretical considerations along the Hofmeister series as well as experimentally evaluated phase behavior. Biotechnol. Bioeng. 2017;114: 1170-1183. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lara Galm
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Sven Amrhein
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Engler-Bunte-Ring 3, 76131, Karlsruhe, Germany
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30
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Tsuda S, Mochizuki M, Nishio H, Yoshiya T. Combination of Thiol-Additive-Free Native Chemical Ligation/Desulfurization and Intentional Replacement of Alanine with Cysteine. Chembiochem 2016; 17:2133-2136. [DOI: 10.1002/cbic.201600455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Saito asagi Ibaraki-shi Osaka 567-0085 Japan
| | | | - Hideki Nishio
- Peptide Institute, Inc.; Saito asagi Ibaraki-shi Osaka 567-0085 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Saito asagi Ibaraki-shi Osaka 567-0085 Japan
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31
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Bacchi M, Jullian M, Sirigu S, Fould B, Huet T, Bruyand L, Antoine M, Vuillard L, Ronga L, Chavas LMG, Nosjean O, Ferry G, Puget K, Boutin JA. Total chemical synthesis, refolding, and crystallographic structure of fully active immunophilin calstabin 2 (FKBP12.6). Protein Sci 2016; 25:2225-2242. [PMID: 27670942 DOI: 10.1002/pro.3051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 01/05/2023]
Abstract
Synthetic biology (or chemical biology) is a growing field to which the chemical synthesis of proteins, particularly enzymes, makes a fundamental contribution. However, the chemical synthesis of catalytically active proteins (enzymes) remains poorly documented because it is difficult to obtain enough material for biochemical experiments. We chose calstabin, a 107-amino-acid proline isomerase, as a model. We synthesized the enzyme using the native chemical ligation approach and obtained several tens of milligrams. The polypeptide was refolded properly, and we characterized its biophysical properties, measured its catalytic activity, and then crystallized it in order to obtain its tridimensional structure after X-ray diffraction. The refolded enzyme was compared to the recombinant, wild-type enzyme. In addition, as a first step of validating the whole process, we incorporated exotic amino acids into the N-terminus. Surprisingly, none of the changes altered the catalytic activities of the corresponding mutants. Using this body of techniques, avenues are now open to further obtain enzymes modified with exotic amino acids in a way that is only barely accessible by molecular biology, obtaining detailed information on the structure-function relationship of enzymes reachable by complete chemical synthesis.
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Affiliation(s)
- Marine Bacchi
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Magali Jullian
- Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France
| | - Serena Sirigu
- PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France
| | - Benjamin Fould
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Tiphaine Huet
- PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France
| | - Lisa Bruyand
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Mathias Antoine
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Laurent Vuillard
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Luisa Ronga
- Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France
| | - Leonard M G Chavas
- PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France
| | - Olivier Nosjean
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Gilles Ferry
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
| | - Karine Puget
- Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France
| | - Jean A Boutin
- Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France
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32
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Ekimoto T, Matubayasi N, Ikeguchi M. Finite-size effect on the charging free energy of protein in explicit solvent. J Chem Theory Comput 2016; 11:215-23. [PMID: 26574219 DOI: 10.1021/ct5008394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The finite-size effect in periodic system is examined for the charging free energy of protein in explicit solvent over a variety of charged states. The key to the finite-size correction is the self-energy, which is defined as the interaction energy of the solute with its own periodic images and the neutralizing background. By employing the thermodynamic-integration method with systematically varied sizes of the unit cell of molecular dynamics (MD) simulations, we show for ubiquitin that the self-energy corrects the finite-size effect on the charging free energy within 1 kcal/mol at total charges of -5e, -1e, neutral, and +1e and within 5 kcal/mol even for a highly charged state with +8e. We then sought the additional correction from the solvation effect using the numerical solution to the Poisson equation of the protein with implicit solvent. This correction reduces the cell-size dependence of the charging free energy at +8e to 3 kcal/mol and is well expressed as the self-energy divided by the dielectric constant of solvent water.
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Affiliation(s)
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University , Katsura, Kyoto 615-8520, Japan
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33
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Herbst E, Shabat D. FRET-based cyanine probes for monitoring ligation reactions and their applications to mechanistic studies and catalyst screening. Org Biomol Chem 2016; 14:3715-28. [PMID: 26909686 DOI: 10.1039/c5ob02127h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is an ever-increasing need to design better methods to selectively connect two molecules under mild aqueous conditions on a small scale. The process of finding such methods significantly relies on the employment of an appropriate assay. We report here a modular FRET-based assay to monitor such reactions and illustrate how the assay is used to monitor two particular reactions: native chemical ligation (NCL) and oxime ligation. For both reactions we show that by employing appropriately designed probes FRET measurements could be used to monitor the reaction's progress. We additionally demonstrate the usefulness of the developed probe system to study the mechanisms of the ligation reactions, for example, in monitoring the formation of a trimeric intermediate in the NCL reaction. Finally, we demonstrate that FRET measurements conducted in our system allow the quantification of the reaction yield and we show the application of our FRET-based assay to catalyst screening for the oxime ligation.
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Affiliation(s)
- E Herbst
- School of Chemistry, Department of Organic Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - D Shabat
- School of Chemistry, Department of Organic Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv, 69978 Israel
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34
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Lee CL, Liu H, Wong CTT, Chow HY, Li X. Enabling N-to-C Ser/Thr Ligation for Convergent Protein Synthesis via Combining Chemical Ligation Approaches. J Am Chem Soc 2016; 138:10477-84. [DOI: 10.1021/jacs.6b04238] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Chi Lung Lee
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Han Liu
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Clarence T. T. Wong
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Hoi Yee Chow
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xuechen Li
- Department of Chemistry,
The State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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35
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Tsuda S, Mochizuki M, Nishio H, Yoshiya T, Nishiuchi Y. Development of a sufficiently reactive thioalkylester involving the side-chain thiol of cysteine applicable for kinetically controlled ligation. Biopolymers 2016; 106:503-11. [DOI: 10.1002/bip.22783] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
| | | | - Hideki Nishio
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
- Graduate School of Science; Osaka University; Toyonaka Osaka 560-0043 Japan
| | - Taku Yoshiya
- Peptide Institute, Inc.; Ibaraki Osaka 567-0085 Japan
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36
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37
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Wan J, Alewood PF. Peptide-Decorated Dendrimers and Their Bioapplications. Angew Chem Int Ed Engl 2016; 55:5124-34. [DOI: 10.1002/anie.201508428] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/01/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Jingjing Wan
- Institute of Molecular Bioscience; The University of Queensland; 306 Carmody Road St Lucia QLD 4072 Australia
| | - Paul F. Alewood
- Institute of Molecular Bioscience; The University of Queensland; 306 Carmody Road St Lucia QLD 4072 Australia
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38
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Wan J, Alewood PF. Mit Peptiden dekorierte Dendrimere und ihre biotechnologische Nutzung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jingjing Wan
- Institute of Molecular Bioscience; The University of Queensland; 306 Carmody Road St Lucia QLD 4072 Australien
| | - Paul F. Alewood
- Institute of Molecular Bioscience; The University of Queensland; 306 Carmody Road St Lucia QLD 4072 Australien
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39
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Tang S, Wan Z, Gao Y, Zheng JS, Wang J, Si YY, Chen X, Qi H, Liu L, Liu W. Total chemical synthesis of photoactivatable proteins for light-controlled manipulation of antigen-antibody interactions. Chem Sci 2016; 7:1891-1895. [PMID: 29899912 PMCID: PMC5965250 DOI: 10.1039/c5sc03404c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/19/2015] [Indexed: 01/23/2023] Open
Abstract
We report the chemical synthesis of the first photo-activatable protein antigen that can be used to study antigen-antibody interaction mediated responses in B cells. This strategy facilitated fine tuning of the caged protein antigen to optimize its bioactivity and photochemical properties. One optimal molecule, HEL-K96NPE, was totally inert to hen egg lysozyme (HEL)-specific B cells and could only restore its antigenicity upon photoactivation. Combined with real time live cell imaging, the utility of HEL-K96NPE was demonstrated as a proof of concept to quantify B cell synapse formation and calcium influx responses at the single cell level.
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Affiliation(s)
- Shan Tang
- Tsinghua-Peking Center for Life Sciences , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education) , Department of Chemistry , Tsinghua University , Beijing 100084 , China .
| | - Zhengpeng Wan
- MOE Key Laboratory of Protein Science , Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , School of Life Sciences , Tsinghua University , Beijing , 100084 , China .
| | - Yiren Gao
- MOE Key Laboratory of Protein Science , Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , School of Life Sciences , Tsinghua University , Beijing , 100084 , China .
| | - Ji-Shen Zheng
- High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei , 230031 , China
| | - Jing Wang
- MOE Key Laboratory of Protein Science , Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , School of Life Sciences , Tsinghua University , Beijing , 100084 , China .
| | - Yan-Yan Si
- Tsinghua-Peking Center for Life Sciences , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education) , Department of Chemistry , Tsinghua University , Beijing 100084 , China .
| | - Xin Chen
- Laboratory of Dynamic Immunobiology , School of Medicine , Tsinghua University , Beijing , 100084 , China
| | - Hai Qi
- Laboratory of Dynamic Immunobiology , School of Medicine , Tsinghua University , Beijing , 100084 , China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education) , Department of Chemistry , Tsinghua University , Beijing 100084 , China .
| | - Wanli Liu
- MOE Key Laboratory of Protein Science , Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , School of Life Sciences , Tsinghua University , Beijing , 100084 , China .
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40
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Aihara K, Yamaoka K, Naruse N, Inokuma T, Shigenaga A, Otaka A. One-Pot/Sequential Native Chemical Ligation Using Photocaged Crypto-thioester. Org Lett 2016; 18:596-9. [DOI: 10.1021/acs.orglett.5b03661] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keisuke Aihara
- Institute
of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Kosuke Yamaoka
- Institute
of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Naoto Naruse
- Institute
of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Tsubasa Inokuma
- Institute
of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Akira Shigenaga
- Institute
of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
| | - Akira Otaka
- Institute
of Biomedical Sciences
and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima 770-8505, Japan
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41
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Ali Shah MI, Xu ZY, Liu L, Jiang YY, Shi J. Mechanism for the enhanced reactivity of 4-mercaptoprolyl thioesters in native chemical ligation. RSC Adv 2016. [DOI: 10.1039/c6ra13793h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Ring-strain-precluded strategy benefiting from entropy effects and n → π* orbital interaction, enhances the reactivity of C-terminal prolyl thioesters in NCL.
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Affiliation(s)
| | - Zhe-Yuan Xu
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Lei Liu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yuan-Ye Jiang
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Jing Shi
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
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42
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Chen X, Lu W. Functional Interrogation of the N-Terminal Lid of MDMX in p53 Binding via Native Chemical Ligation. Chem Pharm Bull (Tokyo) 2016; 64:1004-8. [DOI: 10.1248/cpb.c15-00975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Xishan Chen
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education
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43
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Weidmann J, Dimitrijević E, Hoheisel JD, Dawson PE. Boc-SPPS: Compatible Linker for the Synthesis of Peptide o-Aminoanilides. Org Lett 2015; 18:164-7. [DOI: 10.1021/acs.orglett.5b03111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joachim Weidmann
- Division
of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
- Departments of Chemistry and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elena Dimitrijević
- Departments of Chemistry and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jörg D. Hoheisel
- Division
of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Philip E. Dawson
- Departments of Chemistry and Cell & Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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44
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Mayayo C, Montserrat M, Ramos SJ, Martínez-Lorenzo MJ, Calvo M, Sánchez L, Pérez MD. Effect of high pressure and heat treatments on IgA immunoreactivity and lysozyme activity in human milk. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2595-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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45
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Dery S, Reddy PS, Dery L, Mousa R, Dardashti RN, Metanis N. Insights into the deselenization of selenocysteine into alanine and serine. Chem Sci 2015; 6:6207-6212. [PMID: 30090236 PMCID: PMC6054048 DOI: 10.1039/c5sc02528a] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/06/2015] [Indexed: 12/21/2022] Open
Abstract
The deselenization of selenocysteine selectively removes the selenol group to give alanine under anaerobic conditions or serine under aerobic conditions (oxygen saturation).
The development of native chemical ligation coupled with desulfurization has allowed ligation at several new ligation junctions. However, desulfurization also converts all cysteine residues in the protein sequence into alanine. Deselenization of selenocysteine, in contrast, selectively removes the selenol group to give alanine in the presence of unprotected cysteines. In this study we shed more light onto the deselenization mechanism of selenocysteine to alanine and provide optimized conditions for the reaction. The deselenization can be accomplished in one minute under anaerobic conditions to give alanine. Under aerobic conditions (oxygen saturation), selenocysteine is converted into serine.
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Affiliation(s)
- Shahar Dery
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - Post Sai Reddy
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - Linoy Dery
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | - Reem Mousa
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
| | | | - Norman Metanis
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel .
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46
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47
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Seenaiah M, Jbara M, Mali SM, Brik A. Convergent Versus Sequential Protein Synthesis: The Case of Ubiquitinated and Glycosylated H2B. Angew Chem Int Ed Engl 2015; 54:12374-8. [DOI: 10.1002/anie.201503309] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/13/2015] [Indexed: 11/11/2022]
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48
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Seenaiah M, Jbara M, Mali SM, Brik A. Convergent Versus Sequential Protein Synthesis: The Case of Ubiquitinated and Glycosylated H2B. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503309] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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49
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Tsuda S, Yoshiya T, Mochizuki M, Nishiuchi Y. Synthesis of Cysteine-Rich Peptides by Native Chemical Ligation without Use of Exogenous Thiols. Org Lett 2015; 17:1806-9. [DOI: 10.1021/acs.orglett.5b00624] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shugo Tsuda
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
| | | | - Yuji Nishiuchi
- Peptide Institute, Inc., Ibaraki, Osaka 567-0085, Japan
- Graduate
School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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50
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Malins LR, Payne RJ. Synthetic Amino Acids for Applications in Peptide Ligation–Desulfurization Chemistry. Aust J Chem 2015. [DOI: 10.1071/ch14568] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Native chemical ligation is a powerful tool for the convergent assembly of homogeneous peptide and protein targets from unprotected peptide fragments. The method involves the chemoselective coupling of a peptide thioester with a peptide bearing an N-terminal cysteine (Cys) residue and is mediated by the nucleophilic Cys thiol functionality. A widely adopted extension of the technique for the disconnection of protein targets at alanine (Ala) ligation junctions has been the application of post-ligation desulfurization protocols for the mild removal of the Cys thiol moiety. Recently, attention has turned to the construction of synthetic amino acid building blocks bearing suitably positioned β-, γ-, or δ-thiol ligation auxiliaries with a view to expanding the scope of the ligation–desulfurization manifold. To date, several thiol-derived amino acids have been prepared, greatly increasing the generality and flexibility of chemoselective ligation technologies for the chemical synthesis of diverse protein targets. This review will highlight the current synthetic approaches to these important amino acid building blocks.
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