1
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Liu GX, Jie XT, Niu GJ, Yang LS, Li XL, Luo J, Hu WH. Palladium-catalyzed three-component radical-polar crossover carboamination of 1,3-dienes or allenes with diazo esters and amines. Beilstein J Org Chem 2024; 20:661-671. [PMID: 38590540 PMCID: PMC10999982 DOI: 10.3762/bjoc.20.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Herein, we report a visible-light-mediated palladium-catalyzed three-component radical-polar crossover carboamination of 1,3-dienes or allenes with diazo esters and amines, affording unsaturated γ- and ε-amino acid derivatives with diverse structures. In this methodology, the diazo compound readily transforms into a hybrid α-ester alkylpalladium radical with the release of dinitrogen. The radical intermediate selectively adds to the double bond of a 1,3-diene or allene, followed by the allylpalladium radical-polar crossover path and selective allylic substitution with the amine substrate, thereby leading to a single unsaturated γ- or ε-amino acid derivative. This approach proceeds under mild and simple reaction conditions and shows high functional group tolerance, especially in the incorporation of various bioactive molecules. The studies on scale-up reactions and diverse derivatizations highlight the practical utility of this multicomponent reaction protocol.
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Affiliation(s)
- Geng-Xin Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Xiao-Ting Jie
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Ge-Jun Niu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Li-Sheng Yang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Xing-Lin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Jian Luo
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Wen-Hao Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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2
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Dalal A, Bodak S, Babu SA. Picolinamide-assisted ortho-C-H functionalization of pyrenylglycine derivatives using aryl iodides. Org Biomol Chem 2024; 22:1279-1298. [PMID: 38258893 DOI: 10.1039/d3ob01731a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Chemical transformations involving the pyrenylglycine motif (an unnatural amino acid) and practical methods toward it are seldom known. This work aimed at developing a method for synthesizing novel pyrenylglycine (pyrene-based glycine) unnatural amino acid derivatives. To realize this, initially, a new pyrenylglycine substrate possessing the picolinamide moiety was assembled via the Ugi multicomponent reaction. The picolinamide moiety linked to amine substrates is a well-known bidentate directing group for accomplishing the site-selective γ-C-H functionalization of amines. Subsequently, it was aimed at using a Pd(II)-catalyzed bidentate directing group-aided γ-C-H arylation strategy for generating a wide range of unprecedented examples of C(2)-H arylated pyrenylglycines. Accordingly, pyrenylglycine possessing the picolinamide moiety was subjected to Pd(II)-catalyzed C(2)-H arylation in the non-K-region to afford a library of C(2)-arylated pyrenylglycines (π-extended pyrenes). Additionally, pyrenylglycine-based small peptides were assembled using C(2)-arylated pyrenylglycines. The X-ray structure of a representative compound was obtained, which corroborated the structure of pyrenylglycine and the regioselectivity of C(2)-H arylation of the pyrene in the non-K-region.
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Affiliation(s)
- Arup Dalal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Subhankar Bodak
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306, India.
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3
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Terasawa K, Seike T, Sakamoto K, Ohtake K, Terada T, Iwata T, Watabe T, Yokoyama S, Hara‐Yokoyama M. Site-specific photo-crosslinking/cleavage for protein-protein interface identification reveals oligomeric assembly of lysosomal-associated membrane protein type 2A in mammalian cells. Protein Sci 2023; 32:e4823. [PMID: 37906694 PMCID: PMC10659947 DOI: 10.1002/pro.4823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023]
Abstract
Genetic code expansion enables site-specific photo-crosslinking by introducing photo-reactive non-canonical amino acids into proteins at defined positions during translation. This technology is widely used for analyzing protein-protein interactions and is applicable in mammalian cells. However, the identification of the crosslinked region still remains challenging. Here, we developed a new method to identify the crosslinked region by pre-installing a site-specific cleavage site, an α-hydroxy acid (Nε -allyloxycarbonyl-α-hydroxyl-l-lysine acid, AllocLys-OH), into the target protein. Alkaline treatment cleaves the crosslinked complex at the position of the α-hydroxy acid residue and thus helps to identify which side of the cleavage site, either closer to the N-terminus or C-terminus, the crosslinked site is located within the target protein. A series of AllocLys-OH introductions narrows down the crosslinked region. By applying this method, we identified the crosslinked regions in lysosomal-associated membrane protein type 2A (LAMP2A), a receptor of chaperone-mediated autophagy, in mammalian cells. The results suggested that at least two interfaces are involved in the homophilic interaction, which requires a trimeric or higher oligomeric assembly of adjacent LAMP2A molecules. Thus, the combination of site-specific crosslinking and site-specific cleavage promises to be useful for revealing binding interfaces and protein complex geometries.
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Affiliation(s)
- Kazue Terasawa
- Department of Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
- LiberoThera Co., Ltd.Chuo‐kuJapan
| | - Tatsuro Seike
- Department of Periodontology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Kensaku Sakamoto
- Laboratory for Nonnatural Amino Acid TechnologyRIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
- Department of Drug Target Protein ResearchShinshu University School of MedicineNaganoJapan
| | - Kazumasa Ohtake
- Laboratory for Nonnatural Amino Acid TechnologyRIKEN Center for Biosystems Dynamics ResearchYokohamaJapan
- Department of Electrical Engineering and BioscienceWaseda UniversityTokyoJapan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Shigeyuki Yokoyama
- Department of Drug Target Protein ResearchShinshu University School of MedicineNaganoJapan
- Laboratory for Protein Function and Structural BiologyRIKEN Cluster for Science, Technology and Innovation HubYokohamaJapan
- Department of Structural Biology and Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
| | - Miki Hara‐Yokoyama
- Department of Biochemistry, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
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4
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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [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: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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5
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Hecht SM. Expansion of the Genetic Code Through the Use of Modified Bacterial Ribosomes. J Mol Biol 2022; 434:167211. [PMID: 34419431 PMCID: PMC9990327 DOI: 10.1016/j.jmb.2021.167211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Biological protein synthesis is mediated by the ribosome, and employs ~20 proteinogenic amino acids as building blocks. Through the use of misacylated tRNAs, presently accessible by any of several strategies, it is now possible to employ in vitro and in vivo protein biosynthesis to elaborate proteins containing a much larger variety of amino acid building blocks. However, the incorporation of this broader variety of amino acids is limited to those species utilized by the ribosome. As a consequence, virtually all of the substrates utilized over time have been L-α-amino acids. In recent years, a variety of structural and biochemical studies have provided important insights into those regions of the 23S ribosomal RNA that are involved in peptide bond formation. Subsequent experiments, involving the randomization of key regions of 23S rRNA required for peptide bond formation, have afforded libraries of E. coli harboring plasmids with the rrnB gene modified in the key regions. Selections based on the use of modified puromycin derivatives with altered amino acids then identified clones uniquely sensitive to individual puromycin derivatives. These clones often recognized misacylated tRNAs containing altered amino acids similar to those in the modified puromycins, and incorporated the amino acid analogues into proteins. In this fashion, it has been possible to realize the synthesis of proteins containing D-amino acids, β-amino acids, phosphorylated amino acids, as well as long chain and cyclic amino acids in which the nucleophilic amino group is not in the α-position. Of special interest have been dipeptides and dipeptidomimetics of diverse utility.
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Affiliation(s)
- Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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6
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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7
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Tomar R, Suwasia S, Choudhury AR, Venkataramani S, Babu SA. Azobenzene-based unnatural amino acid scaffolds via a Pd( ii)-catalyzed C(sp 3)–H arylation strategy. Chem Commun (Camb) 2022; 58:12967-12970. [DOI: 10.1039/d2cc04870a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Azobenzene-based unnatural amino acid motifs were constructed via the Pd(ii)-catalyzed diastereoselective β-C(sp3)–H arylation and Mills azo coupling tactics.
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Affiliation(s)
- Radha Tomar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Sonam Suwasia
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Sugumar Venkataramani
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
| | - Srinivasarao Arulananda Babu
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Manauli P.O. 140306, Mohali, Punjab, India
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8
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Woldegiorgis AG, Han Z, Lin X. Chiral Phosphoric Acid‐Catalyzed Enantioselective Synthesis of Pyrazole‐Based Unnatural α‐Amino Acid Derivatives. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alemayehu Gashaw Woldegiorgis
- Center of Chemistry for Frontier Technologies, Department of Chemistry Zhejiang University Hangzhou 310027 People's Republic of China
| | - Zhao Han
- Center of Chemistry for Frontier Technologies, Department of Chemistry Zhejiang University Hangzhou 310027 People's Republic of China
| | - Xufeng Lin
- Center of Chemistry for Frontier Technologies, Department of Chemistry Zhejiang University Hangzhou 310027 People's Republic of China
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9
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Yi H, Zhang J, Ke F, Guo X, Yang J, Xie P, Liu L, Wang Q, Gao X. Comparative Analyses of the Transcriptome and Proteome of Escherichia coli C321.△A and Further Improving Its Noncanonical Amino Acids Containing Protein Expression Ability by Integration of T7 RNA Polymerase. Front Microbiol 2021; 12:744284. [PMID: 34659179 PMCID: PMC8511705 DOI: 10.3389/fmicb.2021.744284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/30/2021] [Indexed: 01/09/2023] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) into proteins has been proven to be a powerful tool to manipulate protein structure and function, and to investigate many biological processes. Improving the yields of ncAA-containing proteins is of great significance in industrial-scale applications. Escherichia coli C321.ΔA was generated by the replacement of all known amber codons and the deletion of RF1 in the genome and has been proven to be an ideal host for ncAA-containing protein expression using genetic code expansion. In this study, we investigated the transcriptome and proteome profiles of this first codon reassignment strain and found that some functions and metabolic pathways were differentially expressed when compared with those of its parent strain. Genes involved in carbohydrate and energy metabolism were remarkably downregulated. Our results may provide important clues about the growth defects in E. coli C321.ΔA. Furthermore, we improved the yields of ncAA-containing proteins in E. coli C321.ΔA by integrating the T7 RNA polymerase system.
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Affiliation(s)
- Huawei Yi
- Clinical Laboratory, The First Affiliated Hospital of Yangtze University, Jingzhou, China
| | - Jing Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Famin Ke
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiurong Guo
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jian Yang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Peijuan Xie
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Li Liu
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Qin Wang
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiaowei Gao
- School of Pharmacy, Southwest Medical University, Luzhou, China.,Department of Chemistry, Zhejiang University, Hangzhou, China
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10
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Fankhauser D, Alissandratos A, Liutkus M, Easton CJ. Easy Production of "Difficult Peptides" Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site. Chemistry 2021; 27:17487-17494. [PMID: 34651362 DOI: 10.1002/chem.202103161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 11/08/2022]
Abstract
Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.
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Affiliation(s)
- Daniel Fankhauser
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Mantas Liutkus
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
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11
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Zhang C, Talukder P, Dedkova LM, Hecht SM. Facilitated synthesis of proteins containing modified dipeptides. Bioorg Med Chem 2021; 41:116210. [PMID: 34022527 DOI: 10.1016/j.bmc.2021.116210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
The elaboration of peptides and proteins containing non-proteinogenic amino acids has been realized using several complementary strategies, including chemical synthesis, ribosome- or non-ribosome-mediated elaboration, intein-mediated polypeptide rearrangements, or some combination of these strategies. All of these have strengths and limitations, and significant efforts have been focused on minimizing the effects of limitations, to improve the overall utility of individual strategies. Our laboratory has studied ribosomally mediated peptide and protein synthesis involving a wide variety of non-proteinogenic amino acids, and in recent years we have described a novel strategy for the selection of modified bacterial ribosomes. These modified ribosomes have enabled the incorporation into peptides and proteins of numerous modified amino acids not accessible using wild-type ribosomes. This has included d-amino acids, β-amino acids, dipeptides and dipeptidomimetic species, as well as phosphorylated amino acids. Presently, we have considered novel strategies for incorporating non-proteinogenic amino acids in improved yields. This has included the incorporation of non-proteinogenic amino acids into contiguous positions, a transformation known to be challenging. We demonstrate the preparation of this type of protein modification by utilizing a suppressor tRNACUA activated with a dipeptide consisting of two identical non-proteinogenic amino acids, in the presence of modified ribosomes selected to recognize such dipeptides. Also, we demonstrate that the use of bis-aminoacylated suppressor tRNAs, shown previously to increase protein yields significantly in vitro, can be extended to the use of non-proteinogenic amino acids.
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Affiliation(s)
- Chao Zhang
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
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12
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Cao W, Zhang H, Yuan Q, Zhou X, Kass SR, Wang XB. Observation of Conformational Simplification upon N-Methylation on Amino Acid Iodide Clusters. J Phys Chem Lett 2021; 12:2780-2787. [PMID: 33710892 DOI: 10.1021/acs.jpclett.1c00125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This Letter reports a counterintuitive observation that methylation of the glycine-iodide cluster leads to fewer conformations and spectroscopic simplicity. Cryogenic "iodide-tagging" negative ion photoelectron spectroscopy (NIPES) is used to probe specific binding sites of three N-methylated glycine derivatives, i.e., N-methylglycine (sarcosine), N,N-dimethylglycine, and N,N,N-trimethylglycine (glycine betaine). NIPES reveals a progressive spectral simplification of the iodide clusters with increasing methylation due to fewer contributing structures. Low energy conformers and tautomers of each cluster are computationally identified, and those observed in the experiments are assigned based on excellent agreement between the NIPE spectra and theoretical simulations. Zwitterionic cluster structures are found to be less stable than their canonical forms and do not contribute to the observed spectra. This work demonstrates the power of iodide-tagging NIPES in probing conformations of amino acid-iodide clusters and provides a molecular level understanding on the effect of methyl substitution on amino acid binding sites.
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Affiliation(s)
- Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Hanhui Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiaoguo Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Steven R Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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13
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Davison RT, Parker PD, Hou X, Chung CP, Augustine SA, Dong VM. Enantioselective Addition of α-Nitroesters to Alkynes. Angew Chem Int Ed Engl 2021; 60:4599-4603. [PMID: 33411337 DOI: 10.1002/anie.202014015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/16/2020] [Indexed: 11/11/2022]
Abstract
By using Rh-H catalysis, we couple α-nitroesters and alkynes to prepare α-amino-acid precursors. This atom-economical strategy generates two contiguous stereocenters, with high enantio- and diastereocontrol. In this transformation, the alkyne undergoes isomerization to generate a RhIII -π-allyl electrophile, which is trapped by an α-nitroester nucleophile. A subsequent reduction with In powder transforms the allylic α-nitroesters to the corresponding α,α-disubstituted α-amino esters.
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Affiliation(s)
- Ryan T Davison
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Patrick D Parker
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Xintong Hou
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Crystal P Chung
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Sara A Augustine
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Vy M Dong
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
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14
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Davison RT, Parker PD, Hou X, Chung CP, Augustine SA, Dong VM. Enantioselective Addition of α‐Nitroesters to Alkynes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ryan T. Davison
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Patrick D. Parker
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Xintong Hou
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Crystal P. Chung
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Sara A. Augustine
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Vy M. Dong
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
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15
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Staszek P, Gniazdowska A. Peroxynitrite induced signaling pathways in plant response to non-proteinogenic amino acids. PLANTA 2020; 252:5. [PMID: 32535658 PMCID: PMC7293691 DOI: 10.1007/s00425-020-03411-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/06/2020] [Indexed: 05/02/2023]
Abstract
Nitro/oxidative modifications of proteins and RNA nitration resulted from altered peroxynitrite generation are elements of the indirect mode of action of canavanine and meta-tyrosine in plants Environmental conditions and stresses, including supplementation with toxic compounds, are known to impair reactive oxygen (ROS) and reactive nitrogen species (RNS) homeostasis, leading to modification in production of oxidized and nitrated derivatives. The role of nitrated and/or oxidized biotargets differs depending on the stress factors and developmental stage of plants. Canavanine (CAN) and meta-tyrosine (m-Tyr) are non-proteinogenic amino acids (NPAAs). CAN, the structural analog of arginine, is found mostly in seeds of Fabaceae species, as a storage form of nitrogen. In mammalian cells, CAN is used as an anticancer agent due to its inhibitory action on nitric oxide synthesis. m-Tyr is a structural analogue of phenylalanine and an allelochemical found in root exudates of fescues. In animals, m-Tyr is recognized as a marker of oxidative stress. Supplementation of plants with CAN or m-Tyr modify ROS and RNS metabolism. Over the last few years of our research, we have collected the complex data on ROS and RNS metabolism in tomato (Solanum lycopersicum L.) plants exposed to CAN or m-Tyr. In addition, we have shown the level of nitrated RNA (8-Nitro-guanine) in roots of seedlings, stressed by the tested NPAAs. In this review, we describe the model of CAN and m-Tyr mode of action in plants based on modifications of signaling pathways induced by ROS/RNS with a special focus on peroxynitrite induced RNA and protein modifications.
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Affiliation(s)
- Pawel Staszek
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
| | - Agnieszka Gniazdowska
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
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16
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Seligmann H, Warthi G. Natural pyrrolysine-biased translation of stop codons in mitochondrial peptides entirely coded by expanded codons. Biosystems 2020; 196:104180. [PMID: 32534170 DOI: 10.1016/j.biosystems.2020.104180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/02/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022]
Abstract
During the noncanonical deletion transcription, k nucleotides are systematically skipped/deleted after each transcribed trinucleotide producing deletion-RNAs (delRNAs). Peptides matching delRNAs either result from (a) canonical translation of delRNAs; or (b) noncanonical translation of regular transcripts along expanded codons. Only along frame "0" (start site) (a) and (b) produce identical peptides. Here, mitochondrial mass spectrometry data analyses assume expanded codon/del-transcription with 3 + k (k from 0 to 12) nucleotides. Detected peptides map preferentially on previously identified delRNAs. More peptides were detected for k (1-12) when del-transcriptional and expanded codon translations start sites coincide (i.e. the 0th frame) than for frames +1 or +2. Hence, both (a) and (b) produced peptides identified here. Biases for frame 0 decrease for k > 2, reflecting codon/anticodon expansion limits. Further analyses find preferential pyrrolysine insertion at stop codons, suggesting Pyl-specific mitochondrial suppressor tRNAs loaded by Pyl-specific tRNA synthetases with unknown origins. Pyl biases at stops are stronger for regular than expanded codons suggesting that Pyl-tRNAs are less competitive with near-cognate tRNAs in expanded codon contexts. Statistical biases for these findings exclude that detected peptides are experimental and/or bioinformatic artefacts implying both del-transcription and expanded codons translation occur in human mitochondria.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel; Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700, La Tronche, France.
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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17
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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18
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Hintzen JCJ, Poater J, Kumar K, Al Temimi AHK, Pieters BJGE, Paton RS, Bickelhaupt FM, Mecinović J. Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins. Molecules 2020; 25:molecules25081918. [PMID: 32326252 PMCID: PMC7221964 DOI: 10.3390/molecules25081918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 01/31/2023] Open
Abstract
Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish whether trimethylthialysine, a simple trimethyllysine analogue generated through cysteine alkylation, is a good trimethyllysine mimic for studies on molecular recognition by reader proteins. Histone peptides bearing trimethylthialysine and trimethyllysine were examined for binding with five human reader proteins employing a combination of thermodynamic analyses, molecular dynamics simulations and quantum chemical analyses. Collectively, our experimental and computational findings reveal that trimethylthialysine and trimethyllysine exhibit very similar binding characteristics for the association with human reader proteins, thereby justifying the use of trimethylthialysine for studies aimed at dissecting the origin of biomolecular recognition in epigenetic processes that play important roles in human health and disease.
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Affiliation(s)
- Jordi C. J. Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi Poater
- ICREA and Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí I Franquès 1–11, 08028 Barcelona, Spain
| | - Kiran Kumar
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Abbas H. K. Al Temimi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
| | - Bas J. G. E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
| | - Robert S. Paton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
- Correspondence: (R.S.P.); (F.M.B.); (J.M.); Tel.: +45-6550-3603 (J.M.)
| | - F. Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
- Correspondence: (R.S.P.); (F.M.B.); (J.M.); Tel.: +45-6550-3603 (J.M.)
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6522 AJ Nijmegen, The Netherlands
- Correspondence: (R.S.P.); (F.M.B.); (J.M.); Tel.: +45-6550-3603 (J.M.)
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19
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Weitzel CS, Li L, Zhang C, Eilts KK, Bretz NM, Gatten AL, Whitaker RJ, Martinis SA. Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. J Biol Chem 2020; 295:4563-4576. [PMID: 32102848 DOI: 10.1074/jbc.ra118.006481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are ancient enzymes that play a fundamental role in protein synthesis. They catalyze the esterification of specific amino acids to the 3'-end of their cognate tRNAs and therefore play a pivotal role in protein synthesis. Although previous studies suggest that aaRS-dependent errors in protein synthesis can be beneficial to some microbial species, evidence that reduced aaRS fidelity can be adaptive is limited. Using bioinformatics analyses, we identified two distinct leucyl-tRNA synthetase (LeuRS) genes within all genomes of the archaeal family Sulfolobaceae. Remarkably, one copy, designated LeuRS-I, had key amino acid substitutions within its editing domain that would be expected to disrupt hydrolytic editing of mischarged tRNALeu and to result in variation within the proteome of these extremophiles. We found that another copy, LeuRS-F, contains canonical active sites for aminoacylation and editing. Biochemical and genetic analyses of the paralogs within Sulfolobus islandicus supported the hypothesis that LeuRS-F, but not LeuRS-I, functions as an essential tRNA synthetase that accurately charges leucine to tRNALeu for protein translation. Although LeuRS-I was not essential, its expression clearly supported optimal S. islandicus growth. We conclude that LeuRS-I may have evolved to confer a selective advantage under the extreme and fluctuating environmental conditions characteristic of the volcanic hot springs in which these archaeal extremophiles reside.
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Affiliation(s)
| | - Li Li
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Kristen K Eilts
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Nicholas M Bretz
- Department of Chemistry, Illinois State University, Normal, Illinois 61761
| | - Alex L Gatten
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
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20
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Liu X, Boron M, Zhao Y, Sun XL. End-point modification of recombinant thrombomodulin with enhanced stability and anticoagulant activity. Eur J Pharm Sci 2019; 139:105066. [PMID: 31513922 PMCID: PMC6767613 DOI: 10.1016/j.ejps.2019.105066] [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: 05/21/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/17/2022]
Abstract
Thrombomodulin (TM) is an endothelial cell membrane protein that plays essential roles in controlling vascular haemostatic balance. The 4, 5, 6 EGF-like domain of TM (TM456) has cofactor activity for thrombin binding and subsequently protein C activation. Therefore, recombinant TM456 is a promising anticoagulant candidate but has a very short half-life. Ligation of poly (ethylene glycol) to a bioactive protein (PEGylation) is a practical choice to improve stability, extend circulating life, and reduce immunogenicity of the protein. Site-specific PEGylation is preferred as it could avoid the loss of protein activity resulting from nonspecific modification. We report herein two site-specific PEGylation strategies, enzymatic ligation and copper-free click chemistry (CFCC), for rTM456 modification. Recombinant TM456 with a C-terminal LPETG tag (rTM456-LPETG) was expressed in Escherichia coli for its end-point modification with NH2-diglycine-PEG5000-OMe via Sortase A-mediated ligation (SML). Similarly, an azide functionality was easily introduced at the C-terminus of rTM456-LPETG via SML with NH2-diglycine-PEG3-azide, which facilitates a site-specific PEGylation of rTM456via CFCC. Both PEGylated rTM456 conjugates retained protein C activation activity as that of rTM456. Also, they were more stable than rTM456 in Trypsin digestion assay. Further, both PEGylated rTM456 conjugates showed a concentration-dependent prolongation of thrombin clotting time (TCT) compared to non-modified protein, which confirms the effectiveness of these two site-specific PEGylation schemes.
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Affiliation(s)
- Xia Liu
- Department of Chemistry, Chemical and Biomedical Engineering and Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, 2121 Euclid Ave, Cleveland, OH 44115, USA; Biology Teaching and Research Section, Key Laboratory of Tumor Prevention and Treatment of Heilongjiang Province, School of Basic Medical Sciences, Mudanjiang Medical University, Mudanjiang, Heilongjiang Province 157011, China
| | - Mallorie Boron
- Department of Chemistry, Chemical and Biomedical Engineering and Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, 2121 Euclid Ave, Cleveland, OH 44115, USA
| | - Yu Zhao
- Department of Chemistry, Chemical and Biomedical Engineering and Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, 2121 Euclid Ave, Cleveland, OH 44115, USA
| | - Xue-Long Sun
- Department of Chemistry, Chemical and Biomedical Engineering and Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, 2121 Euclid Ave, Cleveland, OH 44115, USA.
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21
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Seligmann H, Warthi G. Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons. Comput Struct Biotechnol J 2019; 17:1195-1202. [PMID: 31534643 PMCID: PMC6742854 DOI: 10.1016/j.csbj.2019.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023] Open
Abstract
Frameshifting protein translation occasionally results from insertion of amino acids at isolated mono- or dinucleotide-expanded codons by tRNAs with expanded anticodons. Previous analyses of two different types of human mitochondrial MS proteomic data (Fisher and Waters technologies) detect peptides entirely corresponding to expanded codon translation. Here, these proteomic data are reanalyzed searching for peptides consisting of at least eight consecutive amino acids translated according to regular tricodons, and at least eight adjacent consecutive amino acids translated according to expanded codons. Both datasets include chimerically translated peptides (mono- and dinucleotide expansions, 42 and 37, respectively). The regular tricodon-encoded part of some chimeric peptides corresponds to standard human mitochondrial proteins (mono- and dinucleotide expansions, six (AT6, CytB, ND1, 2xND2, ND5) and one (ND1), respectively). Chimeric translation probably increases the diversity of mitogenome-encoded proteins, putatively producing functional proteins. These might result from translation by tRNAs with expanded anticodons, or from regular tricodon translation of RNAs where transcription/posttranscriptional edition systematically deleted mono- or dinucleotides after each trinucleotide. The pairwise matched combination of adjacent peptide parts translated from regular and expanded codons strengthens the hypothesis that translation of stretches of consecutive expanded codons occurs. Results indicate statistical translation producing distributions of alternative proteins. Genetic engineering should account for potential unexpected, unwanted secondary products.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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22
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Smolskaya S, Andreev YA. Site-Specific Incorporation of Unnatural Amino Acids into Escherichia coli Recombinant Protein: Methodology Development and Recent Achievement. Biomolecules 2019; 9:biom9070255. [PMID: 31261745 PMCID: PMC6681230 DOI: 10.3390/biom9070255] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 12/13/2022] Open
Abstract
More than two decades ago a general method to genetically encode noncanonical or unnatural amino acids (NAAs) with diverse physical, chemical, or biological properties in bacteria, yeast, animals and mammalian cells was developed. More than 200 NAAs have been incorporated into recombinant proteins by means of non-endogenous aminoacyl-tRNA synthetase (aa-RS)/tRNA pair, an orthogonal pair, that directs site-specific incorporation of NAA encoded by a unique codon. The most established method to genetically encode NAAs in Escherichia coli is based on the usage of the desired mutant of Methanocaldococcus janaschii tyrosyl-tRNA synthetase (MjTyrRS) and cognate suppressor tRNA. The amber codon, the least-used stop codon in E. coli, assigns NAA. Until very recently the genetic code expansion technology suffered from a low yield of targeted proteins due to both incompatibilities of orthogonal pair with host cell translational machinery and the competition of suppressor tRNA with release factor (RF) for binding to nonsense codons. Here we describe the latest progress made to enhance nonsense suppression in E. coli with the emphasis on the improved expression vectors encoding for an orthogonal aa-RA/tRNA pair, enhancement of aa-RS and suppressor tRNA efficiency, the evolution of orthogonal EF-Tu and attempts to reduce the effect of RF1.
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Affiliation(s)
- Sviatlana Smolskaya
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8, bld. 2, 119991 Moscow, Russia.
| | - Yaroslav A Andreev
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8, bld. 2, 119991 Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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23
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Chen Z, Kondrashina A, Greco I, Gamon LF, Lund MN, Giblin L, Davies MJ. Effects of Protein-Derived Amino Acid Modification Products Present in Infant Formula on Metabolic Function, Oxidative Stress, and Intestinal Permeability in Cell Models. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5634-5646. [PMID: 31017422 DOI: 10.1021/acs.jafc.9b01324] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteins present in infant formulas are modified by oxidation and glycation during processing. Modified amino acid residues released from proteins may be absorbed in the gastrointestinal tract, and pose a health risk to infants. In this study, the markers of glycation furosine (1.7-3.5 μg per milligram of protein) and Nε-(carboxymethyl)lysine (28-81 ng per milligram of protein) were quantitated in infant formulas. The effects of these species, and other amino acid modifications, at the levels detected in infant formulas, on 3T3-L1 (murine preadipocyte) and Caco-2 (human intestinal epithelial) cells were assessed. Incubation of 3T3-L1 cells for 48 h with amino acid side chain oxidation and glycation products (1 and 10 μM) resulted in a loss (up to 40%, p < 0.05) of cell thiols and decreased metabolic activity compared with those of the controls. In contrast, Caco-2 cells showed a stimulation (10-50%, p < 0.05) of cellular metabolism on exposure to these products for 24 or 48 h. A 28% ( p < 0.05) increase in protein carbonyls was detected upon incubation with 200 μM modified amino acids for 48 h, although no alteration in transepithelial electrical resistance was detected. Oxidation products were detected in the basolateral compartments of Caco-2 monolayers when modified amino acids were applied to the apical side, consistent with limited permeability (up to 3.4%) across the monolayer. These data indicate that modified amino acids present in infant formulas can induce effects on different cell types, with evidence of bioavailability and induction of cellular stress. This may lead to potential health risks for infants consistently exposed to high levels of infant formulas.
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Affiliation(s)
- Zhifei Chen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Alina Kondrashina
- Teagasc Food Research Centre , Moorepark, Fermoy , County Cork , Ireland
| | - Ines Greco
- Department of Food Science, Faculty of Science , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Luke F Gamon
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Marianne N Lund
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen 2200 , Denmark
- Department of Food Science, Faculty of Science , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Linda Giblin
- Teagasc Food Research Centre , Moorepark, Fermoy , County Cork , Ireland
| | - Michael J Davies
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences , University of Copenhagen , Copenhagen 2200 , Denmark
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24
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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25
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Chen S, Ji X, Gao M, Dedkova LM, Hecht SM. In Cellulo Synthesis of Proteins Containing a Fluorescent Oxazole Amino Acid. J Am Chem Soc 2019; 141:5597-5601. [PMID: 30889951 DOI: 10.1021/jacs.8b12767] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic code expansion has enabled many noncanonical amino acids to be incorporated into proteins in vitro and in cellulo. These have largely involved α-l-amino acids, reflecting the substrate specificity of natural aminoacyl-tRNA synthetases and ribosomes. Recently, modified E. coli ribosomes, selected using a dipeptidylpuromycin analogue, were employed to incorporate dipeptides and dipeptidomimetics. Presently, we report the in cellulo incorporation of a strongly fluorescent oxazole amino acid (lacking an asymmetric center or α-amino group) by using modified ribosomes and pyrrolysyl-tRNA synthetase (PylRS). Initially, a plasmid encoding the RRM1 domain of putative transcription factor hnRNP LL was cotransformed with plasmid pTECH-Pyl-OP in E. coli cells, having modified ribosomes able to incorporate dipeptides. Cell incubation in a medium containing oxazole 2 resulted in the elaboration of RRM1 containing the oxazole. Green fluorescent protein, previously expressed in vitro with several different oxazole amino acids at position 66, was also expressed in cellulo containing oxazole 2; the incorporation was verified by mass spectrometry. Finally, oxazole 2 was incorporated into position 13 of MreB, a bacterial homologue of eukaryotic cytoskeletal protein actin F. Modified MreB expressed in vitro and in cellulo comigrated with wild type. E. coli cells expressing the modified MreB were strongly fluorescent and retained the E. coli cell rod-like phenotype. For each protein studied, the incorporation of oxazole 2 strongly increased oxazole fluorescence, suggesting its potential utility as a protein tag. These findings also suggest the feasibility of dramatically increasing the repertoire of amino acids that can be genetically encoded for protein incorporation in cellulo.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xun Ji
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Mingxuan Gao
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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26
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Abstract
Fourier transform infrared (FTIR) spectroscopy has become one of the major techniques of structural characterization of proteins, peptides, and protein-membrane interactions. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or intermolecular interactions. The sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as 13C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, the structural features of membrane pore forming proteins and peptides, and much more. The purpose of this chapter was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, is also presented.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
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27
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Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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28
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Just D, Hernandez-Guerra D, Kritsch S, Pohl R, Císařová I, Jones PG, Mackman R, Bahador G, Jahn U. Lithium Chloride Catalyzed Asymmetric Domino Aza-Michael Addition/[3 + 2] Cycloaddition Reactions for the Synthesis of Spiro- and Bicyclic α,β,γ-Triamino Acid Derivatives. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Daniel Hernandez-Guerra
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Susanne Kritsch
- Fachbereich Chemie; Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry; Faculty of Science; Charles University; Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Peter G. Jones
- Fachbereich Chemie; Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Richard Mackman
- Gilead Sciences, Inc.; 333 Lakeside Drive 94404 Foster City CA USA
| | - Gina Bahador
- Gilead Sciences, Inc.; 333 Lakeside Drive 94404 Foster City CA USA
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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29
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De Filippis V, Pozzi N, Acquasaliente L, Artusi I, Pontarollo G, Peterle D. Protein engineering by chemical methods: Incorporation of nonnatural amino acids as a tool for studying protein folding, stability, and function. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Nicola Pozzi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Ilaria Artusi
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry, Department of Pharmaceutical & Pharmacological SciencesUniversity of Padua Padua Italy
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30
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Czapla M, Freza S. Functionalized ACC molecule as an effective peptide clasp. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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31
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Ramarathinam SH, Gras S, Alcantara S, Yeung AWS, Mifsud NA, Sonza S, Illing PT, Glaros EN, Center RJ, Thomas SR, Kent SJ, Ternette N, Purcell DFJ, Rossjohn J, Purcell AW. Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics. Proteomics 2018; 18:e1700253. [PMID: 29437277 DOI: 10.1002/pmic.201700253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/29/2018] [Indexed: 12/20/2022]
Abstract
The recognition of pathogen-derived peptides by T lymphocytes is the cornerstone of adaptive immunity, whereby intracellular antigens are degraded in the cytosol and short peptides assemble with class I human leukocyte antigen (HLA) molecules in the ER. These peptide-HLA complexes egress to the cell surface and are scrutinized by cytotoxic CD8+ T-cells leading to the eradication of the infected cell. Here, naturally presented HLA-B*57:01 bound peptides derived from the envelope protein of the human immunodeficiency virus (HIVenv) are identified. HIVenv peptides are present at a very small percentage of the overall HLA-B*57:01 peptidome (<0.1%) and both native and posttranslationally modified forms of two distinct HIV peptides are identified. Notably, a peptide bearing a natively encoded C-terminal tryptophan residue is also present in a modified form containing a kynurenine residue. Kynurenine is a major product of tryptophan catabolism and is abundant during inflammation and infection. Binding of these peptides at a molecular level and their immunogenicity in preliminary functional studies are examined. Modest immune responses are observed to the modified HIVenv peptide, highlighting a potential role for kynurenine-modified peptides in the immune response to HIV and other viral infections.
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Affiliation(s)
- Sri H Ramarathinam
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Stephanie Gras
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Amanda W S Yeung
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Secondo Sonza
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Patricia T Illing
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Elias N Glaros
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Robert J Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.,Burnet Institute, Melbourne, Australia
| | - Shane R Thomas
- Mechanisms of Disease and Translational Medicine, Department of Pathology, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.,Melbourne Sexual Health Centre, Central Clinical School, Monash University, Melbourne, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Australia
| | - Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, Oxford, UK
| | - Damian F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Anthony W Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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32
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Richardson MB, Brown DB, Vasquez CA, Ziller JW, Johnston KM, Weiss GA. Synthesis and Explosion Hazards of 4-Azido-l-phenylalanine. J Org Chem 2018; 83:4525-4536. [PMID: 29577718 DOI: 10.1021/acs.joc.8b00270] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A reliable, scalable, cost-effective, and chromatography-free synthesis of 4-azido-l-phenylalanine beginning from l-phenylalanine is described. Investigations into the safety of the synthesis reveal that the Ullman-like Cu(I)-catalyzed azidation step does not represent a significant risk. The isolated 4-azido-l-phenylalanine product, however, exhibits previously undocumented explosive characteristics.
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Affiliation(s)
- Mark B Richardson
- Department of Chemistry , University of California , 1102 Natural Sciences 2 , Irvine , California 92697-2025 , United States
| | - Derek B Brown
- Amgen Incorporated, One Amgen Center Drive , Thousand Oaks , California 91320 , United States
| | - Carlos A Vasquez
- Department of Chemistry , University of California , 1102 Natural Sciences 2 , Irvine , California 92697-2025 , United States
| | - Joseph W Ziller
- Department of Chemistry , University of California , 1102 Natural Sciences 2 , Irvine , California 92697-2025 , United States
| | - Kevin M Johnston
- Department of Chemistry , University of California , 1102 Natural Sciences 2 , Irvine , California 92697-2025 , United States
| | - Gregory A Weiss
- Department of Chemistry , University of California , 1102 Natural Sciences 2 , Irvine , California 92697-2025 , United States
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33
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De Filippis V, Acquasaliente L, Pontarollo G, Peterle D. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction. Biotechnol Appl Biochem 2018; 65:69-80. [DOI: 10.1002/bab.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
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34
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Po P, Delaney E, Gamper H, Szantai-Kis DM, Speight L, Tu L, Kosolapov A, Petersson EJ, Hou YM, Deutsch C. Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel. J Mol Biol 2017; 429:1873-1888. [PMID: 28483649 DOI: 10.1016/j.jmb.2017.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 12/17/2022]
Abstract
All proteins are synthesized by the ribosome, a macromolecular complex that accomplishes the life-sustaining tasks of faithfully decoding mRNA and catalyzing peptide bond formation at the peptidyl transferase center (PTC). The ribosome has evolved an exit tunnel to host the elongating new peptide, protect it from proteolytic digestion, and guide its emergence. It is here that the nascent chain begins to fold. This folding process depends on the rate of translation at the PTC. We report here that besides PTC events, translation kinetics depend on steric constraints on nascent peptide side chains and that confined movements of cramped side chains within and through the tunnel fine-tune elongation rates.
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Affiliation(s)
- Pengse Po
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Delaney
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - D Miklos Szantai-Kis
- Department of Biochemistry and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lee Speight
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - LiWei Tu
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrey Kosolapov
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Carol Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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35
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Nair RN, Rosnow JJ, Murphree TA, Bowden ME, Lindemann SR, Wright AT. De novo synthesis of alkyne substituted tryptophans as chemical probes for protein profiling studies. Org Chem Front 2017; 4:495-499. [PMID: 28944064 PMCID: PMC5607013 DOI: 10.1039/c6qo00819d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
De novo synthesis of alkynalted tryptophan moieties as chemical probes for protein profilling studies, via an unexpected synthesis of Michael acceptor 12 is reported. Friedel Craft's alkylation of 12 and alkyne substituted indoles gave alkynalated tryptophan moieties, which perform as chemical probe by incorporating into actively translating Escherichia coli cells, whereby the alkyne moiety enables multimodal analyses through click chemistry mediated attachment of reporting groups.
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Affiliation(s)
- R N Nair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland. WA
- R. N. Nair. Current address - David Geffen School of Medicine, Department of Psychiatry and Behavorial Sciences, University of California, Los Angeles
| | - J J Rosnow
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland. WA
| | - T A Murphree
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland. WA
| | - M E Bowden
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland. WA
| | - S R Lindemann
- S. R. Lindemann. Current address - Department of Food Science, Purdue University, West Lafayette, IN
| | - A T Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland. WA
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36
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Donaldson T, Iozzino L, Deacon LJ, Billones H, Ausili A, D'Auria S, Dattelbaum JD. Engineering a switch-based biosensor for arginine using a Thermotoga maritima periplasmic binding protein. Anal Biochem 2017; 525:60-66. [PMID: 28259516 DOI: 10.1016/j.ab.2017.02.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/26/2017] [Accepted: 02/28/2017] [Indexed: 11/26/2022]
Abstract
The Thermotoga maritima arginine-binding protein (TmArgBP) has been modified to create a reagentless fluorescent protein biosensor. Two design methods for biosensor construction are compared: 1) solvent accessibility of environmentally-sensitive probes and 2) fluorescence deactivation due to photo-induced electron transfer (PET). Nine single cysteine TmArgBP mutants were created and labeled with three different environmentally sensitive fluorescent probes. These mutants demonstrated limited changes in fluorescence emission upon the addition of arginine. In contrast, the PET-based biosensor provides significant enhancements over the traditional approach and provides a fluorescence quenching mechanism that was capable of providing quantitative detection of arginine. Site-directed mutagenesis of TmArgBP was used to create attachment points for the fluorescent probe (K145C) and for an internal aromatic residue (D18X) to serve as the PET quencher. Both tyrosine and tryptophan, but not phenylalanine, were able to quench the emission of the fluorescent probe by more than 80% upon the addition of arginine. The dissociation constant for arginine ranged from 0.87 to 1.5 μM across the different sensors. This PET-based strategy provides a simple and broadly applicable approach for the analytical detection of small molecules that may be applied to any protein that exhibits conformational switching in a ligand dependent manner.
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Affiliation(s)
- Teraya Donaldson
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
| | - Luisa Iozzino
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA; Laboratory for Molecular Sensing, ISA-CNR, Via Roma 64, 83100 Avellino, Italy
| | - Lindsay J Deacon
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
| | - Hilbert Billones
- Department of Chemistry, University of Richmond, Richmond, VA, 23173, USA
| | - Alessio Ausili
- Laboratory for Molecular Sensing, ISA-CNR, Via Roma 64, 83100 Avellino, Italy
| | - Sabato D'Auria
- Laboratory for Molecular Sensing, ISA-CNR, Via Roma 64, 83100 Avellino, Italy
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37
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Lee BS, Kim S, Ko BJ, Yoo TH. An efficient system for incorporation of unnatural amino acids in response to the four-base codon AGGA in Escherichia coli. Biochim Biophys Acta Gen Subj 2017; 1861:3016-3023. [PMID: 28212794 DOI: 10.1016/j.bbagen.2017.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Adding new amino acids to the set of building blocks for protein synthesis expands the scope of protein engineering, and orthogonal pairs of tRNA and aminoacyl-tRNA synthetase have been developed for incorporating unnatural amino acids (UAAs) into proteins. While diverse systems have been developed to incorporate UAAs in response to the amber codon, less research has been focused on four-base codons despites their advantages. In this study, we report an efficient method to incorporate UAA in response to an AGGA codon in Escherichia coli. RESULTS The Methanococcus jannaschii tyrosyl-tRNA synthetase-tRNACUA(MjTyrRS-MjtRNACUA) orthogonal pair has been engineered to incorporate diverse UAAs in response to the amber codon. To apply the engineered MjTyrRS enzymes for UAAs to a four-base codon suppression, we developed an MjTyrRS-MjtRNAUCCU pair system that enabled incorporation of UAAs in response to the AGGA codon in E. coli. Using this system, we demonstrated that several UAAs could be incorporated quantitatively in the AGGA site. In addition, multiple AGGA codons were successfully suppressed in an E. coli strain when the endogenous tRNACCUArg gene was knocked out. CONCLUSION An efficient system was developed for the incorporation of UAAs in response to the AGGA four-base codon in E. coli, and the method was successfully demonstrated for several UAAs and for multiple AGGA sites. GENERAL SIGNIFICANCE The developed system can expand the repertoire of protein engineering tools based on amino acid analogues in combination with other UAA incorporation methods. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Suyeon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Byoung Joon Ko
- New Drug Development Center, Osong Medical Innovative Foundation, 123, Osongsaengmyeong-ro, Osong-eup, Cheongju 28160, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea.
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38
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Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics. J Mol Graph Model 2016; 71:192-199. [PMID: 27939931 DOI: 10.1016/j.jmgm.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/28/2022]
Abstract
The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.
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39
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Hicks RP. Antibacterial and anticancer activity of a series of novel peptides incorporating cyclic tetra-substituted Cα amino acids. Bioorg Med Chem 2016; 24:4056-4065. [DOI: 10.1016/j.bmc.2016.06.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 11/26/2022]
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40
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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41
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Liutkus M, Fraser SA, Caron K, Stigers DJ, Easton CJ. Peptide Synthesis through Cell-Free Expression of Fusion Proteins Incorporating Modified Amino Acids as Latent Cleavage Sites for Peptide Release. Chembiochem 2016; 17:908-12. [PMID: 26918308 DOI: 10.1002/cbic.201600091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Indexed: 01/03/2023]
Abstract
Chlorinated analogues of Leu and Ile are incorporated during cell-free expression of peptides fused to protein, by exploiting the promiscuity of the natural biosynthetic machinery. They then act as sites for clean and efficient release of the peptides simply by brief heat treatment. Dehydro analogues of Leu and Ile are similarly incorporated as latent sites for peptide release through treatment with iodine under cold conditions. These protocols complement enzyme-catalyzed methods and have been used to prepare calcitonin, gastrin-releasing peptide, cholecystokinin-7, and prolactin-releasing peptide prohormones, as well as analogues substituted with unusual amino acids, thus illustrating their practical utility as alternatives to more traditional chemical peptide synthesis.
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Affiliation(s)
- Mantas Liutkus
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Samuel A Fraser
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Karine Caron
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Dannon J Stigers
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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42
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Cell-Free Synthesis of Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27165320 DOI: 10.1007/978-3-319-27216-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Cell-free protein synthesis based on E. coli cell extracts has been described for the first time more than 50 years ago. To date, cell-free synthesis is widely used for the preparation of toxic proteins, for studies of the translation process and its regulation as well as for the incorporation of artificial or labeled amino acids into a polypeptide chain. Many efforts have been directed towards establishing cell-free expression as a standard method for gene expression, with limited success. In this chapter we will describe the state-of-the-art of cell-free expression, extract preparation methods and recent examples for successful applications of cell-free synthesis of macromolecular complexes.
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43
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Cabral WF, Machado AH, Santos GM. Exogenous nucleosome-binding molecules: a potential new class of therapeutic drugs. Drug Discov Today 2016; 21:707-11. [DOI: 10.1016/j.drudis.2016.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 12/15/2022]
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44
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Clark TD, Bartolotti L, Hicks RP. The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids. Biopolymers 2016; 99:548-61. [PMID: 23712491 DOI: 10.1002/bip.22215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 01/14/2013] [Accepted: 01/25/2013] [Indexed: 11/11/2022]
Abstract
Anionic and zwitterionic micelles are often used as simple models for the lipids found in bacterial and mammalian cell membranes to investigate antimicrobial peptide-lipid interactions. In our laboratory we have employed a variety of 1D, 2D, and diffusion ordered (DOSY) NMR experiments to investigate the interactions of antimicrobial peptides containing unnatural amino acids with SDS and DPC micelles. Complete assignment of the proton spectra of these peptides is prohibited by the incorporation of a high percentage of unnatural amino acids which don't contain amide protons into the backbone. However preliminary assignment of the TOCSY spectra of compound 23 in the presence of both micelles indicated multiple conformers are present as a result of binding to these micelles. Chemical Shift Indexing agreed with previously collected CD spectra that indicated on binding to SDS micelles compound 23 adopts a mixture of α-helical structures and on binding to DPC micelles this peptide adopts a mixture of helical and β-turn/sheet like structures. DOSY NMR experiments also indicated that the total positive charge and the relative placement of that charge at the N-terminus or C-terminus are important in determining the mole fraction of the peptide that will bind to the different micelles. DOSY and (1) H-NMR experiments indicated that the length of Spacer #1 plays a major role in defining the binding conformation of these analogs with SDS micelles. Results obtained from molecular simulations studies of the binding of compounds 23 and 36 with SDS micelles were consistent with the observed NMR results.
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Affiliation(s)
- Tiffany D Clark
- Department of Chemistry, East Carolina University, Science and Technology Building, Greenville, NC 27858, USA
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45
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McKenney KM, Alfonzo JD. From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. Life (Basel) 2016; 6:E13. [PMID: 26985907 PMCID: PMC4810244 DOI: 10.3390/life6010013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/27/2016] [Accepted: 03/07/2016] [Indexed: 12/13/2022] Open
Abstract
All nucleic acids in cells are subject to post-transcriptional chemical modifications. These are catalyzed by a myriad of enzymes with exquisite specificity and that utilize an often-exotic array of chemical substrates. In no molecule are modifications more prevalent than in transfer RNAs. In the present document, we will attempt to take a chemical rollercoaster ride from prebiotic times to the present, with nucleoside modifications as key players and tRNA as the centerpiece that drove the evolution of biological systems to where we are today. These ideas will be put forth while touching on several examples of tRNA modification enzymes and their modus operandi in cells. In passing, we submit that the choice of tRNA is not a whimsical one but rather highlights its critical function as an essential invention for the evolution of protein enzymes.
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Affiliation(s)
- Katherine M McKenney
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Juan D Alfonzo
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.
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46
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Davenport KR, Smith CA, Hofstetter H, Horn JR, Hofstetter O. Site-directed immobilization of a genetically engineered anti-methotrexate antibody via an enzymatically introduced biotin label significantly increases the binding capacity of immunoaffinity columns. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:114-121. [PMID: 26809205 DOI: 10.1016/j.jchromb.2016.01.021] [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: 04/02/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
In this study, the effect of random vs. site-directed immobilization techniques on the performance of antibody-based HPLC columns was investigated using a single-domain camelid antibody (VHH) directed against methotrexate (MTX) as a model system. First, the high flow-through support material POROS-OH was activated with disuccinimidyl carbonate (DSC), and the VHH was bound in a random manner via amines located on the protein's surface. The resulting column was characterized by Frontal Affinity Chromatography (FAC). Then, two site-directed techniques were explored to increase column efficiency by immobilizing the antibody via its C-terminus, i.e., away from the antigen-binding site. In one approach, a tetra-lysine tail was added, and the antibody was immobilized onto DSC-activated POROS. In the second site-directed approach, the VHH was modified with the AviTag peptide, and a biotin-residue was enzymatically incorporated at the C-terminus using the biotin ligase BirA. The biotinylated antibody was subsequently immobilized onto NeutrAvidin-derivatized POROS. A comparison of the FAC analyses, which for all three columns showed excellent linearity (R(2)>0.999), revealed that both site-directed approaches yield better results than the random immobilization; the by far highest efficiency, however, was determined for the immunoaffinity column based on AviTag-biotinylated antibody. As proof of concept, all three columns were evaluated for quantification of MTX dissolved in phosphate buffered saline (PBS). Validation using UV-detection showed excellent linearity in the range of 0.04-12μM (R(2)>0.993). The lower limit of detection (LOD) and lower limit of quantification (LLOQ) were found to be independent of the immobilization strategy and were 40nM and 132nM, respectively. The intra- and inter-day precision was below 11.6%, and accuracy was between 90.7% and 112%. To the best of our knowledge, this is the first report of the AviTag-system in chromatography, and the first application of immunoaffinity chromatography for the analysis of MTX.
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Affiliation(s)
- Kaitlynn R Davenport
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Christopher A Smith
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Heike Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA
| | - Oliver Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115-2862, USA.
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47
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Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C, Plateau P. Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Proteins 2016; 84:240-53. [PMID: 26676967 DOI: 10.1002/prot.24972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/30/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022]
Abstract
D-Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl-tRNA synthetases (aaRSs), and this strategy might be applicable to D-amino acids. Several aaRSs can aminoacylate their tRNA with a D-amino acid; of these, tyrosyl-tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its D-Tyr binding further, relative to L-Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain L-Tyr/D-Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge-altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards D-Tyr; one of these has an inverted stereospecificity, with a large preference for D-Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled.
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Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | | | - Zoltan Palmai
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Najette Amara
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Sandra Wydau-Dematteis
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Erwan Bigan
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Karen Druart
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Clara Moch
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Pierre Plateau
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
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48
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Dinman JD. Pathways to Specialized Ribosomes: The Brussels Lecture. J Mol Biol 2016; 428:2186-94. [PMID: 26764228 DOI: 10.1016/j.jmb.2015.12.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/17/2022]
Abstract
"Specialized ribosomes" is a topic of intense debate and research whose provenance can be traced to the earliest days of molecular biology. Here, the history of this idea is reviewed, and critical literature in which the specialized ribosomes have come to be presently defined is discussed. An argument supporting the evolution of a variety of ribosomes with specialized functions as a consequence of selective pressures acting on a near-infinite set of possible ribosomes is presented, leading to a discussion of how this may also serve as a biological buffering mechanism. The possible relationship between specialized ribosomes and human health is explored. A set of criteria and possible approaches are also presented to help guide the definitive identification of "specialized" ribosomes, and this is followed by a discussion of how synthetic biology approaches might be used to create new types of special ribosomes.
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Affiliation(s)
- Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, 4062 Campus Drive, College Park, MD 20742, USA.
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49
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Zemella A, Thoring L, Hoffmeister C, Kubick S. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems. Chembiochem 2015; 16:2420-31. [PMID: 26478227 PMCID: PMC4676933 DOI: 10.1002/cbic.201500340] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/07/2023]
Abstract
From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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50
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Druart K, Palmai Z, Omarjee E, Simonson T. Protein:Ligand binding free energies: A stringent test for computational protein design. J Comput Chem 2015; 37:404-15. [PMID: 26503829 DOI: 10.1002/jcc.24230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/29/2023]
Abstract
A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl-tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l-tyrosine (l-Tyr), compared to the analogs d-Tyr, p-acetyl-, and p-azido-phenylalanine (ac-Phe, az-Phe). We simulate l- and d-Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous "MD/GBSA" procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l-Tyr, ac- and az-Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l-Tyr or d-Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l-Tyr is the ligand and a d-Tyr specific mutant when d-Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln.
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Affiliation(s)
- Karen Druart
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Zoltan Palmai
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Eyaz Omarjee
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
| | - Thomas Simonson
- Laboratoire De Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, Palaiseau, France
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