1
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Niu W, Guo J. Co-translational Installation of Posttranslational Modifications by Non-canonical Amino Acid Mutagenesis. Chembiochem 2023; 24:e202300039. [PMID: 36853967 PMCID: PMC10202221 DOI: 10.1002/cbic.202300039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/02/2023]
Abstract
Protein posttranslational modifications (PTMs) play critical roles in regulating cellular activities. Here we provide a survey of genetic code expansion (GCE) methods that were applied in the co-translational installation and studies of PTMs through noncanonical amino acid (ncAA) mutagenesis. We begin by reviewing types of PTM that have been installed by GCE with a focus on modifications of tyrosine, serine, threonine, lysine, and arginine residues. We also discuss examples of applying these methods in biological studies. Finally, we end the piece with a short discussion on the challenges and the opportunities of the field.
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Affiliation(s)
- Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, N-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE-68588, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE-68588, USA
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2
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Toyobe M, Yakushiji F. Synthetic modifications of histones and their functional evaluation. Chem Asian J 2022; 17:e202200197. [PMID: 35489041 DOI: 10.1002/asia.202200197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/22/2022] [Indexed: 11/07/2022]
Abstract
Post-transrational modifications (PTMs) of histones play a key role in epigenetic regulation. Unraveling the roles of each epigenetic mark can provide new insights into their biological mechanisms. On the other hand, it is generally difficult to prepare homogeneously-modified histones/nucleosomes to investigate their specific functions. Therefore, synthetic approaches to acquire precisely mimicked histones/nucleosomes are in great demand, and further development of this research field is anticipated. In this review, synthetic strategies to modify histones/nucleosomes, including cysteine modifications, transformations of dehydroalanine residues and lysine acylation using a catalyst system, are cited. In addition, the functional evaluation of synthetically modified histones/nucleosomes is described.
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Affiliation(s)
- Moe Toyobe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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3
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Griffiths RC, Smith FR, Long JE, Scott D, Williams HEL, Oldham NJ, Layfield R, Mitchell NJ. Site-Selective Installation of N ϵ -Modified Sidechains into Peptide and Protein Scaffolds via Visible-Light-Mediated Desulfurative C-C Bond Formation. Angew Chem Int Ed Engl 2022; 61:e202110223. [PMID: 34713958 PMCID: PMC9299887 DOI: 10.1002/anie.202110223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Indexed: 01/07/2023]
Abstract
Post-translational modifications (PTMs) enhance the repertoire of protein function and mediate or influence the activity of many cellular processes. The preparation of site-specifically and homogeneously modified proteins, to apply as tools to understand the biological role of PTMs, is a challenging task. Herein, we describe a visible-light-mediated desulfurative C(sp3 )-C(sp3 ) bond forming reaction that enables the site-selective installation of Nϵ -modified sidechains into peptides and proteins of interest. Rapid, operationally simple, and tolerant to ambient atmosphere, we demonstrate the installation of a range of lysine (Lys) PTMs into model peptide systems and showcase the potential of this technology by site-selectively installing an Nϵ Ac sidechain into recombinantly expressed ubiquitin (Ub).
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Affiliation(s)
- Rhys C. Griffiths
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Frances R. Smith
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Jed E. Long
- Biodiscovery InstituteUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Daniel Scott
- School of Life Sciences, Queen's Medical CentreUniversity of NottinghamNottinghamNG7 2UHUK
| | - Huw E. L. Williams
- Biodiscovery InstituteUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Neil J. Oldham
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Robert Layfield
- School of Life Sciences, Queen's Medical CentreUniversity of NottinghamNottinghamNG7 2UHUK
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4
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Griffiths RC, Smith FR, Long JE, Scott D, Williams HEL, Oldham NJ, Layfield R, Mitchell NJ. Site‐Selective Installation of N
ϵ
‐Modified Sidechains into Peptide and Protein Scaffolds via Visible‐Light‐Mediated Desulfurative C–C Bond Formation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rhys C. Griffiths
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Frances R. Smith
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Jed E. Long
- Biodiscovery Institute University of Nottingham University Park Nottingham NG7 2RD UK
| | - Daniel Scott
- School of Life Sciences, Queen's Medical Centre University of Nottingham Nottingham NG7 2UH UK
| | - Huw E. L. Williams
- Biodiscovery Institute University of Nottingham University Park Nottingham NG7 2RD UK
| | - Neil J. Oldham
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
| | - Robert Layfield
- School of Life Sciences, Queen's Medical Centre University of Nottingham Nottingham NG7 2UH UK
| | - Nicholas J. Mitchell
- School of Chemistry University of Nottingham University Park Nottingham NG7 2RD UK
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5
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Cao L, Liu J, Ghelichkhani F, Rozovsky S, Wang L. Genetic Incorporation of ϵ-N-Benzoyllysine by Engineering Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase. Chembiochem 2021; 22:2530-2534. [PMID: 34118176 PMCID: PMC8406699 DOI: 10.1002/cbic.202100218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Indexed: 01/24/2023]
Abstract
Post-translational modifications regulate protein structure and function. Lysine benzoylation is a newly discovered histone modification with unique physiological relevance. To construct proteins with this modification site-specifically, we generated orthogonal tRNAPyl -MaBzKRS pairs by engineering Methanomethylophilus alvus pyrrolysyl-tRNA synthetase, allowing the genetic incorporation of ϵ-N-benzoyllysine (BzK) into proteins with high efficiency in E. coli and mammalian cells. Two types of MaBzKRS were identified to incorporate BzK using mutations located at different positions of the amino acid binding pocket. These MaBzKRS are small in size and highly expressed, which will afford broad utilities in studying the biological effects of lysine benzoylation.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Farid Ghelichkhani
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
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6
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Walther R, Monge P, Pedersen AB, Benderoth A, Pedersen JN, Farzadfard A, Mandrup OA, Howard KA, Otzen DE, Zelikin AN. Per-glycosylation of the Surface-Accessible Lysines: One-Pot Aqueous Route to Stabilized Proteins with Native Activity. Chembiochem 2021; 22:2478-2485. [PMID: 33998129 DOI: 10.1002/cbic.202100228] [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: 05/11/2021] [Indexed: 11/11/2022]
Abstract
Chemical glycosylation of proteins is a powerful tool applied widely in biomedicine and biotechnology. However, it is a challenging undertaking and typically relies on recombinant proteins and site-specific conjugations. The scope and utility of this nature-inspired methodology would be broadened tremendously by the advent of facile, scalable techniques in glycosylation, which are currently missing. In this work, we investigated a one-pot aqueous protocol to achieve indiscriminate, surface-wide glycosylation of the surface accessible amines (lysines and/or N-terminus). We reveal that this approach afforded minimal if any change in the protein activity and recognition events in biochemical and cell culture assays, but at the same time provided a significant benefit of stabilizing proteins against aggregation and fibrillation - as demonstrated on serum proteins (albumins and immunoglobulin G, IgG), an enzyme (uricase), and proteins involved in neurodegenerative disease (α-synuclein) and diabetes (insulin). Most importantly, this highly advantageous result was achieved via a one-pot aqueous protocol performed on native proteins, bypassing the use of complex chemical methodologies and recombinant proteins.
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Affiliation(s)
- Raoul Walther
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| | - Pere Monge
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| | | | - Anja Benderoth
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
| | | | - Azad Farzadfard
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
| | - Ole A Mandrup
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
| | - Kenneth A Howard
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Alexander N Zelikin
- Department of Chemistry, Aarhus University, Aarhus, 8000, Denmark
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, 8000, Denmark
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7
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Gang D, Park HS. Noncanonical Amino Acids in Synthetic Biosafety and Post-translational Modification Studies. Chembiochem 2020; 22:460-468. [PMID: 32794239 DOI: 10.1002/cbic.202000437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/11/2020] [Indexed: 11/06/2022]
Abstract
The incorporation of noncanonical amino acids (ncAAs) has been extensively studied because of its broad applicability. In the past decades, various in vitro and in vivo ncAA incorporation approaches have been developed to generate synthetic recombinant proteins. Herein, we discuss the methodologies for ncAA incorporation, and their use in diverse research areas, such as in synthetic biosafety and for studies of post-translational modifications.
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Affiliation(s)
- Donghyeok Gang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 341418, Korea
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8
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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9
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Chambers KA, Abularrage NS, Hill CJ, Khan IH, Scheck RA. A Chemical Probe for Dehydrobutyrine. Angew Chem Int Ed Engl 2020; 59:7350-7355. [DOI: 10.1002/anie.202003631] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Kaitlin A. Chambers
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Nile S. Abularrage
- Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Caitlin J. Hill
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Imran H. Khan
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Rebecca A. Scheck
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
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10
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Chambers KA, Abularrage NS, Hill CJ, Khan IH, Scheck RA. A Chemical Probe for Dehydrobutyrine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kaitlin A. Chambers
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Nile S. Abularrage
- Department of Chemistry Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Caitlin J. Hill
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Imran H. Khan
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
| | - Rebecca A. Scheck
- Department of Chemistry Tufts University 62 Talbot Avenue Medford MA 02155 USA
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11
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew Chem Int Ed Engl 2019; 58:17930-17952. [DOI: 10.1002/anie.201812164] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
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12
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemische Epigenetik: der Einfluss chemischer und chemo‐biologischer Techniken auf die Zielstruktur‐Validierung von Bromodomänen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
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13
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Aydillo C, Mazo N, Navo CD, Jiménez‐Osés G. Elusive Dehydroalanine Derivatives with Enhanced Reactivity. Chembiochem 2019; 20:1246-1250. [DOI: 10.1002/cbic.201800758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Carlos Aydillo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- Department of Pharmaceutical Technology and ChemistryFaculty of Pharmacy and NutritionUniversity of Navarra Irunlarrea 3 31008 Pamplona Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA) Irunlarrea 3 31008 Pamplona Spain
| | - Nuria Mazo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
| | - Claudio D. Navo
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
| | - Gonzalo Jiménez‐Osés
- Departamento de QuímicaUniversidad de La Rioja Madre de Dios, 53 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
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14
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Jiménez-Andreu MM, Sayago FJ, Cativiela C. An Improved Synthesis of the Antibiotic Dehydrophos. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- M. Mercedes Jiménez-Andreu
- Departamento de Química Orgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; 50009 Zaragoza Spain
| | - Francisco J. Sayago
- Departamento de Química Orgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; 50009 Zaragoza Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica; Instituto de Síntesis Química y Catálisis Homogénea (ISQCH); CSIC-Universidad de Zaragoza; 50009 Zaragoza Spain
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15
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Navo CD, Asín A, Gómez-Orte E, Gutiérrez-Jiménez MI, Compañón I, Ezcurra B, Avenoza A, Busto JH, Corzana F, Zurbano MM, Jiménez-Osés G, Cabello J, Peregrina JM. Cell-Penetrating Peptides Containing Fluorescent d
-Cysteines. Chemistry 2018; 24:7991-8000. [DOI: 10.1002/chem.201800603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Claudio D. Navo
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Alicia Asín
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Eva Gómez-Orte
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Marta I. Gutiérrez-Jiménez
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Ismael Compañón
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Begoña Ezcurra
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Alberto Avenoza
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Jesús H. Busto
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Francisco Corzana
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - María M. Zurbano
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Gonzalo Jiménez-Osés
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
| | - Juan Cabello
- Center for Biomedical Research of La Rioja (CIBIR); C/ Piqueras, 98 26006 Logroño La Rioja Spain
| | - Jesús M. Peregrina
- Dpto. de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; C/ Madre de Dios, 53 26006 Logroño La Rioja Spain
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16
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Xu AM, Wang DS, Shieh P, Cao Y, Melosh NA. Direct Intracellular Delivery of Cell-Impermeable Probes of Protein Glycosylation by Using Nanostraws. Chembiochem 2017; 18:623-628. [PMID: 28130882 DOI: 10.1002/cbic.201600689] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Bioorthogonal chemistry is an effective tool for elucidating metabolic pathways and measuring cellular activity, yet its use is currently limited by the difficulty of getting probes past the cell membrane and into the cytoplasm, especially if more complex probes are desired. Here we present a simple and minimally perturbative technique to deliver functional probes of glycosylation into cells by using a nanostructured "nanostraw" delivery system. Nanostraws provide direct intracellular access to cells through fluid conduits that remain small enough to minimize cell perturbation. First, we demonstrate that our platform can deliver an unmodified azidosugar, N-azidoacetylmannosamine, into cells with similar effectiveness to a chemical modification strategy (peracetylation). We then show that the nanostraw platform enables direct delivery of an azidosugar modified with a charged uridine diphosphate group (UDP) that prevents intracellular penetration, thereby bypassing multiple enzymatic processing steps. By effectively removing the requirement for cell permeability from the probe, the nanostraws expand the toolbox of bioorthogonal probes that can be used to study biological processes on a single, easy-to-use platform.
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Affiliation(s)
- Alexander M Xu
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA.,Present address: Chemistry and Chemical Engineering Division, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91106, USA
| | - Derek S Wang
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| | - Peyton Shieh
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA, 94305, USA
| | - Yuhong Cao
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, 476 Lomita Mall, Stanford, CA, 94305, USA
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17
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 397] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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Spicer CD, Davis BG. Selective chemical protein modification. Nat Commun 2014; 5:4740. [PMID: 25190082 DOI: 10.1038/ncomms5740] [Citation(s) in RCA: 718] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
Chemical modification of proteins is an important tool for probing natural systems, creating therapeutic conjugates and generating novel protein constructs. Site-selective reactions require exquisite control over both chemo- and regioselectivity, under ambient, aqueous conditions. There are now various methods for achieving selective modification of both natural and unnatural amino acids--each with merits and limitations--providing a 'toolkit' that until 20 years ago was largely limited to reactions at nucleophilic cysteine and lysine residues. If applied in a biologically benign manner, this chemistry could form the basis of true Synthetic Biology.
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Affiliation(s)
- Christopher D Spicer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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Yanagisawa T, Umehara T, Sakamoto K, Yokoyama S. Expanded Genetic Code Technologies for Incorporating Modified Lysine at Multiple Sites. Chembiochem 2014; 15:2181-7. [DOI: 10.1002/cbic.201402266] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 01/08/2023]
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Yanagisawa T, Takahashi M, Mukai T, Sato S, Wakamori M, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S. Multiple Site-Specific Installations ofNε-Monomethyl-L-Lysine into Histone Proteins by Cell-Based and Cell-Free Protein Synthesis. Chembiochem 2014; 15:1830-8. [DOI: 10.1002/cbic.201402291] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 12/12/2022]
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Kim CH, Kang M, Kim HJ, Chatterjee A, Schultz PG. Site-specific incorporation of ε-N-crotonyllysine into histones. Angew Chem Int Ed Engl 2012; 51:7246-9. [PMID: 22689270 DOI: 10.1002/anie.201203349] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Indexed: 11/10/2022]
Abstract
A novel post-translationally modified amino acid, crotonyllysine (Kcr), was genetically incorporated into proteins in bacterial and mammalian cells using an evolved pyrrolysyl-tRNA/synthetase-tRNA pair. The ability to produce histones with homogenous, site-specific Kcr modifications will be valuable in elucidating the biological role of this recently identified post-translational modification.
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Affiliation(s)
- Chan Hyuk Kim
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Chalker JM, Lercher L, Rose NR, Schofield CJ, Davis BG. Conversion of Cysteine into Dehydroalanine Enables Access to Synthetic Histones Bearing Diverse Post-Translational Modifications. Angew Chem Int Ed Engl 2012; 51:1835-9. [DOI: 10.1002/anie.201106432] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Revised: 11/15/2011] [Indexed: 11/10/2022]
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Chalker JM, Lercher L, Rose NR, Schofield CJ, Davis BG. Conversion of Cysteine into Dehydroalanine Enables Access to Synthetic Histones Bearing Diverse Post-Translational Modifications. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201106432] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Li F, Allahverdi A, Yang R, Lua GBJ, Zhang X, Cao Y, Korolev N, Nordenskiöld L, Liu CF. A Direct Method for Site-Specific Protein Acetylation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103754] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Li F, Allahverdi A, Yang R, Lua GBJ, Zhang X, Cao Y, Korolev N, Nordenskiöld L, Liu CF. A direct method for site-specific protein acetylation. Angew Chem Int Ed Engl 2011; 50:9611-4. [PMID: 21922615 DOI: 10.1002/anie.201103754] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/02/2011] [Indexed: 01/22/2023]
Affiliation(s)
- Fupeng Li
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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Yang YY, Hang HC. Chemical approaches for the detection and synthesis of acetylated proteins. Chembiochem 2011; 12:314-22. [PMID: 21243719 DOI: 10.1002/cbic.201000558] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Indexed: 12/17/2022]
Affiliation(s)
- Yu-Ying Yang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
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Chalker JM, Bernardes GJL, Lin YA, Davis BG. Chemical modification of proteins at cysteine: opportunities in chemistry and biology. Chem Asian J 2009; 4:630-40. [PMID: 19235822 DOI: 10.1002/asia.200800427] [Citation(s) in RCA: 469] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Chemical modification of proteins is a rapidly expanding area in chemical biology. Selective installation of biochemical probes has led to a better understanding of natural protein modification and macromolecular function. In other cases such chemical alterations have changed the protein function entirely. Additionally, tethering therapeutic cargo to proteins has proven invaluable in campaigns against disease. For controlled, selective access to such modified proteins, a unique chemical handle is required. Cysteine, with its unique reactivity, has long been used for such modifications. Cysteine has enjoyed widespread use in selective protein modification, yet new applications and even new reactions continue to emerge. This Focus Review highlights the enduring utility of cysteine in protein modification with special focus on recent innovations in chemistry and biology associated with such modifications.
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Affiliation(s)
- Justin M Chalker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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