1
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Larsen CK, Lindquist P, Rosenkilde M, Madsen AR, Haselmann K, Glendorf T, Olesen K, Kodal ALB, Tørring T. Using LanM Enzymes to Modify Glucagon-Like Peptides 1 and 2 in E.coli. Chembiochem 2024; 25:e202400201. [PMID: 38701360 DOI: 10.1002/cbic.202400201] [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: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/05/2024]
Abstract
Selective modification of peptides is often exploited to improve pharmaceutically relevant properties of bioactive peptides like stability, circulation time, and potency. In Nature, natural products belonging to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs) are known to install a number of highly attractive modifications with high selectivity. These modifications are installed by enzymes guided to the peptide by corresponding leader peptides that are removed as the last step of biosynthesis. Here, we exploit leader peptides and their matching enzymes to investigate the installation of D-Ala post-translationally in a critical position in the hormones, glucagon-like peptides (GLP) 1 and 2. We also offer insight into how precursor peptide design can modulate the modification pattern achieved.
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Affiliation(s)
- Camilla K Larsen
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus C, Denmark
- Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Peter Lindquist
- Department of Biomedical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Mette Rosenkilde
- Department of Biomedical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | | | | | | | | | | | - Thomas Tørring
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus C, Denmark
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2
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Nguyen DD, Kim I. Vibrational circular dichroism unveils hidden clues. LIGHT, SCIENCE & APPLICATIONS 2023; 12:210. [PMID: 37652916 PMCID: PMC10471598 DOI: 10.1038/s41377-023-01239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Infrared chiral plasmonic metamaterials based on perpendicularly positioned nanorods enable surface-enhanced vibrational circular dichroism for more selective and sensitive identification of protein fingerprints and enantioselective sensing, which creates a new pathway for chemical or biomedical applications.
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Affiliation(s)
- Dang Du Nguyen
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Inki Kim
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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3
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Fontecilla-Camps JC, Volbeda A. Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis. Chem Rev 2022; 122:12110-12131. [PMID: 35536891 DOI: 10.1021/acs.chemrev.1c00869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activation energy barrier of biochemical reactions is normally lowered by an enzyme catalyst, which directly helps the weakening of the bond(s) to be broken. In many metalloenzymes, this is a first coordination sphere effect. Besides having a direct catalytic action, enzymes can fix their reactive groups and substrates so that they are optimally positioned and also modify the water activity in the system. They can either activate substrates prior to their reaction or bind preactivated substrates, thereby drastically reducing local entropic effects. The latter type is well represented by some bisubstrate reactions, where they have been defined as "entropic traps". These can be described as "second coordination sphere" processes, but enzymes can also control the reactivity beyond this point through local conformational changes belonging to an "outer coordinate sphere" that can be modulated by substrate binding. We have chosen the [4Fe-4S] cluster-dependent enzyme quinolinate synthase to illustrate each one of these processes. In addition, this very old metalloenzyme shows low in vitro substrate binding specificity, atypical reactivity that produces dead-end products, and a unique modulation of its active site volume.
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Affiliation(s)
| | - Anne Volbeda
- Université Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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4
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Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci 2021; 23:ijms23010285. [PMID: 35008708 PMCID: PMC8745688 DOI: 10.3390/ijms23010285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
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Affiliation(s)
- Victor V. Dyakin
- The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Bld. 35. Rom 201-C, Orangeburg, NY 10962, USA
- Correspondence: ; Tel.: +1-845-548-96-94; Fax: +1-845-398-5510
| | - Nuka V. Dyakina-Fagnano
- Child, Adolescent and Young Adult Psychiatry, 36 Franklin Turnpike, Waldwick, NJ 07463, USA;
| | - Laura B. Mcintire
- Department of Pathology and Cell Biology, Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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5
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Hoyas S, Roscioni OM, Tonneaux C, Gerbaux P, Cornil J, Muccioli L. Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations. Biomacromolecules 2021; 22:2573-2581. [PMID: 34009963 DOI: 10.1021/acs.biomac.1c00302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.
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Affiliation(s)
- Sébastien Hoyas
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons, 23 Place du Parc, Mons 7000, Belgium.,Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, 23 Place du Parc, Mons 7000, Belgium
| | - Otello M Roscioni
- Department of Industrial Chemistry ≪ Toso Montanari ≫, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.,MaterialX LTD, Bristol BS2 0XJ, U.K
| | - Corentin Tonneaux
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons, 23 Place du Parc, Mons 7000, Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, 23 Place du Parc, Mons 7000, Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons, 23 Place du Parc, Mons 7000, Belgium
| | - Luca Muccioli
- Department of Industrial Chemistry ≪ Toso Montanari ≫, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
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6
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Chiral discrimination in a mutated IDH enzymatic reaction in cancer: a computational perspective. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:549-559. [PMID: 32880665 DOI: 10.1007/s00249-020-01460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Chiral discrimination in biological systems, such as L-amino acids in proteins and d-sugars in nucleic acids, has been proposed to depend on various mechanisms, and chiral discrimination by mutated enzymes mediating cancer cell signaling is important in current research. We have explored how mutated isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate which in turn is converted to d-2-hydroxyglutatrate (d-2HG) as a preferred product instead of l-2-hydroxyglutatrate (l-2HG) according to quantum chemical calculations. Using transition state structure modeling, we delineate the preferred product formation of d-2HG over l-2HG in an IDH active site model. The mechanisms for the formation of d-2HG over l-2HG are assessed by identifying transition state structures and activation energy barriers in gas and solution phases. The calculated reaction energy profile for the formation of d-2HG and l-2HG metabolites shows a 29 times higher value for l-2HG as compared to d-2HG. Results for second-order Møller-Plesset perturbation theory (MP2) do not alter the observed trend based on Density Functional Theory (DFT). The observed trends in reaction energy profile explain why the formation of D-2HG is preferred over l-2HG and reveal why mutation leads to the formation of d-2HG instead of l-2HG. For a better understanding of the observed difference in the activation barrier for the formation of the two alternative products, we performed natural bond orbital analysis, non-covalent interactions analysis and energy decomposition analysis. Our findings based on computational calculations clearly indicate a role for chiral discrimination in mutated enzymatic pathways in cancer biology.
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7
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Bettini S, Syrgiannis Z, Ottolini M, Bonfrate V, Giancane G, Valli L, Prato M. Supramolecular Chiral Discrimination of D-Phenylalanine Amino Acid Based on a Perylene Bisimide Derivative. Front Bioeng Biotechnol 2020; 8:160. [PMID: 32195240 PMCID: PMC7064719 DOI: 10.3389/fbioe.2020.00160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/17/2020] [Indexed: 11/17/2022] Open
Abstract
The interaction between homochiral substituted perylene bisimide (PBI) molecule and the D enantiomer of phenylalanine amino acid was monitored. Spectroscopic transitions of PBI derivative in aqueous solution in the visible range were used to evaluate the presence of D-phenylalanine. UV-visible, fluorescence, FT-IR, and AFM characterizations showed that D-phenylalanine induces significant variations in the chiral perylene derivative aggregation state and the mechanism is enantioselective as a consequence of the 3D analyte structure. The interaction mechanism was further investigated in presence of interfering amino acid (D-serine and D-histidine) confirming that both chemical structure and its 3D structure play a crucial role for the amino acid discrimination. A D-phenylalanine fluorescence sensor based on perylene was proposed. A limit of detection (LOD) of 64.2 ± 0.38 nM was calculated in the range 10-7-10-5 M and of 1.53 ± 0.89 μM was obtained in the range 10-5 and 10-3 M.
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Affiliation(s)
- Simona Bettini
- Department of Innovation Engineering, Campus University Ecotekne, University of Salento, Lecce, Italy
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Florence, Italy
| | - Zois Syrgiannis
- Simpson Querrey Institute, Northwestern University, Chicago, IL, United States
- Center of Excellence for Nanostructured Materials (CENMAT) and INSTM, Unit of Trieste, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Michela Ottolini
- Department of Innovation Engineering, Campus University Ecotekne, University of Salento, Lecce, Italy
| | - Valentina Bonfrate
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Gabriele Giancane
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Florence, Italy
- Department of Cultural Heritage, University of Salento, Lecce, Italy
| | - Ludovico Valli
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Florence, Italy
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Maurizio Prato
- Center of Excellence for Nanostructured Materials (CENMAT) and INSTM, Unit of Trieste, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Carbon Nanobiotechnology Laboratory, CIC biomaGUNE, Donostia-San Sebastian, Spain
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8
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Rybak MY, Rayevsky AV, Gudzera OI, Tukalo MA. Stereospecificity control in aminoacyl-tRNA-synthetases: new evidence of d-amino acids activation and editing. Nucleic Acids Res 2019; 47:9777-9788. [PMID: 31504788 PMCID: PMC6765224 DOI: 10.1093/nar/gkz756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/14/2019] [Accepted: 08/21/2019] [Indexed: 02/02/2023] Open
Abstract
The homochirality of amino acids is vital for the functioning of the translation apparatus. l-Amino acids predominate in proteins and d-amino acids usually represent diverse regulatory functional physiological roles in both pro- and eukaryotes. Aminoacyl-tRNA-synthetases (aaRSs) ensure activation of proteinogenic or nonproteinogenic amino acids and attach them to cognate or noncognate tRNAs. Although many editing mechanisms by aaRSs have been described, data about the protective role of aaRSs in d-amino acids incorporation remained unknown. Tyrosyl- and alanyl-tRNA-synthetases were represented as distinct members of this enzyme family. To study the potential to bind and edit noncognate substrates, Thermus thermophilus alanyl-tRNA-synthetase (AlaRS) and tyrosyl-tRNA-synthetase were investigated in the context of d-amino acids recognition. Here, we showed that d-alanine was effectively activated by AlaRS and d-Ala-tRNAAla, formed during the erroneous aminoacylation, was edited by AlaRS. On the other hand, it turned out that d-aminoacyl-tRNA-deacylase (DTD), which usually hydrolyzes d-aminoacyl-tRNAs, was inactive against d-Ala-tRNAAla. To support the finding about DTD, computational docking and molecular dynamics simulations were run. Overall, our work illustrates the novel function of the AlaRS editing domain in stereospecificity control during translation together with trans-editing factor DTD. Thus, we propose different evolutionary strategies for the maintenance of chiral selectivity during translation.
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Affiliation(s)
- Mariia Yu Rybak
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
| | - Alexey V Rayevsky
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, 150 Zabolotnogo Street, 03143, Kyiv, Ukraine
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9
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Tian F, Chen R. Pd-Mediated Synthesis of Ag33 Chiral Nanocluster with Core–Shell Structure in T Point Group. J Am Chem Soc 2019; 141:7107-7114. [DOI: 10.1021/jacs.9b02162] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fan Tian
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Donghu New & High Technology Development Zone, Wuhan 430205, PR China
| | - Rong Chen
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Donghu New & High Technology Development Zone, Wuhan 430205, PR China
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10
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Jiang Y, Liu C, Wang X, Wang T, Jiang J. Fluorescent Phthalocyanine Assembly Distinguishes Chiral Isomers of Different Types of Amino Acids and Sugars. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7239-7247. [PMID: 28675790 DOI: 10.1021/acs.langmuir.7b01602] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The functions of some natural supramolecular architectures, such as ribosomes, are dependent on the recognition of different types of chiral biomolecules. However, the recognition of different types of chiral molecules (multiobject chiral recognition), such as amino acids and sugars, by independent and identically artificial supramolecular assembly, was rarely achieved. In this article, simple amphiphilic achiral phthalocyanine was found to form supramolecular chiral assemblies with charged water-soluble polymers upon host-guest interactions at the air/water interface. Among these systems, one identical phthalocyanine/poly(l-lysine) assembly not only can distinguish enantiomers of different amino acids but also can recognize several epimers of monose. The chiral recognitions were achieved by comparing either the steady-state fluorescence intensity or fluorescence quenching rate of phthalocyanine/poly(l-lysine) assemblies, before and after interaction with different small chiral molecules. It was demonstrated that the interactions between poly(l-lysine) and different small chiral molecules could change the aggregation of phthalocyanines. And the sensitivity of fluorescence and the excellent multiobject chiral recognition properties of the phthalocyanine/poly(l-lysine) assembly are dependent on the subtle molecular packing mode and the cooperation of different noncovalent interactions.
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Affiliation(s)
- Yuying Jiang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Chenxi Liu
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Xiqian Wang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Tianyu Wang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing , Beijing 100083, P.R. China
| | - Jianzhuang Jiang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing , Beijing 100083, P.R. China
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11
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Yang X, van der Donk WA. Post-translational Introduction of D-Alanine into Ribosomally Synthesized Peptides by the Dehydroalanine Reductase NpnJ. J Am Chem Soc 2015; 137:12426-9. [PMID: 26361061 PMCID: PMC4599312 DOI: 10.1021/jacs.5b05207] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomally synthesized peptides are generally limited to L-amino acid building blocks. Given the advantageous properties of peptides containing D-amino acids such as stabilization of certain turns and against proteolytic degradation, methods to introduce D-stereocenters are valuable. Here we report the first in vitro reconstitution and characterization of a dehydrogenase that carries out the asymmetric reduction of dehydroalanine. NpnJA reduces dehydroalanine to D-Ala using NAPDH as cosubstrate. The enzyme displays high substrate tolerance allowing introduction of D-Ala into a range of non-native substrates. In addition to the in vitro reactions, we describe five examples of using Escherichia coli as biosynthetic host for D-alanine introduction into ribosomal peptides. A deuterium-label-based coupled-enzyme assay was used to rapidly determine the stereochemistry of the newly installed alanine.
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Affiliation(s)
- Xiao Yang
- Howard Hughes Medical Institute and Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
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12
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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13
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Hg2+
-Induced In Situ Generated Radical Cation of (S
)-BINOL-Based Polymer for Highly Enantioselective Recognition of Phenylalaninol. Macromol Rapid Commun 2014; 35:1443-9. [DOI: 10.1002/marc.201400248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/06/2014] [Indexed: 12/26/2022]
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14
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Vondenhoff GH, Pugach K, Gadakh B, Carlier L, Rozenski J, Froeyen M, Severinov K, Van Aerschot A. N-alkylated aminoacyl sulfamoyladenosines as potential inhibitors of aminoacylation reactions and microcin C analogues containing D-amino acids. PLoS One 2013; 8:e79234. [PMID: 24223911 PMCID: PMC3817062 DOI: 10.1371/journal.pone.0079234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/19/2013] [Indexed: 11/18/2022] Open
Abstract
Microcin C analogues were recently envisaged as important compounds for the development of novel antibiotics. Two issues that may pose problems to these potential antibiotics are possible acquisition of resistance through acetylation and in vivo instability of the peptide chain. N-methylated aminoacyl sulfamoyladenosines were synthesized to investigate their potential as aminoacyl tRNA synthetase inhibitors and to establish whether these N-alkylated analogues would escape the natural inactivation mechanism via acetylation of the alpha amine. It was shown however, that these compounds are not able to effectively inhibit their respective aminoacyl tRNA synthetase. In addition, we showed that (D)-aspartyl-sulfamoyladenosine (i.e. with a (D)-configuration for the aspartyl moiety), is a potent inhibitor of aspartyl tRNA synthetase. However, we also showed that the inhibitory effect of (D)- aspartyl-sulfamoyladenosine is relatively short-lasting. Microcin C analogues with (D)-amino acids throughout from positions two to six proved inactive. They were shown to be resistant against metabolism by the different peptidases and therefore not able to release the active moiety. This observation could not be reversed by incorporation of (L)-amino acids at position six, showing that none of the available peptidases exhibit endopeptidase activity.
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Affiliation(s)
- Gaston H. Vondenhoff
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Ksenia Pugach
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Bharat Gadakh
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Laurence Carlier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Mathy Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | - Konstantin Severinov
- Department of Molecular Biology and Biochemistry Waksman Institute, Rutgers, the State University, Piscataway, New Jersey, United States of America
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Arthur Van Aerschot
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
- * E-mail:
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