Recent Development of Genetic Code Expansion for Posttranslational Modification Studies

Chen, Hao; Venkat, Sumana; McGuire, Paige; Gan, Qinglei; Fan, Chenguang

doi:10.3390/molecules23071662

Cited by 37 publications

(33 citation statements)

References 149 publications

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“…We can expect that more and more amino acids will be discovered and synthesized in the future. Incorporating unnatural amino acids into peptide and protein sequences is the object of intensive investigations [ 52 , 53 , 54 ].…”

Section: Annotation Of Amino Acids and Phosphate Groupsmentioning

confidence: 99%

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

et al. 2021

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Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.

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Section: Annotation Of Amino Acids and Phosphate Groupsmentioning

confidence: 99%

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

et al. 2021

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“…Genetic code expansion is a powerful tool for studying post‐translational modification (PTM)‐containing proteins because this method is site‐specific, does not require modifying enzymes, and can produce enough homogeneously modified proteins for biochemical and biophysical analyses . In recent years, genetic code expansion techniques with orthogonal tRNA/tRNA synthetase pairs have been widely applied to introduce a great many unnatural amino acids into specific proteins .…”

Section: Figurementioning

confidence: 99%

Identification of Human IDO1 Enzyme Activity by Using Genetically Encoded Nitrotyrosine

Zheng

Guo

et al. 2020

ChemBioChem

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Humani ndoleamine 2,3-dioxygenase 1( IDO1) hasb ecome an increasingly valuable target for cancer immunotherapy because it promotes immune escape by tumor cells. To date, the functiono fp ost-translational modifications (PTMs) on IDO1 has not been fully elucidated. Among the many forms of PTMs, it has been identified that three tyrosine sites (Y15, Y345, and Y353) on IDO1a re nitrated and play important roles in catalytic function. Herein, by genetically encoding 3-nitro-ltyrosine into the tyrosine nitration sites of IDO1, the homogeneous and native nitrated IDO1 have been obtained. It is found that the nitration of differentt yrosine sites has different effects on the IDO1 structurea nd enzyme activity.N itration at positionY 15 has an egligible effect, but nitration at Y345 or Y353 decreases the enzyme activity,e specially Y353. Furthermore, these results demonstrate that the regulationo ft he catalytic function caused by tyrosine nitration is relatedt op erturbation of the protein structure and heme-binding disruption.Humani ndoleamine 2,3-dioxygenase 1( IDO1) is am etalloenzyme with heme as ac ofactor that catalyzest he metabolism of l-Trp to N-formylkynurenine (NFK), which is the first and rate-determining step of the kynurenine pathway. [1] In this pathway,I DO1 consumes l-Trp, causing al ack of tryptophan in the local microenvironment,a nd produces many immunosuppressives econdary metabolites, such as kynureninic acid (KA) and quinolinic acid (QA), whichare involved in several different immune signaling processes. [2] Consequently,t he cycle of Tlymphocytes is restricted to the G1 phase and proliferation is inhibited. Additionally,t hese signaling processes trigger the generation and activation of Tr egulatory cells. Finally,alocal immunosuppressivee nvironment is formed. [3] Therefore, the enzymea ctivity of IDO1 plays ac rucial role in IDO1-mediated immune tolerance.It has been confirmed that three tyrosine residues (Y15, Y345, and Y353) in IDO1 can undergo nitration modification by peroxynitrite, such as 3-(4-morpholinyl)sydnonimine. [4] As previously reported, the THP-1 and PBMC cells with induced IDO1 expression, or purified recombinant IDO1 protein treated with the peroxynitrite generator, can cause IDO1 tyrosine nitration modification at three sites, which results in ad ecrease in IDO1 enzyme activity. [4b] To clarify at which site tyrosine nitration has the most significant impact on IDO1 enzymea ctivity,t yrosine was mutated to phenylalanine, the peroxynitrite experiment was repeated, and it was found that nitration of the Y15 residue was the most important factor in the inactivation of IDO1. [4b] However,m utation of tyrosine to phenylalanine may directly change the conformation of IDO1, and thus, affect its enzymea ctivity.M oreover,t he in vitro reactiono fI DO1 protein with peroxynitrite may directly affect its enzymea ctivity due to nonspecific tyrosine oxidative modification. Hence, it might not be accurate to study the effects of tyrosine nitration based on the nonspecific reaction.Genet...

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“…Besides being mostly reversible, competitions among different PTMs for the same residues and limited knowledge of modifying enzymes make it difficult to synthesize homogeneously modified proteins for studying. To overcome these challenges, the genetic code expansion strategy has been applied in PTM studies ( Liu et al., 2011 ; Chen et al., 2018 ). Here, we summarized the applications of CFPS in generating proteins with PTMs through the genetic code expansion strategy.…”

Section: Cell-free Protein Synthesis For Post-translational Modificatmentioning

confidence: 99%

The Application of Cell-Free Protein Synthesis in Genetic Code Expansion for Post-translational Modifications

et al. 2019

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The translation system is a sophisticated machinery that synthesizes proteins from 20 canonical amino acids. Recently, the repertoire of such composition has been expanded by the introduction of non-canonical amino acids (ncAAs) with the genetic code expansion strategy, which provides proteins with designed properties and structures for protein studies and engineering. Although the genetic code expansion strategy has been mostly implemented by using living cells as the host, a number of limits such as poor cellular uptake or solubility of specific ncAA substrates and the toxicity of target proteins have hindered the production of certain ncAA-modified proteins. To overcome those challenges, cell-free protein synthesis (CFPS) has been applied as it allows the precise control of reaction components. Several approaches have been recently developed to increase the purity and efficiency of ncAA incorporation in CFPS. Here, we summarized recent development of CFPS with an emphasis on its applications in generating site-specific protein post-translational modifications by the genetic code expansion strategy.

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Recent Development of Genetic Code Expansion for Posttranslational Modification Studies

Cited by 37 publications

References 149 publications

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

Identification of Human IDO1 Enzyme Activity by Using Genetically Encoded Nitrotyrosine

The Application of Cell-Free Protein Synthesis in Genetic Code Expansion for Post-translational Modifications

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