At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code

Xiao, Han; Schultz, Peter G.

doi:10.1101/cshperspect.a023945

Cited by 115 publications

(96 citation statements)

References 129 publications

(125 reference statements)

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“…Site-specific halogenases of tryptophan have also been developed for the preparation of halotryptophans. [35][36][37][38]76,77] Complex protein substrates that contain halogenated residues and which are not accessible via chemical synthesis could also be specifically obtained by means of auxotrophic strains or reassignment of stop codons [78,79]. Pioneering work by the group of P. G. Schultz expanded the genetic code via a unique tRNA/aminoacyl-tRNA synthetase pair, resulting in a solid protocol to insert 4-iodophenylalanine [80] and 4-boronophenylalanine [81].…”

Section: Access To and Derivatization Of (Pseudo)halogenated Aromaticmentioning

confidence: 99%

The Suzuki–Miyaura Cross-Coupling as a Versatile Tool for Peptide Diversification and Cyclization

et al. 2017

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Abstract:The (site-selective) derivatization of amino acids and peptides represents an attractive field with potential applications in the establishment of structure-activity relationships and labeling of bioactive compounds. In this respect, bioorthogonal cross-coupling reactions provide valuable means for ready access to peptide analogues with diversified structure and function. Due to the complex and chiral nature of peptides, mild reaction conditions are preferred; hence, a suitable cross-coupling reaction is required for the chemical modification of these challenging substrates. The Suzuki reaction, involving organoboron species, is appropriate given the stability and environmentally benign nature of these reactants and their amenability to be applied in (partial) aqueous reaction conditions, an expected requirement upon the derivatization of peptides. Concerning the halogenated reaction partner, residues bearing halogen moieties can either be introduced directly as halogenated amino acids during solid-phase peptide synthesis (SPPS) or genetically encoded into larger proteins. A reversed approach building in boron in the peptidic backbone is also possible. Furthermore, based on this complementarity, cyclic peptides can be prepared by halogenation, and borylation of two amino acid side chains present within the same peptidic substrate. Here, the Suzuki-Miyaura reaction is a tool to induce the desired cyclization. In this review, we discuss diverse amino acid and peptide-based applications explored by means of this extremely versatile cross-coupling reaction. With the advent of peptide-based drugs, versatile bioorthogonal conversions on these substrates have become highly valuable.

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Section: Access To and Derivatization Of (Pseudo)halogenated Aromaticmentioning

confidence: 99%

The Suzuki–Miyaura Cross-Coupling as a Versatile Tool for Peptide Diversification and Cyclization

et al. 2017

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“…Their ground‐truth is the physics of molecular interactions, rather than analogies to previously determined structures. Thus, they can be applied to modified RNAs, including those with unnatural modifications developed for synthetic biology . Physics‐based methods predict a molecule's thermodynamic ensemble, which is the most important determinant of its function.…”

Section: Introductionmentioning

confidence: 99%

Physics‐based all‐atom modeling of RNA energetics and structure

et al. 2017

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The Potential, U, is Essential: The many conformations from a simulation produce a free energy surface. The surface is realistic, if the force field, FF, is. The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined NMR and x-ray structures, but are less reliable for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA.

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“…[5] A number of ncAAs with electrophilic side chains that can react with adjacent nucleophilic residues (usually Cys or Lys) in a target protein to form intra- or intermolecular crosslinks, have been developed. These reactive groups include reactive halides, [6] Michael acceptors [7] and an aryl isothiocyanate.…”

mentioning

confidence: 99%

Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains

2017

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The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions and improve the pharmacological properties of proteins. Here we report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that can site-specifically incorporate PheK and FPheK into proteins in both E. coli and mammalian cells. PheK and FPheK when incorporated into proteins showed good stability during protein expression and purification; crosslinking required incubation under weakly basic condition. We demonstrated that FPheK can react with adjacent Lys, Cys and Tyr residues in thioredoxin in high yields. In addition, crosslinks could be formed between FPheK and Lys residue of two interacting proteins, including the heavy chain and light chain of an antibody Fab. The high efficiency and specificity of FPheK crosslinking may make it a practical tool to engineer proteins with unnatural covalent linkages.

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At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code

Cited by 115 publications

References 129 publications

The Suzuki–Miyaura Cross-Coupling as a Versatile Tool for Peptide Diversification and Cyclization

The Suzuki–Miyaura Cross-Coupling as a Versatile Tool for Peptide Diversification and Cyclization

Physics‐based all‐atom modeling of RNA energetics and structure

Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains

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