Genetically Encoded Photocaged Proteinogenic and Non-Proteinogenic Amino Acids.

Photocaged amino acids could be genetically encoded into proteins via genetic code expansion (GCE) and constitute unique tools for innovative protein engineering. There are a number of photocaged proteinogenic amino acids that allow strategic conversion of proteins into their photocaged variants, thus enabling spatiotemporal and non-invasive regulation of protein functions using light. Meanwhile, there are a hand of photocaged non-proteinogenic amino acids that address the challenges in directly encoding certain non-canonical amino acids (ncAAs) that structurally resemble proteinogenic ones or possess highly reactive functional groups. Herein, we would like to summarize the efforts in encoding photocaged proteinogenic and non-proteinogenic amino acids, hoping to draw more attention to this fruitful and exciting scientific campaign.

{Mo4}-directed structural evolution of highly reduced molybdenum red clusters for efficient proton conduction.

A series of highly reduced Mo red clusters {Mo28} (1), {Mo30} (2), and {Mo40} (3) are synthesized from the rational assembly of planar {MoV4} building blocks and employed for proton conduction. 3 exhibits the best conductivity of 7.56 × 10-3 S cm-1 under optimal conditions due to the most efficient hydrogen-bonding network.

Pinpointing Acidic Residues in Proteins.

It is of great importance to pinpoint specific residues or sites of a protein in biological contexts to enable desired mechanism of action for small molecules or to precisely control protein function. In this regard, acidic residues including aspartic acid (Asp) and glutamic acid (Glu) hold great potential due to their great prevalence and unique function. To unlock the largely untapped potential, great efforts have been made recently by synthetic chemists, chemical biologists and pharmacologists. Herein, we would like to highlight the remarkable progress and particularly introduce the electrophiles that exhibit reactivity to carboxylic acids, the light-induced reactivities to carboxylic acids and the genetically encoded noncanonical amino acids that allow protein manipulations at acidic residues. We also comment on certain unresolved challenges, hoping to draw more attention to this rapidly developing area.

Anderson-type polyoxometalate-based metal-organic framework as an efficient heterogeneous catalyst for selective oxidation of benzylic C-H bonds.

Oxidative transformation of benzylic C-H bonds into functional carbonyl groups under mild conditions represents an efficient method for the synthesis of aromatic carboxylic acids and ketones. Here we report a high-efficiency catalyst system constructed from an Anderson-type polyoxometalate-based metal-Organic framework (POMOF-1) and N-hydroxyphthalimide (NHPI) for selective oxidation of methylarenes and alkylarenes under 1 atm O2 atmosphere. POMOF-1 exerted a synergistic effect originating from the well-aligned Anderson {CrMo6} clusters and Cu centers within the framework, and this entailed good cooperation with NHPI to catalyze the selective oxidation. Accordingly, the reactions exhibit good tolerance and chemical selectivity for a wide range of substrates bearing diverse substituent groups, and the corresponding carboxylic acids and ketones were harvested in good yields under mild conditions. Mechanism study reveals that POMOF-1 worked synergistically with NPHI to activate the benzylic C-H bonds of substrates, which are sequentially oxidized by oxygen and HOO˙ to give rise to the products. This work may pave a way to design high-efficiency catalysts by integration of polyoxometalate-based materials with NPHI for challenging C-H activation.

A Sirtuin-Dependent T7 RNA Polymerase Variant.

Transcriptional regulation is of great significance for cells to maintain homeostasis and, meanwhile, represents an innovative but less explored means to control biological processes in synthetic biology and bioengineering. Herein we devised a T7 RNA polymerase (T7RNAP) variant through replacing an essential lysine located in the catalytic core (K631) with Nε-acetyl-l-lysine (AcK) via genetic code expansion. This T7RNAP variant requires the deacetylase activity of NAD-dependent sirtuins to recover its enzymatic activities and thereby sustains sirtuin-dependent transcription of the gene of interest in live cells including bacteria and mammalian cells as well as in in vitro systems. This T7RNAP variant could link gene transcription to sirtuin expression and NAD availability, thus holding promise to support some relevant research.

A porous Anderson-type polyoxometalate-based metal-organic framework as a multifunctional platform for selective oxidative coupling with amines.

Incorporating catalytic units into a crystalline porous matrix represents a facile way to build high-efficiency heterogeneous catalysts, and by rational design of the porous skeleton with appropriate building blocks the catalytic performance can be significantly enhanced for a series of organic transformations owing to the synergistic effect from the multicomponent and confined porous microenvironment around catalytically active sites. Herein, we demonstrate that the design and synthesis of a porous polyoxometalate-based metal-organic framework YL2(H2O)2[CrMo6O18(PET)2]·4H2O (POMOF-1) constructed from Anderson-type [CrMo6O18(PET)2] (PET = pentaerythritol), which can be employed as a multifunctional platform for synthesis of N-containing compounds via selective oxidative coupling with amines. POMOF-1 features microporous 1D channels defined by Y3+ and L, with [CrMo6O18(PET)2] arranged orderly between adjacent Lvia electrostatic interactions. Upon using POMOF-1 as a catalyst and H2O2 as an oxidant, a variety of amines could be effectively converted to value-added amides, imines and azobenzenes via the oxidative cross-coupling with alcohols or homo-coupling. In particular, POMOF-1 showed dramatically improved activity for the N-formylation reaction owing to the synergistic and confinement effect, with the yield of amides up to 95% and 4 times higher than that of homogeneous [CrMo6O18(PET)2]. Meanwhile, the oxidative homo-coupling of arylmethylamines and arylamines can be facilely tuned by adjustment of the amount of oxidant, solvent and additive, affording imines and azobenzenes in high selectivity and yield, respectively. POMOF-1 is robust and can be reused for 5 cycles with little loss of catalytic activity and structural integrity. The work demonstrates that the combination of catalytically active POMs with crystalline porous MOFs holds great potential to build robust and recyclable heterogeneous systems with enhanced activity and selectivity for multifunctional catalysis.

Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid.

Genetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.

Semisynthesis of Glutamine-Methylated Proteins Enabled by Genetic Code Expansion.

Gln methylation is a newly identified histone mark and mediates ribosomal biogenesis. Site-specifically Gln-methylated proteins are valuable tools to elucidate the biological implications of this modification. Herein, we describe a protocol to generate histones with site-specific Gln methylation in a semisynthetic manner. Firstly, an esterified glutamic acid analogue (BnE) is genetically encoded into proteins by genetic code expansion with high efficiency, which can be quantitatively converted into an acyl hydrazide via hydrazinolysis. Then, through a reaction with acetyl acetone, the acyl hydrazide is converted to reactive Knorr pyrazole. Finally, the in situ generated Knorr pyrazole is incubated with methylamine to give Gln methylation.

Bioconjugation via Hetero-Selective Clamping of Two Different Amines with ortho-Phthalaldehyde.

Amino groups are common in both natural and synthetic compounds and offer a very attractive class of endogenous handles for bioconjugation. However, the ability to differentiate two types of amino groups and join them with high hetero-selectivity and efficiency in a complex setting remains elusive. Herein, we report a new method for bioconjugation via one-pot chemoselective clamping of two different amine nucleophiles using a simple ortho-phthalaldehyde (OPA) reagent. Various α-amino acids, aryl amines, and secondary amines can be crosslinked to the ϵ-amino side chain of lysine on peptides or proteins with high efficiency and hetero-selectivity. This method offers a simple and powerful means to crosslink small molecule drugs, imaging probes, peptides, proteins, carbohydrates, and even virus particles without any pre-functionalization.

N-Glycan Engineering: Constructing the N-GlcNAc Stump.

N-Glycosylation is often essential for the structure and function of proteins. However, N-glycosylated proteins from natural sources exhibit considerable heterogeneity in the appended oligosaccharides, bringing daunting challenges to corresponding basic research and therapeutic applications. To address this issue, various synthetic, enzymatic, and chemoenzymatic approaches have been elegantly designed. Utilizing the endoglycosidase-catalyzed transglycosylation method, a single N-acetylglucosamine (N-GlcNAc, analogous to a tree stump) on proteins can be converted to various homogeneous N-glycosylated forms, thereby becoming the focus of research efforts. In this concept article, we briefly introduce the methods that allow the generation of N-GlcNAc and its close analogues on proteins and peptides and highlight the current challenges and opportunities the scientific community is facing.

Expanding the Scope of Genetically Encoded Lysine Post-Translational Modifications with Lactylation, ß-Hydroxybutyrylation and Lipoylation.

Post-translational modifications (PTMs) occurring on lysine residues, especially diverse forms of acylations, have seen rapid growth over the past two decades. Among them, lactylation and ß-hydroxybutyrylation of lysine side-chains are newly identified histone marks and their implications in physiology and diseases have aroused broad research interest. Meanwhile, lysine lipoylation is highly conserved in diverse organisms and well known for its pivotal role in central metabolic pathways. Recent findings in the proteomic profiling of protein lipoylation have nonetheless suggested a pressing need for an extensive investigation. For both basic and applied research, it is necessary to prepare PTM-bearing proteins particularly in a site-specific manner. Herein, we use genetic code expansion to site-specifically generate these lysine PTMs, including lactylation, ß-hydroxybutyrylation and lipoylation in proteins in E. coli and mammalian cells. Notably, using strategies including activity-based selection, screening and rational design, unique pyrrolysyl-tRNA synthetase variants were successfully evolved for each of the three non-canonical amino acids, which enabled efficient production of recombinant proteins. Through encoding these ncAAs, we examined the deacylase activities of mammalian sirtuins to these modifications, and importantly we unfold the lipoamidase activity of several sirtuins.

Cerium-oxo clusters for photocatalytic aerobic oxygenation of sulfides to sulfoxides.

Two cerium-oxo clusters (COCs) 1 and 2 are constructed by self-assembly of cerium ions and carboxylate ligands. Both clusters feature spherical structures resembling the key moiety of fluorite phase CeO2, and 1 exhibits high activity and selectivity for the photocatalytic aerobic oxygenation of sulfides to sulfoxides based on the switch between the Ce(IV/III) redox couple.

Sirtuin-Derived Covalent Binder for the Selective Recognition of Protein Crotonylation.

Lysine crotonylation (Kcr) is increasingly recognized as a key protein post-translational modification. However, selective detection and enrichment of crotonylated proteins remains a challenging task. Herein we present a covalent binder for the selective recognition of protein crotonylation. Based on proximity-induced crosslinking, a bacterial sirtuin (CobB) was remodeled with genetically installed thiol-bearing noncanonical amino acids at the Kcr-interacting site, which subsequently could react with Kcr sites in a unique NAD+ -dependent manner. The covalent binder has been used to selectively recognize crotonylated proteins in extracted histone samples and in fixed cells.

Site-Specific Protein Modification with Reducing Carbohydrates.

Protein glycosylation plays critical roles in many biological processes. However, the fundamental study and application of glycobiology are hindered by the heterogeneousness of oligosaccharides in natural glycoproteins and the difficulty in constructing glycoproteins of human design. Herein, we describe a semisynthetic method to site-specifically modify proteins with reducing carbohydrates. The method involves the genetic incorporation of a side-chain-esterified aspartate, which was subsequently quantitatively converted into alanine-ß-hydrazide (Aßz), and chemoselective conjugation of Aßz with a range of readily available reducing carbohydrates. The resulting Aßz-linked GlcNAc is a close mimic of native N-GlcNAc and could be installed on various proteins, including IL-17A and RNase A. Notably, Aßz-linked GlcNAc on proteins reacted with biantennary oligosaccharide oxazoline derivatives through endoglycosidase-catalyzed transglycosylation reactions to enable the assembly of homogeneous glycans on proteins.

Transformation of polyvinyl chloride (PVC) into a versatile and efficient adsorbent of Cu(II) cations and Cr(VI) anions through hydrothermal treatment and sulfonation.

The reuse of waste polyvinyl chloride (PVC) has drawn much attention as it can reduce plastic waste and associated pollution, and provide valuable raw materials and products. In this study, sulfonated PVC-derived hydrochar (HS-PVC) was synthesized by two-stage hydrothermal treatment (HT) and sulfonation, and shown to be a versatile adsorbent. The removal of Cu(II) cations and Cr(VI) anions using HS-PVC reached 81.2 ± 1.6% and 60.3 ± 3.8%, respectively. The first stage of HT was crucial for the dichlorination of PVC and the formation of an aromatic structure. This stage guaranteed the introduction of -SO3H onto PVC-derived hydrochar through subsequent sulfonation. HT intensities (i.e., temperature and time) and sulfonation intensity strongly determined the adsorption capacity of HS-PVC. Competitive adsorption between Cu(II) and Cr(VI) onto HS-PVC was demonstrated by binary and preloading adsorption. The proposed Cu(II) cations adsorption mechanism was electrostatic adsorption, while Cr(VI) were possibly complexed by the phenolic -OH and reduced to Cr(III) cations by CC groups in HS-PVC. In addition, HS-PVC derived from PVC waste pipes performed better than PVC powder for Cu(II) and Cr(VI) removal (＞90%). This study provides an efficient method for recycling waste PVC and production of efficient adsorbents.

Toward an Orthogonal Protein Lysine Acylation and Deacylation System.

Lysine acetylation is one of the most basic molecular mechanisms to mediate protein functions in living organisms, and its abnormal regulation has been linked to many diseases. The drug development associated to this process is of great significance but severely hindered by the complex interplay of lysine acetylation and deacetylation in thousands of proteins, and we reasoned that targeting a specific protein acetylation or deacetylation event instead of the related enzymes should be a feasible solution to this issue. Toward this goal, we devised an orthogonal lysine acylation and deacylation (OKAD) system, which potentially could precisely dissect the biological consequence of an individual acetylation or deacetylation event in living cells. The system includes a genetically encoded acylated lysine (PhOAcK) that is not a substrate of endogenous deacetylases, and an evolved sirtuin (CobB2/CobB3) that displays PhOAcK deacylase activities as well as reduced deacetylase activities. We believe the strategy introduced here holds potential for future in-depth biological applications.

Diverse protein manipulations with genetically encoded glutamic acid benzyl ester.

Site-specific modification of proteins has significantly advanced the use of proteins in biological research and therapeutics development. Among various strategies aimed at this end, genetic code expansion (GCE) allows structurally and functionally distinct non-canonical amino acids (ncAAs) to be incorporated into specific sites of a protein. Herein, we genetically encode an esterified glutamic acid analogue (BnE) into proteins, and demonstrate that BnE can be applied in different types of site-specific protein modifications, including N-terminal pyroglutamation, caging Glu in the active site of a toxic protein, and endowing proteins with metal chelator hydroxamic acid and versatile reactive handle acyl hydrazide. Importantly, novel epigenetic mark Gln methylation is generated on histones via the derived acyl hydrazide handle. This work provides useful and unique tools to modify proteins at specific Glu or Gln residues, and complements the toolbox of GCE.

A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition.

Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.

Genetically encoding ε-N-benzoyllysine in proteins.

Lysine ε-N-benzoylation is a recently identified PTM occurring on histone proteins, and herein we genetically encoded ε-N-benzoyl-lysine (BzK) into recombinant proteins in E. coli and mammalian cells, and applied it for the modification of histone proteins and the analysis of sirtuin debenzoylase activity.