New enzyme insights drive advances in commercial ethanol production.
Abstract Innovations at a small scale through enzyme discovery in the laboratory can have large scale impacts when rolled out in an industrial process, and this is evidenced in recent advances for commercial ethanol production. In the starch to ethanol processes, new enzyme product launches squeeze even more value from an already efficient process, as evidenced in new use of proteases for oil release and cellulases for downstream processing and ethanol yield. As for biomass to ethanol, diverse new thermophilic enzymes, expansins and auxiliary activity (AA) collections are growing rapidly. Our mechanistic understan...
Source: Current Opinion in Chemical Biology - March 25, 2014 Category: Biochemistry Authors: Harris PV, Xu F, Kreel NE, Kang C, Fukuyama S Tags: Curr Opin Chem Biol Source Type: research

Hemoprotein-based supramolecular assembling systems.
Abstract Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures...
Source: Current Opinion in Chemical Biology - March 19, 2014 Category: Biochemistry Authors: Oohora K, Hayashi T Tags: Curr Opin Chem Biol Source Type: research

Model complexes of key intermediates in fungal cytochrome P450 nitric oxide reductase (P450nor).
Abstract Denitrifying bacteria and fungi efficiently detoxify the toxic metabolite nitric oxide (NO) through reduction to nitrous oxide (N2O) using nitric oxide reductase (NOR) enzymes. In fungi, for example Fusarium oxysporum, NO is reduced by a Cytochrome P450 NOR (P450nor). This enzyme contains a heme b center coordinated to a proximal cysteinate ligand in the active site. In the proposed mechanism of P450nor, the ferric heme binds NO first to form a ferric heme-nitrosyl complex, which is subsequently reduced by NAD(P)H to generate a ferrous HNO species as the next key intermediate. Recently, key progress has b...
Source: Current Opinion in Chemical Biology - March 11, 2014 Category: Biochemistry Authors: McQuarters AB, Wirgau NE, Lehnert N Tags: Curr Opin Chem Biol Source Type: research

Expanding P450 catalytic reaction space through evolution and engineering.
Abstract Advances in protein and metabolic engineering have led to wider use of enzymes to synthesize important molecules. However, many desirable transformations are not catalyzed by any known enzyme, driving interest in understanding how new enzymes can be created. The cytochrome P450 enzyme family, whose members participate in xenobiotic metabolism and natural products biosynthesis, catalyzes an impressive range of difficult chemical reactions that continues to grow as new enzymes are characterized. Recent work has revealed that P450-derived enzymes can also catalyze useful reactions previously accessible only ...
Source: Current Opinion in Chemical Biology - March 11, 2014 Category: Biochemistry Authors: McIntosh JA, Farwell CC, Arnold FH Tags: Curr Opin Chem Biol Source Type: research

Recent achievments in the design and engineering of artificial metalloenzymes.
TR Abstract Herein, we highlight a selection of recent successes in the creation of artificial metalloenzymes. A particular emphasis is set on different anchoring methods to incorporate the abiotic metal cofactor within the host protein as well as promising strategies for the de novo design of artificial metalloenzymes. Both approaches yield promiscuous catalytic activities which expand the catalytic repertoire of biocatalysis and synthetic biology. Moreover, we summarize laboratory evolution protocols which have contributed to unravel the full potential of artificial metalloenzymes. PMID: 24608081 [PubMed -...
Source: Current Opinion in Chemical Biology - March 5, 2014 Category: Biochemistry Authors: Dürrenberger M, Ward TR Tags: Curr Opin Chem Biol Source Type: research

New developments in 'ene'-reductase catalysed biological hydrogenations.
Abstract Asymmetric biocatalytic hydrogenations are important reactions performed primarily by members of the Old Yellow Enzyme family. These reactions have great potential in the chemosynthesis of a variety of industrially useful synthons due to the generation of up to two stereogenic centres. In this review, additional enzyme classes capable of asymmetric hydrogenations will be discussed, as will examples of multienzyme cascading reactions. New and improved technology that enhances the commercial viability of biotransformations are included, such as the nicotinamide coenzyme-independent reactions. This review wi...
Source: Current Opinion in Chemical Biology - March 5, 2014 Category: Biochemistry Authors: Toogood HS, Scrutton NS Tags: Curr Opin Chem Biol Source Type: research

Artificial metalloenzymes for enantioselective catalysis.
Abstract Artificial metalloenzymes have emerged over the last decades as an attractive approach towards combining homogeneous catalysis and biocatalysis. A wide variety of catalytic transformations have been established by artificial metalloenzymes, thus establishing proof of concept. The field is now slowly transforming to take on new challenges. These include novel designs, novel catalytic reactions, some of which have no equivalent in both homogenous catalysis and biocatalysis and the incorporation of artificial metalloenzymes in chemoenzymatic cascades. Some of these developments represent promising steps towa...
Source: Current Opinion in Chemical Biology - March 5, 2014 Category: Biochemistry Authors: Bos J, Roelfes G Tags: Curr Opin Chem Biol Source Type: research

Metal-based anticancer chemotherapeutic agents.
We describe here some most recent progresses on Pt(IV) prodrugs which can be activated once enter tumor cells, polynuclear Pt(II) complexes which have unique DNA binding ability and mode, anti-metastatic Ru(II)/Ru(III) complexes, and Au(I)/Au(III) and Ti(IV) antitumor active complexes. The key focuses of these studies lie in finding novel metal complexes which could potentially overcome the hurdles of current clinical drugs including toxicity, resistance and other pharmacological deficiencies. PMID: 24608084 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - March 5, 2014 Category: Biochemistry Authors: Muhammad N, Guo Z Tags: Curr Opin Chem Biol Source Type: research

De novo protein components for oxidoreductase assembly and biological integration.
Abstract Manmade protein design is founded on the concept that a protein with minimal evolutionary complexity is a viable scaffold for incorporating simple engineering elements responsible for function in natural proteins and enzymes. There has been significant, recent success both in fabricating manmade protein components that exhibit functional elements inspired by natural oxidoreductases, and the functional integration of this componentry with natural proteins and biochemical pathways. Here we discuss the state of the art in de novo oxidoreductase construction, focusing on the diverse manmade componentry availa...
Source: Current Opinion in Chemical Biology - March 4, 2014 Category: Biochemistry Authors: Watkins DW, Armstrong CT, Anderson JR Tags: Curr Opin Chem Biol Source Type: research

Oxidations catalyzed by fungal peroxygenases.
Abstract The enzymatic oxyfunctionalization of organic molecules under physiological conditions has attracted keen interest from the chemical community. Unspecific peroxygenases (EC 1.11.2.1) secreted by fungi represent an intriguing enzyme type that selectively transfers peroxide-borne oxygen with high efficiency to diverse substrates including unactivated hydrocarbons. They are glycosylated heme-thiolate enzymes that form a separate superfamily of heme proteins. Among the catalyzed reactions are hydroxylations, epoxidations, dealkylations, oxidations of organic hetero atoms and inorganic halides as well as one-e...
Source: Current Opinion in Chemical Biology - March 4, 2014 Category: Biochemistry Authors: Hofrichter M, Ullrich R Tags: Curr Opin Chem Biol Source Type: research

Metal complexes as structural templates for targeting proteins.
This article reviews recent advances in the design and discovery of inert metal complexes as protein binders. In these metal-based probes or drug candidates, the metal is supposed to exert a purely structural role by organizing the coordinating ligands in the three dimensional space to achieve a shape and functional group complementarity with the targeted protein pockets. Presented examples of sandwich, half-sandwich and octahedral d(6)-metal complexes reinforce previous perceptions that metal complexes are highly promising scaffolds for the design of small-molecule protein binders and complement the molecular diversity of...
Source: Current Opinion in Chemical Biology - February 18, 2014 Category: Biochemistry Authors: Dörr M, Meggers E Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Arrays.
PMID: 24525056 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - February 10, 2014 Category: Biochemistry Authors: Matson RS, Smith DF Tags: Curr Opin Chem Biol Source Type: research

Metalloenzyme design and engineering through strategic modifications of native protein scaffolds.
Abstract Metalloenzymes are among the major targets of protein design and engineering efforts aimed at attaining novel and efficient catalysis for biochemical transformation and biomedical applications, due to the diversity of functions imparted by the metallo-cofactors along with the versatility of the protein environment. Naturally evolved protein scaffolds can often serve as robust foundations for sustaining artificial active sites constructed by rational design, directed evolution, or a combination of the two strategies. Accumulated knowledge of structure-function relationship and advancement of tools such as ...
Source: Current Opinion in Chemical Biology - February 7, 2014 Category: Biochemistry Authors: Petrik ID, Liu J, Lu Y Tags: Curr Opin Chem Biol Source Type: research

The neoglycolipid (NGL)-based oligosaccharide microarray system poised to decipher the meta-glycome.
Abstract The neoglycolipid (NGL) technology is the basis of a state-of-the-art oligosaccharide microarray system. The NGL-based microarray system in the Glycosciences Laboratory Imperial College London (http://www3.imperial.ac.uk/glycosciences) is one of the two leading platforms for glycan microarrays, being offered for screening analyses to the broad biomedical community. Highlighted in this review are the sensitivity of the analysis system and, coupled with mass spectrometry, the provision for generating 'designer' microarrays from glycomes to identify novel ligands of biological relevance. Among recent applica...
Source: Current Opinion in Chemical Biology - February 5, 2014 Category: Biochemistry Authors: Palma AS, Feizi T, Childs RA, Chai W, Liu Y Tags: Curr Opin Chem Biol Source Type: research

The application of glycosphingolipid arrays to autoantibody detection in neuroimmunological disorders.
Abstract Humans with autoimmune peripheral neuropathies frequently harbour serum antibodies to single glycosphingolipids, especially gangliosides. Recently it has been appreciated that glycolipid and lipid complexes, formed from two or more individual species, can interact to create molecular shapes capable of being recognised by these autoantibodies whilst not binding to the single individuals. As a result of this, novel autoantibody targets have been identified. This newly termed 'combinatorial glycomic' approach has provided the impetus to redesigning the assay methodologies traditionally used in the neuropathy...
Source: Current Opinion in Chemical Biology - February 1, 2014 Category: Biochemistry Authors: Galban-Horcajo F, Halstead SK, McGonigal R, Willison HJ Tags: Curr Opin Chem Biol Source Type: research

Arraying the post-translational glycoproteome (PTG).
Abstract Glycosylation is chemically the most complex post-translational modification of proteins and therefore understanding the structural and biological implications of post-translational glycosylation is a major challenge. The need for rapid and reliable investigations of protein-glycan interaction events and the substantial efforts required to synthesize glycans and glycopeptides with a variety of structures has called for the development of miniaturized analytical techniques. In the last decade, glycan and glycopeptide microarrays have enabled high-throughput analysis of diverse protein-glycan interactions. ...
Source: Current Opinion in Chemical Biology - January 29, 2014 Category: Biochemistry Authors: Blixt O, Westerlind U Tags: Curr Opin Chem Biol Source Type: research

Chemistry of natural glycan microarrays.
Abstract Glycan microarrays have become indispensable tools for studying protein-glycan interactions. Along with chemo-enzymatic synthesis, glycans isolated from natural sources have played important roles in array development and will continue to be a major source of glycans. N-glycans and O-glycans from glycoproteins, and glycans from glycosphingolipids (GSLs) can be released from corresponding glycoconjugates with relatively mature methods, although isolation of large numbers and quantities of glycans is still very challenging. Glycosylphosphatidylinositol (GPI) anchors and glycosaminoglycans (GAGs) are less re...
Source: Current Opinion in Chemical Biology - January 29, 2014 Category: Biochemistry Authors: Song X, Heimburg-Molinaro J, Cummings RD, Smith DF Tags: Curr Opin Chem Biol Source Type: research

Using glycan microarrays to understand immunity.
Abstract Host immunity represents a complex array of factors that evolved to provide protection against potential pathogens. While many factors regulate host immunity, glycan binding proteins (GBPs) appear to play a fundamental role in orchestrating this process. In addition, GBPs also reside at the key interface between host and pathogen. While early studies sought to understand GBP glycan binding specificity, limitations in the availability of test glycans made it difficult to elucidate a detailed understanding of glycan recognition. Recent developments in glycan microarray technology revolutionized analysis of ...
Source: Current Opinion in Chemical Biology - January 28, 2014 Category: Biochemistry Authors: Arthur CM, Cummings RD, Stowell SR Tags: Curr Opin Chem Biol Source Type: research

Recent developments in copper and zinc homeostasis in bacterial pathogens.
Abstract Copper and zinc homeostasis systems in pathogenic bacteria are required to resist host efforts to manipulate the availability and toxicity of these metal ions. Central to this microbial adaptive response is the involvement of metal-trafficking and metal-sensing proteins that ultimately exercise control of metal speciation in the cell. Cu-specific and Zn-specific metalloregulatory proteins regulate the transcription of metal-responsive genes while metallochaperones and related proteins ensure that these metals are appropriately buffered by the intracellular milieu and delivered to correct intracellular tar...
Source: Current Opinion in Chemical Biology - January 21, 2014 Category: Biochemistry Authors: Braymer JJ, Giedroc DP Tags: Curr Opin Chem Biol Source Type: research

DNA directed immobilization glycocluster array: applications and perspectives.
van F Abstract The present review concerns the recent advances in DNA directed immobilization (DDI) based glycocluster array. The impact of glycan immobilization on subsequent interactions with protein is discussed and the consequent pros and cons of DDI-based glycocluster array are reviewed. Finally, application in the discovery of anti-pathogen molecules is illustrated by screening for galactose or fucose glycoclusters targeting two Pseudomonas aeruginosa virulence factors (PA-IL and PA-IIL). PMID: 24440778 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - January 15, 2014 Category: Biochemistry Authors: Chevolot Y, Laurenceau E, Phaner-Goutorbe M, Monnier V, Souteyrand E, Meyer A, Géhin T, Vasseur JJ, Morvan F Tags: Curr Opin Chem Biol Source Type: research

Synthetic biology.
PMID: 24268561 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - November 20, 2013 Category: Biochemistry Authors: Arkin AP, Fussenegger M Tags: Curr Opin Chem Biol Source Type: research

A wise consistency: engineering biology for conformity, reliability, predictability.
Abstract The next generation of synthetic biology applications will increasingly involve engineered organisms that exist in intimate contact with humans, animals and the rest of the environment. Examples include cellular and viral approaches for maintaining and improving health in humans and animals. The need for reliable and specific function in these environments may require more complex system designs than previously. In these cases the uncertainties in the behavior of biological building blocks, their hosts and their environments present a challenge for design of predictable and safe systems. Here, we review s...
Source: Current Opinion in Chemical Biology - November 20, 2013 Category: Biochemistry Authors: Arkin AP Tags: Curr Opin Chem Biol Source Type: research

Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression.
Abstract Cells use regulatory networks to perform computational operations to respond to their environment. Reliably manipulating such networks would be valuable for many applications in biotechnology; for example, in having genes turn on only under a defined set of conditions or implementing dynamic or temporal control of expression. Still, building such synthetic regulatory circuits remains one of the most difficult challenges in genetic engineering and as a result they have not found widespread application. Here, we review recent advances that address the key challenges in the forward design of genetic circuits...
Source: Current Opinion in Chemical Biology - November 19, 2013 Category: Biochemistry Authors: Nielsen AA, Segall-Shapiro TH, Voigt CA Tags: Curr Opin Chem Biol Source Type: research

Pairwise interactions in collagen and the design of heterotrimeric helices.
Abstract A comprehensive survey of single amino acid substitutions in the canonical Xaa-Yaa-Gly repeat has laid the ground work for our understanding of the collagen triple helix. Building upon this foundation requires understanding pairwise amino acid interactions which will allow us to prepare heterotrimeric helices with great specificity in addition to an overall improved control over helix structure and stability. Furthermore, detailed studies on these interactions will help us understand collagen's n structure, assembly mechanism and stability. The most important pairwise interaction so far identified in the ...
Source: Current Opinion in Chemical Biology - November 16, 2013 Category: Biochemistry Authors: Jalan AA, Hartgerink JD Tags: Curr Opin Chem Biol Source Type: research

Synthetic biomolecules.
PMID: 24211050 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - November 6, 2013 Category: Biochemistry Authors: Woolfson DN, Hung SC Tags: Curr Opin Chem Biol Source Type: research

Targeting and mimicking collagens via triple helical peptide assembly.
Abstract As the major structural component of the extracellular matrix, collagen plays a crucial role in tissue development and regeneration. Since structural and metabolic abnormalities of collagen are associated with numerous debilitating diseases and pathologic conditions, the ability to target collagens of diseased tissues could lead to new diagnostics and therapeutics. Collagen is also a natural biomaterial widely used in drug delivery and tissue engineering, and construction of synthetic collagen-like materials is gaining interests in the biomaterials community. The unique triple helical structure of collage...
Source: Current Opinion in Chemical Biology - November 5, 2013 Category: Biochemistry Authors: Li Y, Yu SM Tags: Curr Opin Chem Biol Source Type: research

Incorporating metals into de novo proteins.
Abstract The de novo design of artificial metalloproteins from first-principles is a powerful strategy with which to establish the minimum structure required for function, as well as to identify the important design features for tuning the chemistry of the coordinated metal ion. Herein we describe recent contributions to this field, covering metallo-porphyrin, mononuclear and multinuclear metal ion sites engineered into de novo proteins. Using miniature artificial scaffolds these examples demonstrate that complex natural protein folds are not required to mimic naturally occurring metal ion sites in proteins. More ...
Source: Current Opinion in Chemical Biology - October 31, 2013 Category: Biochemistry Authors: Peacock AF Tags: Curr Opin Chem Biol Source Type: research

New designed protein assemblies.
ala R Abstract Self-assembly is an essential concept of all organisms. Polypeptides self-assemble either within a single polypeptide chain or through assembly of protein domains. Recent advances in designed protein assemblies were achieved by genetic or chemical linkage of oligomerization domains and by engineering new interaction interfaces, which resulted in formation of lattices and cage-like protein assemblies. The absence of new experimentally determined protein folds in the last few years underlines the challenge of designing new folds. Recently a new strategy for designing self-assembly of a polypeptide fol...
Source: Current Opinion in Chemical Biology - October 31, 2013 Category: Biochemistry Authors: Božič S, Doles T, Gradišar H, Jerala R Tags: Curr Opin Chem Biol Source Type: research

Druggable protein-protein interactions-from hot spots to hot segments.
Abstract Protein-Protein Interactions (PPIs) mediate numerous biological functions. As such, the inhibition of specific PPIs has tremendous therapeutic value. The notion that these interactions are 'undruggable' has petered out with the emergence of more and more successful examples of PPI inhibitors, expanding considerably the scope of potential drug targets. The accumulated data on successes in the inhibition of PPIs allow us to analyze the features that are required for such inhibition. Whereas it has been suggested and shown that targeting hot spots at PPI interfaces is a good strategy to achieve inhibition, i...
Source: Current Opinion in Chemical Biology - October 31, 2013 Category: Biochemistry Authors: London N, Raveh B, Schueler-Furman O Tags: Curr Opin Chem Biol Source Type: research

Innovation by homologous recombination.
Abstract Swapping fragments among protein homologs can produce chimeric proteins with a wide range of properties, including properties not exhibited by the parents. Computational methods that use information from structures and sequence alignments have been used to design highly functional chimeras and chimera libraries. Recombination has generated proteins with diverse thermostability and mechanical stability, enzyme substrate specificity, and optogenetic properties. Linear regression, Gaussian processes, and support vector machine learning have been used to model sequence-function relationships and predict usefu...
Source: Current Opinion in Chemical Biology - October 29, 2013 Category: Biochemistry Authors: Trudeau DL, Smith MA, Arnold FH Tags: Curr Opin Chem Biol Source Type: research

Synthetic heparin and heparan sulfate oligosaccharides and their protein interactions.
Abstract Heparin and heparan sulfate bind a host of basic proteins that take advantage of the sugar's dense structural information. The significance of these interactions in various aspects of development, physiology, and disease stimulated keen interest in evaluating structure-activity relationships. The well-defined heparin and heparan sulfate oligosaccharides needed for these studies can be mainly accessed by chemical synthesis and, more recently by chemoenzymatic means. The various synthetic strategies available to chemical synthesis have recently enabled the acquisition of several regular and irregular sequen...
Source: Current Opinion in Chemical Biology - October 29, 2013 Category: Biochemistry Authors: Zulueta MM, Lin SY, Hu YP, Hung SC Tags: Curr Opin Chem Biol Source Type: research

Synthesis of sialic acid-containing saccharides.
Abstract Sialic acids are a diverse family of negatively charged monosaccharides with a shared nine-carbon carboxylated backbone, and they often serve as the terminal positions of cell surface glycoproteins and glycolipids. Sialic acids play essential roles in mediating or modulating numerous pathological, biological, and immunological recognition events. Advances in synthesis have provided chemically well-defined and structurally homogeneous sialic acid-containing carbohydrates that are crucial for studying glycobiology. This review highlights recent innovations in the chemical and chemoenzymatic synthesis of dif...
Source: Current Opinion in Chemical Biology - October 29, 2013 Category: Biochemistry Authors: Adak AK, Yu CC, Liang CF, Lin CC Tags: Curr Opin Chem Biol Source Type: research

In vivo chemistry.
PMID: 24156981 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - October 21, 2013 Category: Biochemistry Authors: Bertozzi CR, Wu P Tags: Curr Opin Chem Biol Source Type: research

Synthetic probes of glycosaminoglycan function.
Abstract Glycosaminoglycans (GAGs) participate in many critical biological processes by modulating the activities of a wide range of proteins, including growth factors, chemokines, and viral receptors. Recent studies using synthetic oligosaccharides and glycomimetic polymers have established the importance of specific structural determinants in controlling GAG function. These findings illustrate the power of synthetic molecules to elucidate glycan-mediated signaling events, as well as the prospect of further advancements to understand the roles of GAGs in vivo and explore their therapeutic potential. PMID: 24...
Source: Current Opinion in Chemical Biology - October 19, 2013 Category: Biochemistry Authors: Griffin ME, Hsieh-Wilson LC Tags: Curr Opin Chem Biol Source Type: research

Recent progress in synthetic and biological studies of GPI anchors and GPI-anchored proteins.
Abstract Covalent attachment of glycosylphosphatidylinositols (GPIs) to the protein C-terminus is one of the most common posttranslational modifications in eukaryotic cells. In addition to anchoring surface proteins to the cell membrane, GPIs also have many other important biological functions, determined by their unique structure and property. This account has reviewed the recent progress made in disclosing GPI and GPI-anchored protein biosynthesis, in the chemical and chemoenzymatic synthesis of GPIs and GPI-anchored proteins, and in understanding the conformation, organization, and distribution of GPIs in the l...
Source: Current Opinion in Chemical Biology - October 12, 2013 Category: Biochemistry Authors: Yu S, Guo Z, Johnson C, Gu G, Wu Q Tags: Curr Opin Chem Biol Source Type: research

Synthetic Biology: evolution or revolution? A co-founder's perspective.
Abstract In this article, we relate the story of Synthetic Biology's birth, from the perspective of a co-founder, and consider its original premise-that standardization and abstraction of biological components will unlock the full potential of biological engineering. The standardization ideas of Synthetic Biology emerged in the late 1990s from a convergence of research on cellular computing, and were motivated by an array of applications from tissue regeneration to bio-sensing to mathematical programming. As the definition of Synthetic Biology has grown to be synonymous with Biological Engineering and Biotechnolog...
Source: Current Opinion in Chemical Biology - October 11, 2013 Category: Biochemistry Authors: Gardner TS, Hawkins K Tags: Curr Opin Chem Biol Source Type: research

A journey toward Bioorthogonal Profiling of Protein Methylation inside living cells.
Abstract Human protein methyltransferases (PMTs) play essential roles through methylating histone and nonhistone targets. It is very challenging to profile global methylation (or methylome) in the context of relevant cellular settings. Unlike other posttranslational modifications such as lysine acetylation or Ser/Thr/Tyr/His phosphorylation, methylation of lysine or arginine does not significantly alter its physical properties (e.g. charge and size) and therefore may not be probed readily by conventional biological tools such antibodies. It is also not trivial to assign unambiguously dynamic methylation events to ...
Source: Current Opinion in Chemical Biology - September 12, 2013 Category: Biochemistry Authors: Wang R, Luo M Tags: Curr Opin Chem Biol Source Type: research

Expanding room for tetrazine ligations in the in vivo chemistry toolbox.
Abstract There is tremendous interest in developing and refining methods to predictably perform chemical reactions within the framework of living systems. Here we review recent advances in applying tetrazine cycloadditions to live cell and in vivo chemistry. We highlight new syntheses of the tetrazine and dienophile precursors useful for in vivo studies. We briefly overview the use of this reaction in combination with unnatural amino acid technology and discuss applications involving the imaging of glycans on live cells. An emerging area is the use of tetrazine ligations for the development of in vivo imaging prob...
Source: Current Opinion in Chemical Biology - September 7, 2013 Category: Biochemistry Authors: Sečkutė J, Devaraj NK Tags: Curr Opin Chem Biol Source Type: research

Editorial overview.
PMID: 24018167 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - September 6, 2013 Category: Biochemistry Authors: Novotny MV, Kennedy RT Tags: Curr Opin Chem Biol Source Type: research

Developing top down proteomics to maximize proteome and sequence coverage from cells and tissues.
Abstract Mass spectrometry based proteomics generally seeks to identify and characterize protein molecules with high accuracy and throughput. Recent speed and quality improvements to the independent steps of integrated platforms have removed many limitations to the robust implementation of top down proteomics (TDP) for proteins below 70kDa. Improved intact protein separations coupled to high-performance instruments have increased the quality and number of protein and proteoform identifications. To date, TDP applications have shown>1000 protein identifications, expanding to an average of ∼3-4 more proteoform...
Source: Current Opinion in Chemical Biology - August 26, 2013 Category: Biochemistry Authors: Ahlf DR, Thomas PM, Kelleher NL Tags: Curr Opin Chem Biol Source Type: research

trans-Cyclooctene-a stable, voracious dienophile for bioorthogonal labeling.
Abstract Discussed herein is the development and advancement of trans-cyclooctene as a tool for facilitating bioorthogonal labeling through reactions with s-tetrazines. While a number of strained alkenes have been shown to combine with tetrazines for applications in bioorthogonal labeling, trans-cyclooctene enables fastest reactivity at low concentration with rate constants in excess of k2=10(6)M(-1)s(-1). In the present article, we describe advances in computation and synthesis that have enabled applications in chemical biology and nuclear medicine. PMID: 23978373 [PubMed - as supplied by publisher] (Source:...
Source: Current Opinion in Chemical Biology - August 23, 2013 Category: Biochemistry Authors: Selvaraj R, Fox JM Tags: Curr Opin Chem Biol Source Type: research

Single-cell imaging mass spectrometry.
In this report, we estimate the availability of proteins and lipids in a single cell and discuss strategies employed to improve sensitivity at the single-cell level. PMID: 23948695 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 12, 2013 Category: Biochemistry Authors: Passarelli MK, Ewing AG Tags: Curr Opin Chem Biol Source Type: research

Teaching old NCATs new tricks: using non-canonical amino acid tagging to study neuronal plasticity.
Abstract The non-canonical amino acid labeling techniques BONCAT (bioorthogonal non-canonical amino acid tagging) and FUNCAT (fluorescent non-canonical amino acid tagging) enable the specific identification and visualization of newly synthesized proteins. Recently, these techniques have been applied to neuronal systems to elucidate protein synthesis dynamics during plasticity, identify stimulation-induced proteomes and subproteomes and to investigate local protein synthesis in specific subcellular compartments. The next generation of tools and applications, reviewed here, includes the development of new tags, the ...
Source: Current Opinion in Chemical Biology - August 9, 2013 Category: Biochemistry Authors: Hinz F, Dieterich D, Schuman E Tags: Curr Opin Chem Biol Source Type: research

Cell-selective metabolic labeling of biomolecules with bioorthogonal functionalities.
Abstract Metabolic labeling of biomolecules with bioorthogonal functionalities enables visualization, enrichment, and analysis of the biomolecules of interest in their physiological environments. This versatile strategy has found utility in probing various classes of biomolecules in a broad range of biological processes. On the other hand, metabolic labeling is nonselective with respect to cell type, which imposes limitations for studies performed in complex biological systems. Herein, we review the recent methodological developments aiming to endow metabolic labeling strategies with cell-type selectivity. The cel...
Source: Current Opinion in Chemical Biology - August 5, 2013 Category: Biochemistry Authors: Xie R, Hong S, Chen X Tags: Curr Opin Chem Biol Source Type: research

High sensitivity capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for the rapid analysis of complex proteomes.
Abstract The vast majority of bottom-up proteomic studies employ reversed-phase separation of tryptic digests coupled with electrospray ionization tandem mass spectrometry. These studies are remarkably successful for the analysis of samples containing micrograms of protein. However, liquid chromatography tends to perform poorly for samples containing nanogram amounts of protein, presumably due to loss of trace-level peptides within the chromatographic system. Capillary zone electrophoresis provides a much simpler flow system and would appear to be an attractive alternative to liquid chromatography for separation o...
Source: Current Opinion in Chemical Biology - August 1, 2013 Category: Biochemistry Authors: Sun L, Zhu G, Yan X, Dovichi NJ Tags: Curr Opin Chem Biol Source Type: research

Tools for probing and perturbing O-GlcNAc in cells and in vivo.
Abstract Intracellular glycosylation of nuclear and cytoplasmic proteins involves the addition of N-acetylglucosamine (O-GlcNAc) to serine and threonine residues. This dynamic modification occurs on hundreds of proteins and is involved in various essential biological processes. Because O-GlcNAc is substoichiometric and labile, identifying proteins and sites of modification has been challenging and generally requires proteome enrichment. Here we review recent advances on the implementation of chemical tools to perturb, to detect, and to map O-GlcNAc in living systems. Metabolic and chemoenzymatic labels along with ...
Source: Current Opinion in Chemical Biology - July 30, 2013 Category: Biochemistry Authors: Cecioni S, Vocadlo DJ Tags: Curr Opin Chem Biol Source Type: research

Radical S-adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis.
MA Abstract Sactipeptides represent a new emerging class of ribosomally assembled and posttranslationally modified peptides that show diverse bioactivities. Their common hallmark is an intramolecular thioether bond that crosslink the sulfur atom of a cysteine residue with the α-carbon of an acceptor amino acid. This review summarizes recent achievements concerning the biosynthesis of sactipeptides in general and with special focus on the common enzymatic radical SAM mechanism leading to the thioether linkage formation. In addition this mechanism is compared to the mechanism of thioether bond formation durin...
Source: Current Opinion in Chemical Biology - July 24, 2013 Category: Biochemistry Authors: Flühe L, Marahiel MA Tags: Curr Opin Chem Biol Source Type: research

Natural product biosynthesis-a Renaissance.
PMID: 23891474 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - July 24, 2013 Category: Biochemistry Authors: Liu HW, Begley T Tags: Curr Opin Chem Biol Source Type: research

Current development in isoprenoid precursor biosynthesis and regulation.
Abstract Isoprenoids are one of the largest classes of natural products and all of them are constructed from two precursors, isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). For decades, the mevalonic acid (MVA) pathway was proposed to be the only IPP and DMAPP biosynthetic pathway. This review summarizes the newly discovered IPP and DMAPP production pathways since late 1990s, their distribution among different kingdoms, and their roles in secondary metabolite production. These new IPP and DMAPP production pathways include the methylerythritol phosphate (MEP) pathway, a modified MVA ...
Source: Current Opinion in Chemical Biology - July 24, 2013 Category: Biochemistry Authors: Chang WC, Song H, Liu HW, Liu P Tags: Curr Opin Chem Biol Source Type: research

Emerging technologies in molecular imaging: new windows into biology.
PMID: 23886981 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - July 22, 2013 Category: Biochemistry Authors: Chen JK, Kikuchi K Tags: Curr Opin Chem Biol Source Type: research