Phototransformable fluorescent proteins: Future challenges.
Abstract In fluorescence microscopy, the photophysical properties of the fluorescent markers play a fundamental role. The beauty of phototransformable fluorescent proteins (PTFPs) is that some of these properties can be precisely controlled by light. A wide range of PTFPs have been developed in recent years, including photoactivatable, photoconvertible and photoswitchable fluorescent proteins. These smart labels triggered a plethora of advanced fluorescence methods to scrutinize biological cells or organisms dynamically, quantitatively and with unprecedented resolution. Despite continuous improvements, PTFPs still...
Source: Current Opinion in Chemical Biology - June 24, 2014 Category: Biochemistry Authors: Adam V, Berardozzi R, Byrdin M, Bourgeois D Tags: Curr Opin Chem Biol Source Type: research

The bright future of single-molecule fluorescence imaging.
Abstract Single-molecule Förster resonance energy transfer (smFRET) is an essential and maturing tool to probe biomolecular interactions and conformational dynamics in vitro and, increasingly, in living cells. Multi-color smFRET enables the correlation of multiple such events and the precise dissection of their order and timing. However, the requirements for good spectral separation, high time resolution, and extended observation times place extraordinary demands on the fluorescent labels used in such experiments. Together with advanced experimental designs and data analysis, the development of long-lasting, ...
Source: Current Opinion in Chemical Biology - June 20, 2014 Category: Biochemistry Authors: Juette MF, Terry DS, Wasserman MR, Zhou Z, Altman RB, Zheng Q, Blanchard SC Tags: Curr Opin Chem Biol Source Type: research

Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency?
Abstract I discuss some physico-chemical and evolutionary aspects of enzyme accuracy (selectivity, specificity) and speed (turnover rate, processivity). Accuracy can be a beneficial side-product of active-sites being refined to proficiently convert a given substrate into one product. However, exclusion of undesirable, non-cognate substrates is also an explicitly evolved trait that may come with a cost. I define two schematic mechanisms. Ground-state discrimination applies to enzymes where selectivity is achieved primarily at the level of substrate binding. Exemplified by DNA methyltransferases and the ribosome, gr...
Source: Current Opinion in Chemical Biology - June 19, 2014 Category: Biochemistry Authors: Tawfik DS Tags: Curr Opin Chem Biol Source Type: research

Fluorescence cryo-microscopy: current challenges and prospects.
d K Abstract Studying biological structures with fine details does not only require a microscope with high resolution, but also a sample preparation process that preserves the structures in a near-native state. Live-cell imaging is restricted mostly to the field of light microscopy. For studies requiring much higher resolution, fast freezing techniques (vitrification) are successfully used to immobilize the sample in a near-native state for imaging with electron and X-ray cryo-microscopy. Fluorescence cryo-microscopy combines imaging of vitrified samples with the advantages of fluorescence labeling of biological s...
Source: Current Opinion in Chemical Biology - June 18, 2014 Category: Biochemistry Authors: Kaufmann R, Hagen C, Grünewald K Tags: Curr Opin Chem Biol Source Type: research

Synthetic cellularity based on non-lipid micro-compartments and protocell models.
Abstract This review discusses recent advances in the design and construction of protocell models based on the self-assembly or microphase separation of non-lipid building blocks. We focus on strategies involving partially hydrophobic inorganic nanoparticles (colloidosomes), protein-polymer globular nano-conjugates (proteinosomes), amphiphilic block copolymers (polymersomes), and stoichiometric mixtures of oppositely charged biomolecules and polyelectrolytes (coacervates). Developments in the engineering of membrane functionality to produce synthetic protocells with gated responses and control over multi-step reac...
Source: Current Opinion in Chemical Biology - June 18, 2014 Category: Biochemistry Authors: Li M, Huang X, Tang TY, Mann S Tags: Curr Opin Chem Biol Source Type: research

Phosphate analogues in the dissection of mechanism.
Abstract Phosphoryl group transfer is central to genetic replication, cellular signalling and many metabolic processes. Understanding the mechanisms of phosphorylation and phosphate ester and anhydride cleavage is key to efforts towards biotechnological and biomedical exploitation of phosphate-handling enzymes. Analogues of phosphate esters and anhydrides are indispensable tools, alongside protein mutagenesis and computational methods, for the dissection of phosphoryl transfer mechanisms. Hydrolysable and non-hydrolysable phosphate analogues have provided insight into the nature and sites of phosphoryl transfer pr...
Source: Current Opinion in Chemical Biology - May 27, 2014 Category: Biochemistry Authors: Korhonen HJ, Conway LP, Hodgson DR Tags: Curr Opin Chem Biol Source Type: research

Nitrogen-Vacancy color center in diamond-emerging nanoscale applications in bioimaging and biosensing.
We present emerging applications such as single molecule spin imaging, nanoscale imaging of biomagnetic fields, sensing molecular fluctuations and temperatures in live cellular environments. We summarize other current advances and future prospects of NV diamond for imaging and sensing pertaining to bio-medical applications. PMID: 24875635 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - May 26, 2014 Category: Biochemistry Authors: Balasubramanian G, Lazariev A, Arumugam SR, Duan DW Tags: Curr Opin Chem Biol Source Type: research

Advances in live-cell single-particle tracking and dynamic super-resolution imaging.
Abstract Resolving the movement of individual molecules in living cells by single particle tracking methods has allowed many molecular behaviors to be deciphered over the past three decades. These methods have increasingly benefited from advances in microscopy of single nano-objects such as fluorescent dye molecules, proteins or nanoparticles as well as tiny absorbing metal nanoparticles. In parallel to these efforts aiming at tracking ever smaller and more photostable nano-objects in living cells, the development of localization-based super-resolution imaging provided means to increase the number of single molecu...
Source: Current Opinion in Chemical Biology - May 26, 2014 Category: Biochemistry Authors: Cognet L, Leduc C, Lounis B Tags: Curr Opin Chem Biol Source Type: research

Live-cell reporters for fluorescence imaging.
a IR Abstract Advances in the development of new fluorescent reporters and imaging techniques have revolutionized our ability to directly visualize biological processes in living systems. Real-time analysis of protein localization, dynamics, and interactions has been made possible by site-specific protein labeling with custom designed probes. This review outlines some of the most recent advances in the design and application of live-cell imaging probes, with a particular focus on SNAP-tag technology. Specific examples illustrating applications in superresolution and single-molecule imaging, protein trafficking and...
Source: Current Opinion in Chemical Biology - May 14, 2014 Category: Biochemistry Authors: Corrêa IR Tags: Curr Opin Chem Biol Source Type: research

Chromophore chemistry of fluorescent proteins controlled by light.
We describe both the fundamental principles and the specific molecular mechanisms underlying the irreversible and reversible chromophore photoconversions. We discuss advancements in super-resolution microscopy that became possible due to the engineering of new protein phenotypes and understanding of their chromophore transformations. PMID: 24819887 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - May 9, 2014 Category: Biochemistry Authors: Shcherbakova DM, Verkhusha VV Tags: Curr Opin Chem Biol Source Type: research

Faster fluorescence microscopy: advances in high speed biological imaging.
Abstract The past decade has seen explosive growth in new high speed imaging methods. These can broadly be classified as either point-scanning (which offer better depth penetration) or parallelized systems (which offer higher speed). We discuss each class generally, and cover specific advances in diffraction-limited microscopes (laser-scanning confocal, spinning-disk, and light-sheet) and superresolution microscopes (single-molecule imaging, stimulated emission-depletion, and structured illumination). A theme of our review is that there is no free lunch: each technique has strengths and weaknesses, and an advance ...
Source: Current Opinion in Chemical Biology - May 8, 2014 Category: Biochemistry Authors: Winter PW, Shroff H Tags: Curr Opin Chem Biol Source Type: research

The organisation of the cell membrane: do proteins rule lipids?
Abstract Cell membranes are a complex adaptive system: they are constantly re-organised in response to extra- and intracellular inputs and their local and global structure ultimately determines how, where and when these inputs are processed. This requires a tight coupling of signalling and membranes in localised and specialised compartments. While lipids are essential components of cell membranes, they mostly lack a direct link to the input signals. Here we review how proteins can deform locally membranes, modify and reorganise lipids to form membrane domains and regulate properties like membrane charges and diffu...
Source: Current Opinion in Chemical Biology - May 8, 2014 Category: Biochemistry Authors: Rossy J, Ma Y, Gaus K Tags: Curr Opin Chem Biol Source Type: research

Applications of imaging fluorescence correlation spectroscopy.
Abstract Imaging fluorescence correlation spectroscopy (imaging FCS), or the acquisition of fluorescence correlation functions at contiguous points in an imaging format, is a recent addition to quantitative bioimaging. Imaging FCS has been implemented in various modalities. These techniques provide excellent time resolution, have single molecules sensitivity and can be combined with super-resolution techniques, thus combining high spatial and temporal resolution. Although still at its beginning it has been applied in different forms to biological problems. This review looks at applications of imaging FCS in the la...
Source: Current Opinion in Chemical Biology - May 7, 2014 Category: Biochemistry Authors: Singh AP, Wohland T Tags: Curr Opin Chem Biol Source Type: research

Computer aided enzyme design and catalytic concepts.
Abstract Gaining a deeper understanding of enzyme catalysis is of great practical and fundamental importance. Over the years it has become clear that despite advances made in experimental mutational studies, a quantitative understanding of enzyme catalysis will not be possible without the use of computer modeling approaches. While we believe that electrostatic preorganization is by far the most important catalytic factor, convincing the wider scientific community of this may require the demonstration of effective rational enzyme design. Here we make the point that the main current advances in enzyme design are bas...
Source: Current Opinion in Chemical Biology - May 6, 2014 Category: Biochemistry Authors: Frushicheva MP, Mills MJ, Schopf P, Singh MK, Prasad RB, Warshel A Tags: Curr Opin Chem Biol Source Type: research

Quantitative super-resolution microscopy: pitfalls and strategies for image analysis.
Abstract Super-resolution microscopy is an enabling technology that allows biologists to visualize cellular structures at nanometer length scales using far-field optics. To break the diffraction barrier, it is necessary to leverage the distinct molecular states of fluorescent probes. At the same time, the existence of these different molecular states and the photophysical properties of the fluorescent probes can complicate data quantification and interpretation. Here, we review the pitfalls in super-resolution data analysis that must be avoided for proper interpretation of images. PMID: 24793374 [PubMed - as ...
Source: Current Opinion in Chemical Biology - April 30, 2014 Category: Biochemistry Authors: Durisic N, Cuervo LL, Lakadamyali M Tags: Curr Opin Chem Biol Source Type: research

Recent applications of superresolution microscopy in neurobiology.
Abstract Chemical synapses in brain are structural differentiations where excitatory or inhibitory signals are vectorially transmitted between two neurons. Excitatory synapses occur mostly on dendritic spines, submicron sized protrusions of the neuronal dendritic arborizations. Axons establish contacts with these tiny specializations purported to be the smallest functional processing units in the central nervous system. The minute size of synapses and their macromolecular constituents creates an inherent difficulty for imaging but makes them an ideal object for superresolution microscopy. Here we discuss some repr...
Source: Current Opinion in Chemical Biology - April 25, 2014 Category: Biochemistry Authors: Willig KI, Barrantes FJ Tags: Curr Opin Chem Biol Source Type: research

Super-resolution microscopy of mitochondria.
Abstract Mitochondria, the powerhouses of the cell, are essential organelles in eukaryotic cells. With their complex inner architecture featuring a smooth outer and a highly convoluted inner membrane, they are challenging objects for microscopy. The diameter of mitochondria is generally close to the resolution limit of conventional light microscopy, rendering diffraction-unlimited super-resolution light microscopy (nanoscopy) for imaging submitochondrial protein distributions often mandatory. In this review, we discuss what can be expected when imaging mitochondria with conventional diffraction-limited and diffrac...
Source: Current Opinion in Chemical Biology - April 24, 2014 Category: Biochemistry Authors: Jakobs S, Wurm CA Tags: Curr Opin Chem Biol Source Type: research

The role of reorganization energy in rational enzyme design.
Abstract Computational design is becoming an integral component in developing novel enzymatic activities. Catalytic efficiencies of man-made enzymes however are far behind their natural counterparts. The discrepancy between laboratory and naturally evolved enzymes suggests that a major catalytic factor is still missing in the computational process. Reorganization energy, which is the origin of catalytic power of natural enzymes, has not been exploited yet for design. As exemplified in case of KE07 Kemp eliminase, this quantity is optimized by directed evolution. Mutations beneficial for evolution, but without dire...
Source: Current Opinion in Chemical Biology - April 23, 2014 Category: Biochemistry Authors: Fuxreiter M, Mones L Tags: Curr Opin Chem Biol Source Type: research

Protein engineering for development of new hydrolytic biocatalysts.
Abstract Hydrolytic enzymes play important roles as biocatalysts in chemical synthesis. The chemical versatility and structurally sturdy features of Candida antarctica lipase B has placed this enzyme as a common utensil in the synthetic tool-box. In addition to catalyzing acyl transfer reactions, a number of promiscuous activities have been described recently. Some of these new enzyme activities have been amplified by mutagenesis. Epoxide hydrolases are of interest due to their potential as catalysts in asymmetric synthesis. This current update discusses recent development in the engineering of lipases and epoxide...
Source: Current Opinion in Chemical Biology - April 22, 2014 Category: Biochemistry Authors: Widersten M Tags: Curr Opin Chem Biol Source Type: research

Looking beneath the surface to determine what makes DNA damage deleterious.
Abstract Apurinic/apyrimidinic and oxidized abasic sites are chemically reactive DNA lesions that are produced by a variety of damaging agents. The effects of these molecules that lack a Watson-Crick base on polymerase enzymes are well documented. More recently, multiple consequences of the electrophilic nature of abasic lesions have been revealed. Members of this family of DNA lesions have been shown to inactivate repair enzymes and undergo spontaneous transformation into more deleterious forms of damage. Abasic site reactivity provides insight into the chemical basis for the cytotoxicity of DNA damaging agents t...
Source: Current Opinion in Chemical Biology - April 21, 2014 Category: Biochemistry Authors: Greenberg MM Tags: Curr Opin Chem Biol Source Type: research

The yeast kinetochore - structural insights from optical microscopy.
Abstract In eukaryotic organisms each chromosome is captured by spindle microtubules. This interaction is mediated by an evolutionarily conserved, multi-protein complex called kinetochore. The main function of the kinetochore is to maintain correct chromosome segregation during cell division by transporting each sister chromatid to the spindle pole bodies localized at the opposite sites of the yeast nucleus. The kinetochore of budding yeast (Saccharomyces cerevisiae) is often used as a model system due to its simple composition compared to higher eukaryotes. This review highlights results obtained using optical im...
Source: Current Opinion in Chemical Biology - April 21, 2014 Category: Biochemistry Authors: Cieśliński K, Ries J Tags: Curr Opin Chem Biol Source Type: research

Catalytic control in terpenoid cyclases: multiscale modeling of thermodynamic, kinetic, and dynamic effects.
Abstract In this Opinion we review some of the key work on terpene biosynthesis using multi-scale simulation approaches. Terpene synthases generate terpenes employing beautiful and rich carbocation chemistry, including highly specific ring formations, hydride, proton, methyl, and methylene migrations, followed by reaction quenching. In spite of the chemical finesse of these enzymes, terpene synthases are highly promiscuous. Incidentally, these mischievous enzymes are very challenging to treat computationally due to the inherent complexity of the potential energy surface in carbocations and the lack of directional ...
Source: Current Opinion in Chemical Biology - April 12, 2014 Category: Biochemistry Authors: Major DT, Freud Y, Weitman M Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Bioinorganic chemistry: Recent advances in bioinorganic chemistry.
PMID: 24731720 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 11, 2014 Category: Biochemistry Authors: Nolan EM, Shionoya M Tags: Curr Opin Chem Biol Source Type: research

Recent achievements in developing the biocatalytic toolbox for chiral amine synthesis.
e M Abstract Novel enzyme activities and chemoenzymatic reaction concepts have considerably expanded the biocatalytic toolbox for chiral amine synthesis. Creating new activities or extending the scope of existing enzymes by protein engineering is a common trend in biocatalysis and in chiral amine synthesis specifically. For instance, an amine dehydrogenase that allows for the direct asymmetric amination of ketones with ammonia was created by mutagenesis of an l-amino acid dehydrogenase. Another trend in chiral amine chemistry is the development of strategies allowing for the synthesis of secondary amines. For exam...
Source: Current Opinion in Chemical Biology - April 7, 2014 Category: Biochemistry Authors: Kohls H, Steffen-Munsberg F, Höhne M Tags: Curr Opin Chem Biol Source Type: research

Combining the 'two worlds' of chemocatalysis and biocatalysis towards multi-step one-pot processes in aqueous media.
l W Abstract The combination of biocatalytic and chemocatalytic reactions leading to one-pot processes in aqueous medium represents an economically and ecologically attractive concept in organic synthesis due to the potential to avoid time and capacity consuming and waste producing work-up steps of intermediates. The use of water as a solvent has many advantages. A key feature is the opportunity it provides as the solvent in nature to make use of the full range of enzymes. In recent years development of chemoenzymatic one-pot processes in water has emerged tremendously, and proof of concepts for the combination of...
Source: Current Opinion in Chemical Biology - April 4, 2014 Category: Biochemistry Authors: Gröger H, Hummel W Tags: Curr Opin Chem Biol Source Type: research

Heavy enzymes-experimental and computational insights in enzyme dynamics.
tilde;ón I Abstract The role of protein motions in the chemical step of enzyme-catalyzed reactions is the subject of an open debate in the scientific literature. The systematic use of isotopically substituted enzymes has been revealed as a useful tool to quantify the role of these motions. According to the Born-Oppenheimer approximation, changing the mass of the protein does not change the forces acting on the system but alters the frequencies of the protein motions, which in turn can affect the rate constant. Experimental and theoretical studies carried out in this field are presented in this article and d...
Source: Current Opinion in Chemical Biology - April 4, 2014 Category: Biochemistry Authors: Swiderek K, Javier Ruiz-Pernía J, Moliner V, Tuñón I Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Biocatalysis and biotransformation: Riding the third wave of biocatalysis.
PMID: 24704005 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 2, 2014 Category: Biochemistry Authors: Moore JC, Bornscheuer UT Tags: Curr Opin Chem Biol Source Type: research

Enzyme architecture: on the importance of being in a protein cage.
Abstract Substrate binding occludes water from the active sites of many enzymes. There is a correlation between the burden to enzymatic catalysis of deprotonation of carbon acids and the substrate immobilization at solvent-occluded active sites for ketosteroid isomerase (KSI-small burden, substrate pKa=13), triosephosphate isomerase (TIM, substrate pKa≈18) and diaminopimelate epimerase (DAP epimerase, large burden, substrate pKa≈29) catalyzed reaction. KSI binds substrates at a surface cleft, TIM binds substrate at an exposed 'cage' formed by closure of flexible loops; and, DAP epimerase binds substrat...
Source: Current Opinion in Chemical Biology - March 31, 2014 Category: Biochemistry Authors: Richard JP, Amyes TL, Goryanova B, Zhai X Tags: Curr Opin Chem Biol Source Type: research

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