Natural and synthetic selenoproteins.
Abstract Once considered highly toxic, the element selenium is now recognized as a micronutrient essential for human health. It is inserted co-translationally into many proteins as the non-canonical amino acid selenocysteine, providing the resulting selenoprotein molecules with a range of valuable redox properties; selenocysteine is also increasingly exploited as a structural and mechanistic probe in synthetic peptides and proteins. Here we review topical investigations into the preparation and characterization of natural and artificial selenoproteins. Such molecules are uniquely suited as tools for protein chemis...
Source: Current Opinion in Chemical Biology - September 25, 2014 Category: Biochemistry Authors: Metanis N, Hilvert D Tags: Curr Opin Chem Biol Source Type: research

Small-molecule control of cytokine function: new opportunities for treating immune disorders.
Abstract Manipulating cytokine function with protein-based drugs has proven effective for treating a wide variety of autoimmune and autoinflammatory disorders. However, the limited ability of protein-based drugs to modulate intracellular targets, including many implicated by studies of the genetics and physiology of these diseases, and to coordinately neutralize redundant inflammatory cytokines, suggests an important and complementary role for small molecules in immunomodulatory drug development. The recent clinical approval of Janus kinase and phosphodiesterase inhibitors, along with emerging evidence from other ...
Source: Current Opinion in Chemical Biology - September 12, 2014 Category: Biochemistry Authors: Sundberg TB, Xavier RJ, Schreiber SL, Shamji AF Tags: Curr Opin Chem Biol Source Type: research

Subunit specific inhibitors of proteasomes and their potential for immunomodulation.
Abstract Specialized variants of the constitutive 20S proteasome in the immune system like the immunoproteasomes and the thymoproteasome contain active site-bearing subunits which differ in their cleavage priorities and substrate binding pockets. The immunoproteasome plays a crucial role in antigen processing and for the differentiation of pro-inflammatory T helper cells which are involved in the pathogenesis of autoimmunity. Selective inhibitors of the immunoproteasome and constitutive proteasome have recently been generated which interfere with the development and progression of autoimmune diseases. Here we desc...
Source: Current Opinion in Chemical Biology - September 11, 2014 Category: Biochemistry Authors: Kisselev AF, Groettrup M Tags: Curr Opin Chem Biol Source Type: research

Endo-lysosomal proteases in antigen presentation.
Abstract Endo-lysosomal proteases have long been attractive, yet elusive, targets for medicinal chemistry. They have found to play key roles in health and disease; with protease under- and over-activity having been implicated in cancer, osteoporosis and Alzheimer's disease. Here we will discuss their role in the adaptive immune response. The crucial roles of these enzymes multiple processes in antigen presentation will be discussed: from activating MHC-II receptors, to the production of epitopes from antigens and the activation of Toll-like receptors. The early efforts at pharmacological interventions in these pat...
Source: Current Opinion in Chemical Biology - September 8, 2014 Category: Biochemistry Authors: van Kasteren SI, Overkleeft HS Tags: Curr Opin Chem Biol Source Type: research

Regulating adaptive immune responses using small molecule modulators of aminopeptidases that process antigenic peptides.
Abstract Antigenic peptide processing by intracellular aminopeptidases has emerged recently as an important pathway that regulates adaptive immune responses. Pathogens and cancer can manipulate the activity of key enzymes of this pathway to promote immune evasion. Furthermore, the activity of these enzymes is naturally variable due to polymorphic variation, contributing to predisposition to disease, most notably autoimmunity. Here, we review recent findings that suggest that the pharmacological regulation of the activity of these aminopeptidases constitutes a valid approach for regulating human immune responses. W...
Source: Current Opinion in Chemical Biology - August 28, 2014 Category: Biochemistry Authors: Stratikos E Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: In vivo chemistry: Pushing the envelope.
PMID: 25139790 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 16, 2014 Category: Biochemistry Authors: Fox JM, Robillard MS Tags: Curr Opin Chem Biol Source Type: research

Turning the spotlight on protein-lipid interactions in cells.
Abstract Protein function is largely dependent on coordinated and dynamic interactions of the protein with biomolecules including other proteins, nucleic acids and lipids. Although powerful methods for global profiling of protein-protein and protein-nucleic acid interactions are available, proteome-wide mapping of protein-lipid interactions is still challenging and rarely performed. The emergence of bifunctional lipid probes with photoactivatable and clickable groups offers new chemical tools for globally profiling protein-lipid interactions under cellular contexts. In this review, we summarize recent advances in ...
Source: Current Opinion in Chemical Biology - August 14, 2014 Category: Biochemistry Authors: Peng T, Yuan X, Hang HC Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Mechanisms: Chemical and computational probes of biological mechanism.
PMID: 25129687 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 13, 2014 Category: Biochemistry Authors: O'Donoghue AC, Kamerlin SC Tags: Curr Opin Chem Biol Source Type: research

Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications.
Abstract The ability to introduce any chemical probe to any endogenous target protein in its native environment, that is in cells and in vivo, is anticipated to provide various new exciting tools for biological and biomedical research. Although still at the prototype stage, the ligand-directed tosyl (LDT) chemistry is a novel type of affinity labeling technique that we developed for such a dream. This chemistry allows for modifying native proteins by various chemical probes with high specificity in various biological settings ranging from in vitro (in test tubes) to in living cells and in vivo. Since the first rep...
Source: Current Opinion in Chemical Biology - August 12, 2014 Category: Biochemistry Authors: Tsukiji S, Hamachi I Tags: Curr Opin Chem Biol Source Type: research

Reconstitution of cytoskeletal protein assemblies for large-scale membrane transformation.
Abstract Membranes determine two-dimensional and three-dimensional biochemical reaction spaces in living systems. Defining size and shape of surfaces and volumes encompassed by membrane is of key importance for cellular metabolism and homeostasis, and the maintenance and controlled transformation of membrane shapes are coordinated by a large number of different protein assemblies. The orchestration of spatial elements over distances orders of magnitudes larger than protein molecules, as required for cell division, is a particularly challenging task, requiring large-scale ordered protein filaments and networks. The...
Source: Current Opinion in Chemical Biology - August 11, 2014 Category: Biochemistry Authors: Rivas G, Vogel SK, Schwille P Tags: Curr Opin Chem Biol Source Type: research

The in vivo chemistry of photoswitched tethered ligands.
Abstract Nature's photoreceptors are typically composed of a chromophore that is covalently bound to a receptor protein at the top of a signaling cascade. The protein can function as a G-protein coupled receptor (GPCR), an ion channel, or as an enzyme. This logic can be mimicked with synthetic photoswitches, such as azobenzenes, that are linked to naturally 'blind' transmembrane proteins using in vivo-chemistry. The resulting semisynthetic receptors can be employed to optically control cellular functions, especially in neurons, and influence the behavior of animals with the exquisite temporal and spatial precision...
Source: Current Opinion in Chemical Biology - August 7, 2014 Category: Biochemistry Authors: Broichhagen J, Trauner D Tags: Curr Opin Chem Biol Source Type: research

Palladium-mediated chemistry in living cells.
Abstract Bioorthogonal metal catalysed chemistry is the application of biocompatible transition metals to catalyse conventional synthetic organic chemistry reactions within a biological environment. Over the past decade, metals which were previously restricted to conventional organic synthesis have begun to be used in an increasing number of biological settings. This has been dominated by copper mediated catalysis of the azide-alkyne Huisgen cycloaddition (1,3-dipolar addition) chemistry but other, less toxic, metals such as palladium are now beginning to establish themselves in the chemical biology/chemical medic...
Source: Current Opinion in Chemical Biology - August 6, 2014 Category: Biochemistry Authors: Chankeshwara SV, Indrigo E, Bradley M Tags: Curr Opin Chem Biol Source Type: research

Building better bioorthogonal reactions.
Abstract Over the past two decades, there has been intense interest in designing and implementing selective (bioorthogonal) reactions for biomolecule tracking. Here we review the most widely used bioorthogonal chemistries in live cells and animals, drawing particular attention to the unique functional groups underlying these transformations. We also describe recent efforts to tune functional group reactivities and stabilities to access even more rapid and selective chemistries. Last, we highlight ongoing challenges in identifying new bioorthogonal reagents and combinations of reactions that can be used concurrentl...
Source: Current Opinion in Chemical Biology - July 30, 2014 Category: Biochemistry Authors: Shih HW, Kamber DN, Prescher JA Tags: Curr Opin Chem Biol Source Type: research

Beyond D-luciferin: expanding the scope of bioluminescence imaging in vivo.
Abstract The light-emitting chemical reaction catalyzed by the enzyme firefly luciferase is widely used for noninvasive imaging in live mice. However, photon emission from the luciferase is crucially dependent on the chemical properties of its substrate, D-luciferin. In this review, we describe recent work to replace the natural luciferase substrate with synthetic analogs that extend the scope of bioluminescence imaging. PMID: 25078002 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - July 28, 2014 Category: Biochemistry Authors: Adams ST, Miller SC Tags: Curr Opin Chem Biol Source Type: research

Positive roles of compartmentalization in internal reactions.
Abstract Recently, many researchers have attempted to construct artificial cell models using a bottom-up approach in which various biochemical reactions that involve a defined set of molecules are reconstructed in cell-like compartments, such as liposomes and water-in-oil droplets. In many of these studies, the cell-like compartments have acted only as containers for the encapsulated biochemical reactions, whereas other studies have indicated that compartmentalization improves the rates and yields of these reactions. Here, we introduce two ways in which compartmentalization can improve internal reactions: the isol...
Source: Current Opinion in Chemical Biology - July 14, 2014 Category: Biochemistry Authors: Ichihashi N, Yomo T Tags: Curr Opin Chem Biol Source Type: research

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.
Abstract Although there have been great strides in defining the mechanisms of RNA strand cleavage by 2'-O-transphosphorylation, long-standing questions remain. How do different catalytic modes such as acid/base and metal ion catalysis influence transition state charge distribution? Does the large rate enhancement characteristic of biological catalysis result in different transition states relative to solution reactions? Answering these questions is important for understanding biological catalysis in general, and revealing principles for designing small molecule inhibitors. Recent application of linear free energy ...
Source: Current Opinion in Chemical Biology - July 11, 2014 Category: Biochemistry Authors: Kellerman DL, York DM, Piccirilli JA, Harris ME Tags: Curr Opin Chem Biol Source Type: research

Strain-promoted cycloadditions involving nitrones and alkynes-rapid tunable reactions for bioorthogonal labeling.
Abstract The development and applications of strain-promoted alkyne-nitrone cycloaddition (SPANC) reactions have brought about new tools for rapid and specific functionalization of biomolecules in different settings. While a number of strain-promoted reactions have been successfully developed, SPANC reactions offer high reactivity with bimolecular rate constants of k2 that are as fast as 60M(-1)s(-1). SPANC reactions also offer stability of starting materials, particularly in the case of endocyclic nitrones, as well as stereoelectronic tunability of the nitrone moiety to optimize reactivity towards different alkyn...
Source: Current Opinion in Chemical Biology - July 10, 2014 Category: Biochemistry Authors: MacKenzie DA, Sherratt AR, Chigrinova M, Cheung LL, Pezacki JP Tags: Curr Opin Chem Biol Source Type: research

Photoclick chemistry: a fluorogenic light-triggered in vivo ligation reaction.
Abstract The ability to use chemical reactivity to monitor and control biomolecular processes with a spatial and temporal precision motivated the development of light-triggered in vivo chemistries. To this end, the photoinduced tetrazole-alkene cycloaddition, also termed 'photoclick chemistry' offers a very rapid chemical ligation platform for the manipulation of biomolecules and matrices in vivo. Here we outline the recent developments in the optimization of this chemistry, ranging from the search for substrates that offer two-photon photoactivatability, superior reaction kinetics, and/or genetic encodability, to...
Source: Current Opinion in Chemical Biology - July 10, 2014 Category: Biochemistry Authors: Ramil CP, Lin Q Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Molecular imaging.
PMID: 24986159 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 28, 2014 Category: Biochemistry Authors: Eggeling C, Heilemann M Tags: Curr Opin Chem Biol Source Type: research

STED microscopy-towards broadened use and scope of applications.
Abstract High resolution Stimulated Emission Depletion (STED) microscopy has been demonstrated for fundamental studies in cells, living tissue and organisms. Today, a major trend in the STED technique development is to make the instruments simpler and more user-friendly, without compromising performance. This has become possible by new low-cost, turn-key laser technology and by implementing specifically designed phase plates and polarization elements, extending and simplifying the shaping of the laser beam profiles. These simpler and cheaper realizations of STED are now becoming more broadly available. In parallel...
Source: Current Opinion in Chemical Biology - June 28, 2014 Category: Biochemistry Authors: Blom H, Widengren J Tags: Curr Opin Chem Biol Source Type: research

Organization and dynamics of AMPA receptors inside synapses-nano-organization of AMPA receptors and main synaptic scaffolding proteins revealed by super-resolution imaging.
Abstract Progresses in microscopy have often led to major discoveries in neuroscience, and the recent advent of super-resolution microscopy is no exception. In this review, we will show how imaging has advanced our modern vision of synaptic function. More particularly, we will emphasize how novel nanoscopy techniques have helped in deciphering the organization of post-synaptic proteins, offering new insight into the mechanism of synaptic transmission. PMID: 24975376 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 26, 2014 Category: Biochemistry Authors: Hosy E, Butler C, Sibarita JB Tags: Curr Opin Chem Biol Source Type: research

Geometry of the nucleus: a perspective on gene expression regulation.
We present the analogies between the emerging understanding of nuclear organization in the field of cell biology, and the more established disciplines of heterogeneous catalysis and the physics of random walks. We provide several recent examples showing how nuclear geometry affects protein reactivity in the nucleus. PMID: 24981829 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 26, 2014 Category: Biochemistry Authors: Woringer M, Darzacq X, Izeddin I Tags: Curr Opin Chem Biol Source Type: research

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