Targeted and proteome-wide analysis of metabolite-protein interactions.
Abstract Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and metabolome of many organisms being readily available, researchers now have the opportunity to dissect how key metabolites regulate complex cellular pathways in vivo. Nonetheless, characterizing the specific and functional protein targets of key metabolites associated with specific cellular phenotypes remains a major challenge. Innovations in chemical biology are now poised to address this fundamental limitation in physiology and disease. In...
Source: Current Opinion in Chemical Biology - November 29, 2019 Category: Biochemistry Authors: Tsukidate T, Li Q, Hang HC Tags: Curr Opin Chem Biol Source Type: research

Glycosphingolipids and lysosomal storage disorders as illustrated by gaucher disease.
Abstract Glycosphingolipids are important building blocks of the outer leaflet of the cell membrane. They are continuously recycled, involving fragmentation inside lysosomes by glycosidases. Inherited defects in degradation cause lysosomal glycosphingolipid storage disorders. The relatively common glycosphingolipidosis Gaucher disease is highlighted here to discuss new insights in the molecular basis and pathophysiology of glycosphingolipidoses reached by fundamental research increasingly using chemical biology tools. We discuss improvements in the detection of glycosphingolipid metabolites by mass spectrometry an...
Source: Current Opinion in Chemical Biology - November 25, 2019 Category: Biochemistry Authors: Aerts JMFG, Kuo CL, Lelieveld LT, Boer DEC, van der Lienden MJC, Overkleeft HS, Artola M Tags: Curr Opin Chem Biol Source Type: research

Metal-based photosensitizers for photodynamic therapy: the future of multimodal oncology?
Abstract Photodynamic therapy (PDT) is an approved medical technique to treat certain forms of cancer. It has been used to complement traditional anticancer modalities such as surgery, chemotherapy or radiotherapy, and in certain cases, to replace these treatments. One critical parameter of PDT is the photosensitizer (PS); historically, a purely organic macrocyclic tetrapyrrole-based structure. This short review surveys two recent clinical examples of metal complexes, namely TOOKAD®-Soluble and TLD-1433, which have ideal photophysical properties to act as PDT PSs. We highlight the important role played by the ...
Source: Current Opinion in Chemical Biology - November 20, 2019 Category: Biochemistry Authors: McFarland SA, Mandel A, Dumoulin-White R, Gasser G Tags: Curr Opin Chem Biol Source Type: research

Molecular scaffolds: when DNA becomes the hardware for single-molecule investigations.
Abstract Over the past few decades, single-molecule manipulation has been widely applied to the real-time analysis of biomolecular interactions. It has enabled researchers to decipher structure-function relationships for polymers, enzymes, and larger-scale molecular machines, in particular by harnessing force to probe both chemical and mechanical stabilities. Nucleic acids have played a central role in this effort because, in addition to their biological significance, they exhibit unique polymeric properties which have recast them as key components participating in numerous experimental designs. In this review, we...
Source: Current Opinion in Chemical Biology - November 20, 2019 Category: Biochemistry Authors: Gosse C, Strick TR, Kostrz D Tags: Curr Opin Chem Biol Source Type: research

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase.
Abstract Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of 'omics', we discuss what makes the larger subunit of this enzyme (RNR-α) so interesting, highlighting its emerging cellular interactome based on its unique oligomeric dynamism that dictates its compartment-specific occupations. Linking the history of the field with the multivariable nature of this exceedingly sophisticated enzyme, we further discuss implications of new data pertaining to DNA-damage...
Source: Current Opinion in Chemical Biology - November 14, 2019 Category: Biochemistry Authors: Long MJC, Van Hall-Beauvais A, Aye Y Tags: Curr Opin Chem Biol Source Type: research

Machine learning for target discovery in drug development.
Abstract The discovery of macromolecular targets for bioactive agents is currently a bottleneck for the informed design of chemical probes and drug leads. Typically, activity profiling against genetically manipulated cell lines or chemical proteomics is pursued to shed light on their biology and deconvolute drug-target networks. By taking advantage of the ever-growing wealth of publicly available bioactivity data, learning algorithms now provide an attractive means to generate statistically motivated research hypotheses and thereby prioritize biochemical screens. Here, we highlight recent successes in machine inte...
Source: Current Opinion in Chemical Biology - November 14, 2019 Category: Biochemistry Authors: Rodrigues T, Bernardes GJL Tags: Curr Opin Chem Biol Source Type: research

Modeling catalytic reaction mechanisms in glycoside hydrolases.
Abstract Modeling catalysis in carbohydrate-active enzymes is a daunting challenge because of the high flexibility and diversity of both enzymes and carbohydrates. Glycoside hydrolases (GHs) are an illustrative example, where conformational changes and subtle interactions have been shown to be critical for catalysis. GHs have pivotal roles in industry (e.g. biofuel or detergent production) and biomedicine (e.g. targets for cancer and diabetes), and thus, a huge effort is devoted to unveil their molecular mechanisms. Besides experimental techniques, computational methods have served to provide an in-depth understan...
Source: Current Opinion in Chemical Biology - November 12, 2019 Category: Biochemistry Authors: Coines J, Raich L, Rovira C Tags: Curr Opin Chem Biol Source Type: research

Photocrosslinking probes for capture of carbohydrate interactions.
Abstract Glycan-mediated interactions are essential in many biological processes and regulate a wide variety of cellular functions. However, characterizing these interactions is difficult because glycan biosynthesis is not template driven and because carbohydrate recognition events are usually of low affinity and transient. Photocrosslinking carbohydrate probes can form a covalent bond with molecules in close proximity on UV irradiation and are capable of capturing interactions between glycans and glycan-binding proteins in situ. Because of these advantages, multiple photocrosslinking carbohydrate probes have...
Source: Current Opinion in Chemical Biology - November 6, 2019 Category: Biochemistry Authors: Wu H, Kohler J Tags: Curr Opin Chem Biol Source Type: research

The physical organic chemistry of glycopyranosyl transfer reactions in solution and enzyme-catalyzed.
Abstract Our understanding of the mechanisms of glycopyranosyl transfer that occur in solution, both for the chemical synthesis of complex structures and that for the cleavage of glycosidic bonds has allowed us to design biologically active molecules. Recent efforts on the reactivity of glycopyranosides, which are critical entities in all biological systems, coupled with the advent of modern spectroscopic instrumentation have allowed physical organic chemists to broaden our knowledge of glycosyl transfer reaction transition states, both in solution and for enzyme-catalyzed processes, and of critical high energy in...
Source: Current Opinion in Chemical Biology - November 1, 2019 Category: Biochemistry Authors: Colombo C, Bennet AJ Tags: Curr Opin Chem Biol Source Type: research

Towards biological applications of nanophotonic tweezers.
Abstract Optical trapping (synonymous with optical tweezers) has become a core biophysical technique widely used for interrogating fundamental biological processes on size scales ranging from the single-molecule to the cellular level. Recent advances in nanotechnology have led to the development of 'nanophotonic tweezers,' an exciting new class of 'on-chip' optical traps. Here, we describe how nanophotonic tweezers are making optical trap technology more broadly accessible and bringing unique biosensing and manipulation capabilities to biological applications of optical trapping. PMID: 31678712 [PubMed - as s...
Source: Current Opinion in Chemical Biology - October 31, 2019 Category: Biochemistry Authors: Badman RP, Ye F, Wang MD Tags: Curr Opin Chem Biol Source Type: research

Chemically engineered glycan-modified cancer vaccines to mobilize skin dendritic cells.
Abstract Dendritic cell (DC)-targeting vaccines show great promise in increasing antitumor immunity. Glycan-engineered vaccines facilitate both DC targeting and increased uptake by DCs for processing and presentation to CD4+ and CD8+ T cells to induce tumor-specific T-cell responses. However, the complexity of various DC subsets in skin tissues, expressing different glycan-binding receptors that can mediate vaccine uptake or drainage of vaccines via lymphatics directly to the lymph node-resident DCs, complicates the success of vaccines. Moreover, the influx of inflammatory immune cells to the site of vac...
Source: Current Opinion in Chemical Biology - October 31, 2019 Category: Biochemistry Authors: Duinkerken S, Li RE, van Haften FJ, de Gruijl TD, Chiodo F, Schetters STT, van Kooyk Y Tags: Curr Opin Chem Biol Source Type: research

Imaging dynamic cell signaling in  vivo with new classes of fluorescent reporters.
Imaging dynamic cell signaling in vivo with new classes of fluorescent reporters. Curr Opin Chem Biol. 2019 Oct 31;54:1-9 Authors: Shu X Abstract Dynamical features of cell signaling are the essence of living organisms. To understand animal development, it is fundamental to investigate signaling dynamics in vivo. Robust reporters are required to visualize spatial and temporal dynamics of enzyme activities and protein-protein interactions involved in signaling pathways. In this review, we summarize recent development in the design of new classes of fluorescent reporters for imaging dynamic ac...
Source: Current Opinion in Chemical Biology - October 31, 2019 Category: Biochemistry Authors: Shu X Tags: Curr Opin Chem Biol Source Type: research

Drugging the gut microbiota: toward  rational modulation of bacterial composition in the gut.
Drugging the gut microbiota: toward rational modulation of bacterial composition in the gut. Curr Opin Chem Biol. 2019 Oct 31;56:10-15 Authors: Altamura F, Maurice CF, Castagner B Abstract The human gastrointestinal tract hosts almost a trillion microorganisms, organized in a complex community known as the gut microbiota, an integral part of human physiology and metabolism. Indeed, disease-specific alterations in the gut microbiota have been observed in several chronic disorders, including obesity and inflammatory bowel diseases. Correcting these alterations could revert the development of such p...
Source: Current Opinion in Chemical Biology - October 31, 2019 Category: Biochemistry Authors: Altamura F, Maurice CF, Castagner B Tags: Curr Opin Chem Biol Source Type: research

Single-molecule manipulation quantification of site-specific DNA binding.
Abstract The execution of functions on DNA relies on complex interactions between DNA and proteins in a sequence and structure dependent manner. Accurate quantification of the affinity and kinetics of these interactions is critical for understanding the molecular mechanisms underlying their corresponding biological functions. The development of single-molecule manipulation technologies in the last two decades has made it possible to apply a mechanical constraint to a single DNA molecule and measure the end-to-end extension changes with nanometer resolution in realtime. While it has been shown that such technologie...
Source: Current Opinion in Chemical Biology - October 30, 2019 Category: Biochemistry Authors: Zhao X, Guo S, Lu C, Chen J, Le S, Fu H, Yan J Tags: Curr Opin Chem Biol Source Type: research

Molecular mechanisms regulating O-linked N-acetylglucosamine (O-GlcNAc)-processing enzymes.
Abstract The post-translational modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc) dynamically programmes cellular physiology to maintain homoeostasis and tailor biochemical pathways to meet context-dependent cellular needs. Despite diverse roles of played by O-GlcNAc, only two enzymes act antagonistically to govern its cycling; O-GlcNAc transferase installs the monosaccharide on target proteins, and O-GlcNAc hydrolase removes it. The recent literature has exposed a network of mechanisms regulating these two enzymes to choreograph global, and target-specific, O-GlcNAc cycling in response to cellul...
Source: Current Opinion in Chemical Biology - October 22, 2019 Category: Biochemistry Authors: King DT, Males A, Davies GJ, Vocadlo DJ Tags: Curr Opin Chem Biol Source Type: research

Recent achievements and current trajectories of diversity-oriented synthesis.
Abstract For two decades, diversity-oriented synthesis (DOS) has facilitated the assembly of small-molecule libraries comprising a variety of complex molecular architectures. Here, we describe some of the recent achievements in this field, many of which promise to contribute to the development of new chemical probes and drug leads. In particular, we report progress along several avenues of bioactive discovery that leverage topographically complex compounds generated using DOS and other methods. We also discuss advances in DNA-compatible chemistry that enable syntheses of more three-dimensionally complex and divers...
Source: Current Opinion in Chemical Biology - October 14, 2019 Category: Biochemistry Authors: Gerry CJ, Schreiber SL Tags: Curr Opin Chem Biol Source Type: research

Emerging technologies in mechanotransduction research.
Abstract Mechanotransduction research focuses on understanding how cells sense and respond to mechanical stimuli by converting mechanical signals into biochemical and biological responses. Cells have been shown to respond to mechanical stimuli through specialized biological machinery such as adhesion complexes. Research in the last two decades helped in identifying key components of cellular mechanotransduction. In recent years, integrated approaches, which are highlighted here, are emerging to provide new insights into the mechanistic and theoretical underpinnings of mechanotransduction. In particular, mathematic...
Source: Current Opinion in Chemical Biology - October 13, 2019 Category: Biochemistry Authors: Shamsan GA, Odde DJ Tags: Curr Opin Chem Biol Source Type: research

Mechanics and structural stability of the collagen triple helix.
Abstract The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing biological pathways including cell signaling, motility, and differentiation. Collagen's unique triple helical structure is thought to impart mechanical stability. However, detailed experimental studies on its molecular mechanics have been only recently emerging. Here, we review the treatment of the triple helix as a homogeneous flexible rod, including bend (standard worm-like...
Source: Current Opinion in Chemical Biology - October 10, 2019 Category: Biochemistry Authors: Kirkness MW, Lehmann K, Forde NR Tags: Curr Opin Chem Biol Source Type: research

Peptides and peptidomimetics as inhibitors of protein-protein interactions involving β-sheet secondary structures.
Peptides and peptidomimetics as inhibitors of protein-protein interactions involving β-sheet secondary structures. Curr Opin Chem Biol. 2019 Oct 04;52:157-167 Authors: Laxio Arenas J, Kaffy J, Ongeri S Abstract Protein-protein interactions involving β-sheet secondary structures have been questioned in many fatal human diseases such as cancer, autoimmune and neurodegenerative diseases. Small selective peptide derivatives and analogues are promising drug candidates for inhibiting this poorly known class of PPIs. In this review, we will highlight the main strategies developed for designing line...
Source: Current Opinion in Chemical Biology - October 4, 2019 Category: Biochemistry Authors: Laxio Arenas J, Kaffy J, Ongeri S Tags: Curr Opin Chem Biol Source Type: research

How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation.
Abstract Dissociation of a protein from DNA is often assumed to be described by an off rate that is independent of other molecules in solution. Recent experiments and computational analyses have challenged this view by showing that unbinding rates (residence times) of DNA-bound proteins can depend on concentrations of nearby molecules that are competing for binding. This 'facilitated dissociation' (FD) process can occur at the single-binding site level via formation of a ternary complex, and can dominate over 'spontaneous dissociation' at low (submicromolar) concentrations. In the crowded intracellular environment...
Source: Current Opinion in Chemical Biology - October 2, 2019 Category: Biochemistry Authors: Erbaş A, Marko JF Tags: Curr Opin Chem Biol Source Type: research

Dynamic bonds and their roles in mechanosensing.
Abstract Mechanical forces are ubiquitous in a cell's internal structure and external environment. Mechanosensing is the process that the cell employs to sense its mechanical environment. In receptor-mediated mechanosensing, cell surface receptors interact with immobilized ligands to provide a specific way to receive extracellular force signals to targeted force-transmitting, force-transducing and force-supporting structures inside the cell. Conversely, forces generated endogenously by the cell can be transmitted via cytoplasmic protein-protein interactions and regulate cell surface receptor activities in an 'insi...
Source: Current Opinion in Chemical Biology - September 26, 2019 Category: Biochemistry Authors: Zhu C, Chen Y, Ju LA Tags: Curr Opin Chem Biol Source Type: research

The continuing expansion of CAZymes and their families.
Abstract Carbohydrate-active enzymes (CAZymes) catalyze the assembly and breakdown of glycans and glycoconjugates. Some have been discovered, studied and exploited for numerous applications long ago. For instance, amylase and invertase were isolated in the second half of the 19th century and lysozyme was the first enzyme whose 3-D structure was determined. In spite of this early start, the number of families of carbohydrate-active enzymes continues to grow steadily in the early 21st century. This review examines the CAZyme families reported during the last two years and posits that the current expansion will conti...
Source: Current Opinion in Chemical Biology - September 20, 2019 Category: Biochemistry Authors: Garron ML, Henrissat B Tags: Curr Opin Chem Biol Source Type: research

Peptide nucleic acid (PNA) and its applications in chemical biology, diagnostics, and therapeutics.
Abstract Peptide nucleic acid (PNA) stands as one of the most successful artificial oligonucleotide mimetics. Salient features include the stability of hybridization complexes (either as duplexes or triplexes), metabolic stability, and ease of chemical modifications. These features have enabled important applications such as antisense agents, gene editing, nucleic acid sensing and as a platform to program the assembly of PNA-tagged molecules. Here, we review recent advances in these areas. PMID: 31541865 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - September 18, 2019 Category: Biochemistry Authors: Saarbach J, Sabale PM, Winssinger N Tags: Curr Opin Chem Biol Source Type: research

Shedding light on complexity of protein-protein interactions in cancer.
Abstract Most cell signaling and surveillance circuits are physically maintained through a dense network of protein-protein interactions (PPIs). Genetic mutations, epigenetic changes as well as alterations in cellular microenvironment can markedly rewire the patterns of PPIs, which leads to neoplastic growth of cancer cells. There are accumulating evidences that drugs that target-specific PPI pairs may provide an opportunity to treat cancers with a higher specificity and efficacy than those inhibiting enzymatic activity of oncogenic proteins. Therefore, identification of driving PPIs in a given cancer not only imp...
Source: Current Opinion in Chemical Biology - August 31, 2019 Category: Biochemistry Authors: Yoon TY, Lee HW Tags: Curr Opin Chem Biol Source Type: research

Probing microscopic conformational dynamics in folding reactions by measuring transition paths.
Abstract Transition paths comprise those parts of a folding trajectory where the molecule passes through the high-energy transition states separating folded and unfolded conformations. The transition states determine the folding kinetics and mechanism but are difficult to observe because of their brief duration. Single-molecule experiments have in recent years begun to characterize transition paths in folding reactions, allowing the microscopic conformational dynamics that occur as a molecule traverses the energy barriers to be probed directly. Here we review single-molecule fluorescence and force spectroscopy mea...
Source: Current Opinion in Chemical Biology - August 30, 2019 Category: Biochemistry Authors: Hoffer NQ, Woodside MT Tags: Curr Opin Chem Biol Source Type: research

Lectin antagonists in infection, immunity, and inflammation.
Abstract Lectins are proteins found in all domains of life with a plethora of biological functions, especially in the infection process, immune response, and inflammation. Targeting these carbohydrate-binding proteins is challenged by the fact that usually low affinity interactions between lectin and glycoconjugate are observed. Nature often circumvents this process through multivalent display of ligand and lectin. Consequently, the vast majority of synthetic antagonists are multivalently displayed native carbohydrates. At the cost of disadvantageous pharmacokinetic properties and possibly a reduced selectivity fo...
Source: Current Opinion in Chemical Biology - August 27, 2019 Category: Biochemistry Authors: Meiers J, Siebs E, Zahorska E, Titz A Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Mammalian synthetic biology: from devices to multicellular systems.
PMID: 31466822 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 26, 2019 Category: Biochemistry Authors: Saito H, Yokobayashi Y Tags: Curr Opin Chem Biol Source Type: research

Chemical tools to characterize peptidoglycan synthases.
Abstract The peptidoglycan cell wall is a unique macromolecular structure in bacteria that defines their shape and confers protection from the surrounding environment. Decades of research has focused on understanding the peptidoglycan synthesis pathway and exploiting its essentiality for antibiotic development. Recently, a new class of peptidoglycan polymerases known as the SEDS (shape, elongation, division and sporulation) proteins were identified; these polytopic membrane proteins function together with the better-known penicillin-binding proteins (PBPs) to build the cell wall. In this review, we will highlight ...
Source: Current Opinion in Chemical Biology - August 26, 2019 Category: Biochemistry Authors: Taguchi A, Kahne D, Walker S Tags: Curr Opin Chem Biol Source Type: research

New insights into lipopolysaccharide assembly and export.
Abstract Lipopolysaccharide is an important immunomodulatory and structural component found in the outer membrane of Gram-negative bacteria. The biosynthesis of this glycoconjugate proceeds by a highly conserved pathway and, as such, is an attractive target for antibiotic action. We highlight here recent work focused on understanding this pathway with an emphasis on new insights related to chain length control and transport across the inner and outer cell membranes. PMID: 31445442 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 21, 2019 Category: Biochemistry Authors: Sweeney RP, Lowary TL Tags: Curr Opin Chem Biol Source Type: research

Bifunctional chemical probes inducing protein-protein interactions.
Abstract Inducing biomolecular interactions with synthetic molecules to impact biological function is a concept of enormous appeal. Recent years have seen a resurgence of interest in designing bispecific molecules that serve as bridging agents to bring proteins together. Pioneering structural and biophysical investigation of ternary complexes formed by mono-functional and bifunctional ligands highlights that proximity-induced stabilization or de novo formation of protein-protein interactions is a common feature of their molecular recognition. In this review, we illustrate these concepts and advances with represent...
Source: Current Opinion in Chemical Biology - August 13, 2019 Category: Biochemistry Authors: Maniaci C, Ciulli A Tags: Curr Opin Chem Biol Source Type: research

An overview of activity-based probes for glycosidases.
GJ Abstract As the scope of modern genomics technologies increases, so does the need for informative chemical tools to study functional biology. Activity-based probes (ABPs) provide a powerful suite of reagents to probe the biochemistry of living organisms. These probes, featuring a specificity motif, a reactive chemical group and a reporter tag, are opening-up large swathes of protein chemistry to investigation in vitro, as well as in cellular extracts, cells and living organisms in vivo. Glycoside hydrolases, by virtue of their prominent biological and applied roles, provide a broad canvas on which ABPs may ill...
Source: Current Opinion in Chemical Biology - August 13, 2019 Category: Biochemistry Authors: Wu L, Armstrong Z, Schröder SP, de Boer C, Artola M, Aerts JM, Overkleeft HS, Davies GJ Tags: Curr Opin Chem Biol Source Type: research

Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking.
cek M Abstract Modification of DNA with reactive groups and their post-synthetic transformations are useful for labelling, imaging, bioconjugations and cross-linking with other (bio)molecules. This review summarizes the recent progress in this field and covers transformations of oxo groups, cycloadditions, conjugate additions, alkylations, cross-couplings and other reactions. Examples of applications are given and the practicability and scope of the reactions are discussed. PMID: 31415984 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - August 12, 2019 Category: Biochemistry Authors: Ivancová I, Leone DL, Hocek M Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Recent advance in chemical genetics and chemical epigenetics.
PMID: 31377107 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - July 31, 2019 Category: Biochemistry Authors: Lei X, Li XD Tags: Curr Opin Chem Biol Source Type: research

Recent developments in spontaneous Raman imaging of living biological cells.
Abstract Raman spectroscopy is a non-invasive optical technique for measuring chemical information from samples including biological cells. With its high sensitivity and compatibility with in vitro samples, Raman spectroscopy is increasing in popularity as a tool for acquiring chemical images of cellular samples in fields including parasitology, pharmacology, and oncology. This review describes emerging technologies that are improving the speed, resolution, and impact of Raman imaging techniques. Topics include novel instrumentation for data acquisition and improvements on techniques for displaying hyperspectral d...
Source: Current Opinion in Chemical Biology - July 22, 2019 Category: Biochemistry Authors: Durrant B, Trappett M, Shipp D, Notingher I Tags: Curr Opin Chem Biol Source Type: research

Towards functional de novo designed proteins.
Abstract Our ability to design completely de novo proteins is improving rapidly. This is true of all three main approaches to de novo protein design, which we define as: minimal, rational and computational design. Together, these have delivered a variety of protein scaffolds characterised to high resolution. This is truly impressive and a major advance from where the field was a decade or so ago. That all said, significant challenges in the field remain. Chief amongst these is the need to deliver functional de novo proteins. Such designs might include selective and/or tight binding of specified small molecules, or...
Source: Current Opinion in Chemical Biology - July 20, 2019 Category: Biochemistry Authors: Dawson WM, Rhys GG, Woolfson DN Tags: Curr Opin Chem Biol Source Type: research

Can single molecule localization microscopy detect nanoclusters in T cells?
Abstract Nanoclusters of cell surface receptors have been detected with single molecule localization microscopy (SMLM) and are thought to mediate signal transduction. Clustering of the T cell receptor (TCR), for example, was reported to control signalling efficiency and antigen discrimination. However, the ability to detect nanoclusters with SMLM has been questioned. Here, we review the detection limits of SMLM as defined by both the physical limits and data processing, as well as evidence for nanoclusters arising from complementary techniques. We conclude with an outlook of how future data analysis can reveal the...
Source: Current Opinion in Chemical Biology - July 17, 2019 Category: Biochemistry Authors: Feher K, Halstead JM, Goyette J, Gaus K Tags: Curr Opin Chem Biol Source Type: research

Editorial overview: Advances and future prospects of molecular imaging for studying and quantifying biological processes.
PMID: 31311706 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - July 13, 2019 Category: Biochemistry Authors: Kukura P, Myong S Tags: Curr Opin Chem Biol Source Type: research

Nucleic acid enzymes based on functionalized nucleosides.
Abstract Nucleic acid-based enzymes have recently joined their proteinaceous counterparts as important biocatalysts. While RNA enzymes (ribozymes) are found in nature, deoxyribozymes or DNAzymes are man-made entities. Numerous ribozymes and DNAzymes have been identified by Darwinian selection methods to catalyze a broad array of chemical transformations. Despite these important advances, practical applications involving nucleic acid enzymes are often plagued by relatively poor pharmacokinetic properties and cellular uptake, rapid degradation by nucleases and/or by the limited chemical arsenal carried by natural DN...
Source: Current Opinion in Chemical Biology - July 12, 2019 Category: Biochemistry Authors: Hollenstein M Tags: Curr Opin Chem Biol Source Type: research

New discoveries in bacterial N-glycosylation to expand the synthetic biology toolbox.
Abstract Historically, protein glycosylation was believed to be restricted to eukaryotes, but now is abundantly represented in all three domains of life. The first bacterial N-linked glycosylation system was discovered in the Gram-negative pathogen, Campylobacter jejuni, and subsequently transferred into the heterologous Escherichia coli host beginning a new era of synthetic bacterial glycoengineering. Since then, additional N-glycosylation pathways have been characterized resembling the classical C. jejuni system and unconventional new approaches for N-glycosylation have been uncovered. These include cytoplasmic ...
Source: Current Opinion in Chemical Biology - July 6, 2019 Category: Biochemistry Authors: Nothaft H, Szymanski CM Tags: Curr Opin Chem Biol Source Type: research

Visualizing transcription: key to understanding gene expression dynamics.
Abstract Visualization of transcription in living cells has taught us that genes are often transcribed in bursts, with periods of gene activity interspersed by periods of inactivity. Recently, technological advances in live-cell imaging have provided a more detailed picture of the characteristics of transcriptional bursts, and have allowed direct visualization of the upstream regulatory steps of bursting at single-molecule resolution. In this review, we highlight the latest insights into transcription dynamics and we discuss recent developments in understanding the regulation of transcriptional bursting through th...
Source: Current Opinion in Chemical Biology - July 5, 2019 Category: Biochemistry Authors: Brouwer I, Lenstra TL Tags: Curr Opin Chem Biol Source Type: research

The role of bacterial lipid diversity and membrane properties in modulating antimicrobial peptide activity and drug resistance.
We describe the current models of membrane disruption caused by AMPs and the changes in the structural properties that microbial membranes undergo in response to AMPs. This is followed by an outline of how the phospholipid composition of microbial membranes contributes to the changes in membrane bilayer structure and how the composition can be analysed in significant detail by modern lipidomic techniques. Finally, we discuss the challenges to fully analyse microbial membrane composition and structure that may occur during the development of resistance to AMPs. PMID: 31260926 [PubMed - as supplied by publisher] (Source...
Source: Current Opinion in Chemical Biology - June 28, 2019 Category: Biochemistry Authors: Lee TH, Hofferek V, Separovic F, Reid GE, Aguilar MI Tags: Curr Opin Chem Biol Source Type: research

High-speed atomic force microscopy.
Abstract High-speed atomic force microscopy (HS-AFM) is a unique tool for molecular imaging. It can directly visualize protein molecules during their functional activity at high spatiotemporal resolution, without a marker being attached to the molecules. Molecular dynamics filmed with HS-AFM can provide mechanistic insights into the functional molecular processes that are hard to be attained with other approaches. In this mini review, I highlight some of recent relevant studies of proteins by HS-AFM imaging after brief descriptions of AFM and HS-AFM. PMID: 31254806 [PubMed - as supplied by publisher] (Source:...
Source: Current Opinion in Chemical Biology - June 26, 2019 Category: Biochemistry Authors: Ando T Tags: Curr Opin Chem Biol Source Type: research

Single-molecule trapping and measurement in solution.
Abstract Trapping of a single molecule in the fluid phase was realized decades following developments in the gas-phase, because in some ways the solution phase posed a greater challenge. The key issues have since been addressed by several different means; techniques to confine nanometer scale entities in solution now abound and are gaining traction in a variety of single molecule studies. Available methods range from pure physical entrapment of a molecule on the one hand to electrokinetic and optical techniques, and approaches that exploit thermodynamic principles on the other. Some trapping techniques have also o...
Source: Current Opinion in Chemical Biology - June 26, 2019 Category: Biochemistry Authors: Bespalova MI, Mahanta S, Krishnan M Tags: Curr Opin Chem Biol Source Type: research

Mammalian synthetic biology by CRISPRs engineering and applications.
Abstract Technologies harnessing CRISPR systems have been rapidly evolving and expanding the capacity of researchers for understanding of mammalian cell behavior and its underlying mechanisms through genome and epigenome manipulations. In this review, we summarized the recent developments of CRISPR-based technologies for genetic and epigenetic modifications that include engineering of Cas9 for PAM simplification, non-cleaving base editing tools and alteration of gene expression. Applications such as genome-wide screening methods or CRISPR-based DNA barcoding for cellular lineage tracking are highlighted. Anticipat...
Source: Current Opinion in Chemical Biology - June 26, 2019 Category: Biochemistry Authors: Katayama K, Mitsunobu H, Nishida K Tags: Curr Opin Chem Biol Source Type: research

Extending fluorescence microscopy into anaerobic environments.
Abstract Fluorescence microscopy is a powerful tool for investigating living cells. While widely used fluorescent proteins, such as green fluorescent protein (GFP), have had huge impact in biological imaging because they provide genetically encoded, highly specific labeling, these probes require oxygen to generate fluorescence. This crucial oxidative step has limited the use of GFP-like proteins in anaerobic bacterial systems and restricted live-cell studies of obligate anaerobes and their biology. This review discusses alternative approaches to labeling proteins in anaerobic bacteria that are compatible with live...
Source: Current Opinion in Chemical Biology - June 25, 2019 Category: Biochemistry Authors: Chia HE, Marsh ENG, Biteen JS Tags: Curr Opin Chem Biol Source Type: research

Aptamer-based and aptazyme-based riboswitches in mammalian cells.
In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. PMID: 31238268 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - June 22, 2019 Category: Biochemistry Authors: Yokobayashi Y Tags: Curr Opin Chem Biol Source Type: research

Strategies for increasing the throughput of super-resolution microscopies.
ley S Abstract Fluorescence microscopy methods have been developed to circumvent the diffraction limit by exploiting nonlinearities in the interactions between light and fluorophores. Initially, these methods were up to orders of magnitude slower than standard microscopies. In recent years, a wide array of technological advances have increased the throughput of super-resolution microscopies, through parallelization, smart scanning or data processing, and sample expansion. Here, we review recent innovations for increased throughput, some applications that have benefitted from them, and how they could be improved in...
Source: Current Opinion in Chemical Biology - June 15, 2019 Category: Biochemistry Authors: Mahecic D, Testa I, Griffié J, Manley S Tags: Curr Opin Chem Biol Source Type: research

Functional super-resolution microscopy of the cell.
Abstract Recent advances in super-resolution fluorescence microscopy have led to ∼10 nm spatial resolution and profound impact on cell biology and beyond. Here we discuss emerging possibilities to encode functional information of intracellular microenvironments, for example, local pH, small-molecule concentrations, chemical polarity (hydrophobicity), and protein activity, into diverse dimensions of the super-resolution signal, hence a class of approaches we collectively refer to as functional super-resolution microscopy. By adding remarkably rich functional information to the already powerful super-reso...
Source: Current Opinion in Chemical Biology - June 15, 2019 Category: Biochemistry Authors: Yan R, Wang B, Xu K Tags: Curr Opin Chem Biol Source Type: research

DNA barcodes evolve for high-resolution cell lineage tracing.
Abstract Mammalian development involves continuous dynamic processes in which cells propagate, differentiate, orchestrate, and decease to produce high-order functions. Although accurate cell lineage information can provide a strong foundation to understand such complex processes, the cell lineages involved in development of the whole mammalian body remain largely unclear, except for in early embryogenesis, which is observable under a microscope. With CRISPR genome editing, the concept of 'evolving DNA barcodes' has rapidly emerged for large-scale, high-resolution cell lineage tracing, where cell-embedded DNA barco...
Source: Current Opinion in Chemical Biology - June 15, 2019 Category: Biochemistry Authors: Masuyama N, Mori H, Yachie N Tags: Curr Opin Chem Biol Source Type: research

Chemoenzymatic synthesis of glycoproteins.
Abstract The majority of the world's best-selling biotherapeutics are glycoproteins. However their production using cellular expression systems invariably produces inseparable mixtures of materials which differ in their attached carbohydrates. As in many cases correct carbohydrate structure is vital for in vivo efficacy, the development of methods for the production of glycoproteins in homogeneous form has become a significant scientific objective. Here a brief overview of recent progress in the production of homogeneous glycoproteins, including monoclonal antibodies, will be discussed, centring on the use of endo...
Source: Current Opinion in Chemical Biology - June 13, 2019 Category: Biochemistry Authors: Fairbanks AJ Tags: Curr Opin Chem Biol Source Type: research