Next generation biofuel engineering in prokaryotes.
Abstract Next-generation biofuels must be compatible with current transportation infrastructure and be derived from environmentally sustainable resources that do not compete with food crops. Many bacterial species have unique properties advantageous to the production of such next-generation fuels. However, no single species possesses all characteristics necessary to make high quantities of fuels from plant waste or CO2. Species containing a subset of the desired characteristics are used as starting points for engineering organisms with all desired attributes. Metabolic engineering of model organisms has yielded hi...
Source: Current Opinion in Chemical Biology - April 23, 2013 Category: Biochemistry Authors: Gronenberg LS, Marcheschi RJ, Liao JC Tags: Curr Opin Chem Biol Source Type: research

Drugging the human methylome: an emerging modality for reversible control of aberrant gene transcription.
Abstract Protein and DNA methylation have emerged as critical mechanisms for the control of regulated gene transcription. In humans, the addition, recognition and removal of methyl groups are orchestrated by at least 344 proteins that we collectively refer to as the 'methylome'. The large size of the methylome likely reflects the importance of precise control over this small covalent modification. An increasing number of reports implicating the misregulation of methylation in disease make the proteins governing this modification attractive target for small molecule drug discovery. In light of the emerging opportun...
Source: Current Opinion in Chemical Biology - April 22, 2013 Category: Biochemistry Authors: Wigle TJ, Copeland RA Tags: Curr Opin Chem Biol Source Type: research

Spectral expansion and antenna reduction can enhance photosynthesis for energy production.
Abstract We consider two approaches for improving the efficiency of photosynthesis: the expansion of the solar spectrum that drives oxygenic photosynthesis and the reduction of antenna systems that couple to the photochemical reaction center. The first approach can possibly result in an increase of 19% in the number of photons available per unit area if the photosynthetically active radiation spectrum is expanded to 750nm. The second approach can in principle shift the photosynthesis light response curve to significantly higher intensities, thereby reducing the amount of excess light, which is absorbed photons in ...
Source: Current Opinion in Chemical Biology - April 18, 2013 Category: Biochemistry Authors: Blankenship RE, Chen M Tags: Curr Opin Chem Biol Source Type: research

Expanding the microalgal industry - continuing controversy or compelling case?
Abstract Herein we examine the potential role that microalgae might play in the approaching challenges of energy and fuel security, and food and water supply. Microalgal production systems remain the subject of controversy however, generally consisting of arguments about the economic and environment sustainability of these systems. We discuss these aspects and draw some parallels with other systems to highlight real advantages and obstacles to expanding the modern microalgal industry. Emerging alternative production models and the relatively early developmental state of the microalgal biofuels industry provide roo...
Source: Current Opinion in Chemical Biology - April 12, 2013 Category: Biochemistry Authors: Stephens E, Ross IL, Hankamer B Tags: Curr Opin Chem Biol Source Type: research

Bispecific antibodies for delivery into the brain.
Abstract The blood-brain barrier (BBB) is a formidable obstacle preventing drug delivery to the brain, particularly for large protein therapeutics. The utilization of endogenous brain endothelial transport pathways, however, represents a promising approach to cross the cellular barrier through receptor-mediated transcytosis. Therapeutics designed to take advantage of this approach require at least two functionalities, one that facilitates transport and the other to provide therapeutic benefit, and bispecific antibodies are ideally suited for this task. PMID: 23570979 [PubMed - as supplied by publisher] (Sourc...
Source: Current Opinion in Chemical Biology - April 6, 2013 Category: Biochemistry Authors: Watts RJ, Dennis MS Tags: Curr Opin Chem Biol Source Type: research

Analytical and bioanalytical technologies for characterizing antibody-drug conjugates.
Abstract Antibody-drug conjugates (ADCs) require multiple assays for analytical and bioanalytical characterization due to their heterogeneous and dynamic nature. These assays can help address questions from the drug-loading distribution following conjugation to exposure-response relationships after dosing in vivo. This review describes new assay technologies that have been developed for physiochemical characterization and determination of pharmacokinetic parameters of ADCs. PMID: 23570980 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 6, 2013 Category: Biochemistry Authors: Alley SC, Anderson KE Tags: Curr Opin Chem Biol Source Type: research

Scope and potential of halogenases in biosynthetic applications.
RJ Abstract A large and diverse series of halogenated natural products exist. In many of these compounds the halogen is important to biological activity and bioavailability. We now recognise that nature has developed many different halogenation strategies for which well-known enzyme classes such as haem oxidases or flavin-dependent oxidases have been adapted. Enzymes capable of halogenating all kinds of different chemical groups from electron-rich to electron-poor, from aromatic to aliphatic have been characterised. Given that synthetic halogenation reactions are not trivial transformations and that halogenated m...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Smith DR, Grüschow S, Goss RJ Tags: Curr Opin Chem Biol Source Type: research

Engineering and application of P450 monooxygenases in pharmaceutical and metabolite synthesis.
Abstract Cytochrome P450 monoxygenase (P450s or CYPs) allow access to drug metabolites, necessary for approval of new therapeutics in one step, with increased success being demonstrated using bacterial and fungal P450s. Moreover, 12 of the 13 products of the human metabolism of verapamil can be accessed through engineered and chimeric bacterial P450s. These P450s are also used in the synthesis of pharmaceuticals themselves, including the semi-synthetic production of artemisinin in an engineered cell. The integration of new technologies including ultrasound and polyfluorinated hydrocarbon solvents offers an attract...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Caswell JM, O'Neill M, Taylor SJ, Moody TS Tags: Curr Opin Chem Biol Source Type: research

On the development of new biocatalytic processes for practical pharmaceutical synthesis.
Abstract Biocatalysis has established itself as a scalable and green technology for the production of a broad range of pharmaceutical APIs and intermediates. The number and scope of biocatalysts employed on large scale to deliver cost-advantaged and quality-advantaged processes to important substances continue to expand. This review discusses the recent developments in the field, including examples of processes leveraging hydrolases, reductases, transaminases, oxidases and other biocatalysts, focused on the preparation of important investigational and launched therapeutics. Biocatalysts recently discovered, and in...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Huisman GW, Collier SJ Tags: Curr Opin Chem Biol Source Type: research

Chelators for investigating zinc metalloneurochemistry.
Abstract The physiology and pathology of mobile zinc signaling has become an important topic in metalloneurochemistry. To study the action of mobile zinc effectively, specialized tools are required that probe the temporal and positional changes of zinc ions within live tissue and cells. In the present article we describe the design and implementation of selective zinc chelators as antagonists to interrogate the function of mobile zinc, with an emphasis on the pools of vesicular zinc in the terminals of hippocampal mossy fiber buttons. PMID: 23478014 [PubMed - in process] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Radford RJ, Lippard SJ Tags: Curr Opin Chem Biol Source Type: research

Squalene hopene cyclases: highly promiscuous and evolvable catalysts for stereoselective CC and CX bond formation.
uer B Abstract We review here how the inherent promiscuous nature, as well as the evolvability of terpene cyclase enzymes enables new applications in chemistry. We mainly focus on squalene hopene cyclases, class II triterpene synthases that use a proton-initiated cationic polycyclization cascade to form carbopolycyclic products. We highlight recent findings to demonstrate that these enzymes are capable of activating different functionalities other than the traditional terminal isoprene CC-group as well as being compatible with a wide range of nucleophiles beyond the 'ene-functionality'. Thus, squalene hopene cycla...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Hammer SC, Syrén PO, Seitz M, Nestl BM, Hauer B Tags: Curr Opin Chem Biol Source Type: research

Using chemistry to study and control metals in biology.
PMID: 23490809 [PubMed - in process] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Chang CJ, He C Tags: Curr Opin Chem Biol Source Type: research

Enzyme catalysed tandem reactions.
eda E Abstract To transfer to the laboratory, the excellent efficiency shown by enzymes in Nature, biocatalysis, had to mimic several synthetic strategies used by the living organisms. Biosynthetic pathways are examples of tandem catalysis and may be assimilated in the biocatalysis field for the use of isolated multi-enzyme systems in the homogeneous phase. The concurrent action of several enzymes that work sequentially presents extraordinary advantages from the synthetic point of view, since it permits a reversible process to become irreversible, to shift the equilibrium reaction in such a way that enantiopure co...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Oroz-Guinea I, García-Junceda E Tags: Curr Opin Chem Biol Source Type: research

De novo enzymes by computational design.
Abstract Computational enzyme design has emerged as a promising tool for generating made-to-order biocatalysts. In addition to improving the reliability of the design cycle, current efforts in this area are focusing on expanding the set of catalyzed reactions and investigating the structure and mechanism of individual designs. Although the activities of de novo enzymes are typically low, they can be significantly increased by directed evolution. Analysis of their evolutionary trajectories provides valuable feedback for the design algorithms and can enhance our understanding of natural protein evolution. PMID:...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Kries H, Blomberg R, Hilvert D Tags: Curr Opin Chem Biol Source Type: research

Alkylating enzymes.
Abstract Chemospecific and regiospecific modifications of natural products by methyl, prenyl, or C-glycosyl moieties are a challenging and cumbersome task in organic synthesis. Because of the availability of an increasing number of stable and selective transferases and cofactor regeneration processes, enzyme-assisted strategies turn out to be promising alternatives to classical synthesis. Two categories of alkylating enzymes become increasingly relevant for applications: firstly prenyltransferases and terpene synthases (including terpene cyclases), which are used in the production of terpenoids such as artemisinin...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Wessjohann LA, Keim J, Weigel B, Dippe M Tags: Curr Opin Chem Biol Source Type: research

Strategies for the discovery and engineering of enzymes for biocatalysis.
UT Abstract Protein engineering is the most important method to overcome the limitations of natural enzymes as biocatalysts. The past few years have seen a tremendous increase in novel concepts to facilitate the design of mutant libraries for focused directed evolution mostly guided by advanced bioinformatic tools. In addition, advanced high-throughput methods were developed using, for example, FACS analysis or microfluidic systems. These achievements significantly facilitate the tailor-made design of enzymes to make them suitable for industrial applications. PMID: 23523243 [PubMed - in process] (Source: Cur...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Davids T, Schmidt M, Böttcher D, Bornscheuer UT Tags: Curr Opin Chem Biol Source Type: research

CC bond formation using ThDP-dependent lyases.
l M Abstract The present review summarizes recent achievements in enzymatic thiamine catalysis during the past three years. With well-established enzymes such as BAL, PDC and TK new reactions have been identified and respective variants were prepared, which enable access to stereoisomeric products. Further we highlight recent progress with 'new' ThDP-dependent enzymes like MenD and PigD, which catalyze the Stetter-like 1,4 addition of aldehydes and YerE, which is the first known ThDP-dependent enzyme accepting ketones as acceptors. PMID: 23523314 [PubMed - in process] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Müller M, Sprenger GA, Pohl M Tags: Curr Opin Chem Biol Source Type: research

Biocatalysis enters a new era.
PMID: 23540295 [PubMed - in process] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Turner NJ, Truppo MD Tags: Curr Opin Chem Biol Source Type: research

Priming ammonia lyases and aminomutases for industrial and therapeutic applications.
Abstract Ammonia lyases (AL) and aminomutases (AM) are emerging in green synthetic routes to chiral amines and an AL is being explored as an enzyme therapeutic for treating phenylketonuria and cancer. Although the restricted substrate range of the wild-type enzymes limits their widespread application, the non-reliance on external cofactors and direct functionalization of an olefinic bond make ammonia lyases attractive biocatalysts for use in the synthesis of natural and non-natural amino acids, including β-amino acids. The approach of combining structure-guided enzyme engineering with efficient mutant library...
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Heberling MM, Wu B, Bartsch S, Janssen DB Tags: Curr Opin Chem Biol Source Type: research

Protein engineering of enzymes for process applications.
This article discusses the challenges involved in enzyme modification focused on process requirements, such as the need to fulfill reaction thermodynamics, specific activity under the required conditions, kinetics at required concentrations, and stability. Finally, future research directions are discussed, including the integration of biocatalysis with neighboring chemical steps. PMID: 23562542 [PubMed - in process] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - April 1, 2013 Category: Biochemistry Authors: Woodley JM Tags: Curr Opin Chem Biol Source Type: research

Carbon partitioning in photosynthesis.
Abstract The work seeks to raise awareness of a fundamental problem that impacts the renewable generation of fuels and chemicals via (photo)synthetic biology. At issue is regulation of the endogenous cellular carbon partitioning between different biosynthetic pathways, over which the living cell exerts stringent control. The regulation of carbon partitioning in photosynthesis is not understood. In plants, microalgae and cyanobacteria, methods need be devised to alter photosynthetic carbon partitioning between the sugar, terpenoid, and fatty acid biosynthetic pathways, to lower the prevalence of sugar biosynthesis ...
Source: Current Opinion in Chemical Biology - March 28, 2013 Category: Biochemistry Authors: Melis A Tags: Curr Opin Chem Biol Source Type: research

Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production.
Abstract Microalgae are among the most diverse organisms on the planet, and as a result of symbioses and evolutionary selection, the configuration of core metabolic networks is highly varied across distinct algal classes. The differences in photosynthesis, carbon fixation and processing, carbon storage, and the compartmentation of cellular and metabolic processes are substantial and likely to transcend into the efficiency of various steps involved in biofuel molecule production. By highlighting these differences, we hope to provide a framework for comparative analyses to determine the efficiency of the different a...
Source: Current Opinion in Chemical Biology - March 25, 2013 Category: Biochemistry Authors: Hildebrand M, Abbriano RM, Polle JE, Traller JC, Trentacoste EM, Smith SR, Davis AK Tags: Curr Opin Chem Biol Source Type: research

Cell-free translation of peptides and proteins:from high throughput screening to clinical production.
Abstract In the past decade, in vitro transcription/translation technologies have emerged as discovery tools for screening large protein expression libraries, for the selection of engineered polypeptide libraries, and as alternatives to conventional heterologous expression for protein production. Therapeutic proteins and peptides discovered using ribosome-based display methods that link genetic information to the encoded polypeptide generated by cell-free extracts, or purified translation components, are beginning to move forward into human clinical trials. This review details the significant progress in in vitro ...
Source: Current Opinion in Chemical Biology - March 14, 2013 Category: Biochemistry Authors: Murray CJ, Baliga R Tags: Curr Opin Chem Biol Source Type: research

Comparing life cycle assessments of different biofuel options.
Abstract Life cycle assessment (LCA) has shown that first generation biofuels provide a little to no benefit for greenhouse gas (GHG) reductions compared to petroleum fuels, particularly when indirect effects are considered. Second generation fuels are intended to achieve greater GHG reductions and avoid other sustainability issues. LCAs of second generation biofuels exhibit great variability and uncertainty, leading to inconclusive results for the performance of particular pathways (combinations of feedstocks and fuels). Variability arises in part because of the prospective nature of LCAs for future fuels; howeve...
Source: Current Opinion in Chemical Biology - March 9, 2013 Category: Biochemistry Authors: Kendall A, Yuan J Tags: Curr Opin Chem Biol Source Type: research

Heme transport and erythropoiesis.
Abstract In humans, systemic heme homeostasis is achieved via coordinated regulation of heme synthesis, transport and degradation. Although the heme biosynthesis and degradation pathways have been well characterized, the pathways for heme trafficking and incorporation into hemoproteins remain poorly understood. In the past few years, researchers have exploited genetic, cellular and biochemical tools, to identify heme transporters and, in the process, reveal unexpected functions for this elusive group of proteins. However, given the complexity of heme trafficking pathways, current knowledge of heme transporters is ...
Source: Current Opinion in Chemical Biology - February 13, 2013 Category: Biochemistry Authors: Yuan X, Fleming MD, Hamza I Tags: Curr Opin Chem Biol Source Type: research

Recent development of phosphorylases possessing large potential for oligosaccharide synthesis.
Abstract Phosphorylases are one group of carbohydrate active enzymes involved in the cleavage and formation of glycosidic linkages together with glycoside hydrolases and sugar nucleotide-dependent glycosyltransferases. Noticeably, the catalyzed phosphorolysis is reversible, making phosphorylases suitable catalysts for efficient synthesis of particular oligosaccharides from a donor sugar 1-phosphate and suitable carbohydrate acceptors with strict regioselectivity. Although utilization of phosphorylases for oligosaccharide synthesis has been limited because only few different enzymes are known, recently the number o...
Source: Current Opinion in Chemical Biology - February 8, 2013 Category: Biochemistry Authors: Nakai H, Kitaoka M, Svensson B, Ohtsubo K Tags: Curr Opin Chem Biol Source Type: research

New technologies and their impact on 'omics' research.
PMID: 23395431 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - February 6, 2013 Category: Biochemistry Authors: Bogyo M, Rudd PM Tags: Curr Opin Chem Biol Source Type: research

Targeted delivery of platinum-based anticancer complexes.
We describe recent progress using functionalized carbon nanotubes (CNTs) and nanorods, hollow Prussian blue (HPB), magnetic iron oxide and gold nanoparticles, liposomes, nanogels and polymers, as well as active targeting by conjugation to biodegradable proteins and peptides (e.g. EGF, heparin, herceptin, somatostatin and TAT). Spatially targeted activation of Pt(IV) prodrugs using light is also a promising approach. Interestingly, use of these new delivery and targeting systems for platinum drugs can lead to species with unusual reactivity which can kill cancer cells by new mechanisms. PMID: 23395452 [PubMed - as supp...
Source: Current Opinion in Chemical Biology - February 6, 2013 Category: Biochemistry Authors: Butler JS, Sadler PJ Tags: Curr Opin Chem Biol Source Type: research

Metal-based methods for protein inactivation.
This article summarizes the chemistry of hydrolytic and oxidative catalysts for protein inactivation. PMID: 23352647 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - January 23, 2013 Category: Biochemistry Authors: Prakash J, Kodanko JJ Tags: Curr Opin Chem Biol Source Type: research

Ubiquitin - omics reveals novel networks and associations with human disease.
Abstract Human neurodegenerative and infectious diseases and tumorigenesis are associated with alterations in ubiquitin pathways. Over 10% of the genome encode for genes that either bind or manipulate ubiquitin to affect a large proportion of biological processes. This has been the basis for the development of approaches allowing the enrichment of ubiquitinated proteins for comparisons using proteomics and mass spectrometry. Tools such as tagged tandem ubiquitin binding domains, chemically derivatized ubiquitin or anti-gly-gly-lys antibodies combined with mass spectrometry have contributed to surveys of poly-ubiqu...
Source: Current Opinion in Chemical Biology - January 19, 2013 Category: Biochemistry Authors: Kessler BM Tags: Curr Opin Chem Biol Source Type: research

Target deconvolution techniques in modern phenotypic profiling.
Abstract The past decade has seen rapid growth in the use of diverse compound libraries in classical phenotypic screens to identify modulators of a given process. The subsequent process of identifying the molecular targets of active hits, also called 'target deconvolution', is an essential step for understanding compound mechanism of action and for using the identified hits as tools for further dissection of a given biological process. Recent advances in 'omics' technologies, coupled with in silico approaches and the reduced cost of whole genome sequencing, have greatly improved the workflow of target deconvolutio...
Source: Current Opinion in Chemical Biology - January 18, 2013 Category: Biochemistry Authors: Lee J, Bogyo M Tags: Curr Opin Chem Biol Source Type: research

The importance of water exchange rates in the design of responsive agents for MRI.
Abstract The rate of water exchange in lanthanide complexes is often overlooked as an important parameter in the design of responsive MR imaging agents. Most often, the number of inner-sphere water coordination sites or the rotational mobility of the complex is considered as the central theme while water exchange is either assumed to be "fast enough" or entirely ignored. On the contrary, relaxation and shift theories predict that water exchange rates may indeed be the key parameter one should consider in any new molecular design. In this short review, the impact of water exchange rates on three classes o...
Source: Current Opinion in Chemical Biology - January 17, 2013 Category: Biochemistry Authors: Sherry AD, Wu Y Tags: Curr Opin Chem Biol Source Type: research

Comprehending dynamic protein methylation with mass spectrometry.
Abstract Protein methylation is a post-translational modification (PTM) which modulates cellular and biological processes including transcription, RNA processing, protein interactions and protein dynamics. Methylation, catalyzed by highly specific methyltransferase enzymes, occurs on several amino acids including arginine, lysine, histidine and dicarboxylic amino acids like glutamate. Mass spectrometry (MS)-based techniques continue to be the methods of choice for the study of protein PTMs. These approaches are powerful and sensitive tools that have been used to identify, quantify and characterize protein methylat...
Source: Current Opinion in Chemical Biology - January 17, 2013 Category: Biochemistry Authors: Afjehi-Sadat L, Garcia BA Tags: Curr Opin Chem Biol Source Type: research

Clawing back: broadening the notion of metal chelators in medicine.
Abstract The traditional notion of chelation therapy is the administration of a chemical agent to remove metals from the body. But formation of a metal-chelate can have biological ramifications that are much broader than metal elimination. Exploring these other possibilities could lead to pharmacological interventions that alter the concentration, distribution, or reactivity of metals in targeted ways for therapeutic benefit. This review highlights recent examples that showcase four general strategies of using principles of metal chelation in medicinal contexts beyond the traditional notion of chelation therapy. T...
Source: Current Opinion in Chemical Biology - January 16, 2013 Category: Biochemistry Authors: Franz KJ Tags: Curr Opin Chem Biol Source Type: research

Peptidomics methods for the identification of peptidase-substrate interactions.
Abstract Peptidases have important roles in controlling physiological signaling through their regulation of bioactive peptides. Understanding and controlling bioactive peptide regulation is of great biomedical interest and approaches that elucidate the interplay between peptidases and their substrates are vital for achieving this goal. Here, we highlight the utility of recent peptidomics approaches in identifying endogenous substrates of peptidases. These approaches reveal bioactive substrates and help characterize the biochemical functions of the enzyme. Most recently, peptidomics approaches have been applied to ...
Source: Current Opinion in Chemical Biology - January 15, 2013 Category: Biochemistry Authors: Lone AM, Kim YG, Saghatelian A Tags: Curr Opin Chem Biol Source Type: research

Emerging roles for protein S-palmitoylation in immunity from chemical proteomics.
Abstract The activation of innate and adaptive immune signaling pathways and effector functions often occur at cellular membranes and are regulated by complex mechanisms. Here we review the growing number of proteins which are known to be regulated by S-palmitoylation in immune cells emerging from recent advances in chemical proteomics. These chemical proteomic studies have highlighted the roles of this dynamic lipid modification in regulating the specificity and strength of immune responses in different lymphocyte populations. PMID: 23332315 [PubMed - as supplied by publisher] (Source: Current Opinion in Chemical Biology)
Source: Current Opinion in Chemical Biology - January 14, 2013 Category: Biochemistry Authors: Yount JS, Zhang MM, Hang HC Tags: Curr Opin Chem Biol Source Type: research

Protein TAILS: when termini tell tales of proteolysis and function.
Abstract Among the hundreds of posttranslational modifications, limited proteolysis, also known as processing, is special: It is irreversible, near ubiquitous, and by trimming peptide chains from their ends or cutting proteins into two, proteolysis forms shorter chains displaying new termini. The unique chemistry and location of α-amino-termini and carboxyl-termini in a protein engender special chemical and physical properties to a protein. Hence, modification of protein termini is often associated with new biological activities of a protein. We highlight recent proteomic developments enabling high throughpu...
Source: Current Opinion in Chemical Biology - January 6, 2013 Category: Biochemistry Authors: Lange PF, Overall CM Tags: Curr Opin Chem Biol Source Type: research

Advances in characterizing ubiquitylation sites by mass spectrometry.
Abstract The attachment of one or more ubiquitin moieties to proteins plays a central regulatory mechanism in eukaryotic cells. Protein ubiquitylation regulates numerous cellular processes, including protein degradation, signal transduction, DNA repair and cell division. The characterization of ubiquitylation is a two-fold challenge that involves the mapping of ubiquitylation sites and the determination of ubiquitin chain topology. This review focuses on the technical advances in the mass spectrometry-based characterization of ubiquitylation sites, which have recently involved the large-scale identification of ubi...
Source: Current Opinion in Chemical Biology - January 5, 2013 Category: Biochemistry Authors: Sylvestersen KB, Young C, Nielsen ML Tags: Curr Opin Chem Biol Source Type: research

Contemporary positional proteomics strategies to study protein processing.
Abstract Positional proteomics refers to mass spectrometry (MS)-driven proteomics technologies by which peptides carrying the amino or carboxyl terminus of proteins are enriched from whole proteomes, and identified by means of MS. Proteases irreversibly modify their substrates by hydrolyzing peptide bonds and have thus profound effects on the biological processes steered by their substrates. Since proteases create novel termini in their substrates, positional proteomics is ideally suited for protease degradomics studies. We here review recent developments in the field of positional proteomics applied to protease r...
Source: Current Opinion in Chemical Biology - January 3, 2013 Category: Biochemistry Authors: Plasman K, Van Damme P, Gevaert K Tags: Curr Opin Chem Biol Source Type: research

Transcriptomics in the RNA-seq era.
Abstract The transcriptomics field has developed rapidly with the advent of next-generation sequencing technologies. RNA-seq has now displaced microarrays as the preferred method for gene expression profiling. The comprehensive nature of the data generated has been a boon in terms of transcript identification but analysis challenges remain. Key among these problems is the development of suitable expression metrics for expression level comparisons and methods for identification of differentially expressed genes (and exons). Several approaches have been developed but as yet no consensus exists on the best pipeline t...
Source: Current Opinion in Chemical Biology - January 2, 2013 Category: Biochemistry Authors: McGettigan PA Tags: Curr Opin Chem Biol Source Type: research

Profiling and inhibiting reversible palmitoylation.
Abstract Protein palmitoylation describes the posttranslational modification of cysteines by a thioester-linked long-chain fatty acid. This modification is critical for membrane association, spatial organization, and the proper activity of hundreds of membrane-associated proteins. Palmitoylation is continuously remodeled, both by spontaneous hydrolysis and enzyme-mediated de-palmitoylation. Bioorthogonal pulse-chase labeling approaches have highlighted the role of protein thioesterases as key regulators of palmitoylation dynamics. Importantly, thioesterases are critical for regulating the spatial organization of k...
Source: Current Opinion in Chemical Biology - December 31, 2012 Category: Biochemistry Authors: Hernandez JL, Majmudar JD, Martin BR Tags: Curr Opin Chem Biol Source Type: research

Glycomics meets genomics, epigenomics and other high throughput omics for system biology studies.
auc G Abstract Majority of eukaryotic proteins are glycosylated and their glycan moieties have numerous important structural, functional and regulatory roles. Because of structural complexity of glycans and technological limitations glycomics, and particularly glycoproteomics was not able to follow rapid progress in genomics and proteomics over last 30 years. However, the field of glycan has been progressing rapidly and first large-scale studies of the glycome have been completed recently. These studies have revealed significant differences in glycome composition between individuals, which may contribute to the hu...
Source: Current Opinion in Chemical Biology - December 31, 2012 Category: Biochemistry Authors: Zoldoš V, Horvat T, Lauc G Tags: Curr Opin Chem Biol Source Type: research

Deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics.
Abstract Bacterial glycoproteins represent an attractive target for new antibacterial treatments, as they are frequently linked to pathogenesis and contain distinctive glycans that are absent in humans. Despite their potential therapeutic importance, many bacterial glycoproteins remain uncharacterized. This review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectin-based microarrays to monitor bacterial glycoprotein dynamics, crosslinking sugars to assess the roles of bacterial glycoproteins, and harness...
Source: Current Opinion in Chemical Biology - December 28, 2012 Category: Biochemistry Authors: Longwell SA, Dube DH Tags: Curr Opin Chem Biol Source Type: research

Chemical proteomics: ligation and cleavage of protein modifications.
Abstract Bioorthogonal ligation and cleavage methods are of major importance in the field of chemical biology. Recently, there has been significant progress in the improvement of classic ligation procedures as well as in the establishment of new ligation methodologies. Furthermore, the design of cleavable linkers for protein enrichment has lately received much attention. These techniques equip researchers with a wealth of tools suitable for proteomic applications. In order to ease navigation through these diverse systems, we here provide a comprehensive overview of methods that are useful for chemical proteomics. ...
Source: Current Opinion in Chemical Biology - December 27, 2012 Category: Biochemistry Authors: Rudolf GC, Heydenreuter W, Sieber SA Tags: Curr Opin Chem Biol Source Type: research

Tuning probe selectivity for chemical proteomics applications.
SH Abstract Covalent chemical probes enable investigation of a desired fraction of the proteome. It is possible to adjust the selectivity of these probes, so they either react with a certain amino acid in all proteins, a class of proteins or only a single protein species. A combination of specific reactive groups with additional recognition elements can fine tune probes to hit the desired proteins, even in the presence of related family members. Using probes of lower or higher selectivity, screening experiments for inhibitor discovery and imaging experiments for localization studies can be performed, showing only...
Source: Current Opinion in Chemical Biology - December 27, 2012 Category: Biochemistry Authors: Haedke U, Küttler EV, Vosyka O, Yang Y, Verhelst SH Tags: Curr Opin Chem Biol Source Type: research