Post-translational modification of proteins and the discovery of new medicine

Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution

Mass spectrometry imaging (MSI) is a powerful tool for label-free mapping of the spatial distribution of proteins in biological tissues. We have previously demonstrated imaging of individual proteoforms in biological tissues using nanospray desorption electrospray ionization (nano-DESI), an ambient liquid extraction-based MSI technique. Nano-DESI MSI generates multiply charged protein ions, which is advantageous for their identification using top-down proteomics analysis. In this study, we demonstrate proteoform mapping in biological tissues with a spatial resolution down to 7 μm using nano-DESI MSI. A substantial decrease in protein signals observed in high-spatial-resolution MSI makes these experiments challenging. We have enhanced the sensitivity of nano-DESI MSI experiments by optimizing the design of the capillary-based probe and the thickness of the tissue section. In addition, we demonstrate that oversampling may be used to further improve spatial resolution at little or no expense to sensitivity. These developments represent a new step in MSI-based spatial proteomics, which complements targeted imaging modalities widely used for studying biological systems.

Proteoform-Selective Imaging of Tissues Using Mass Spectrometry

Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform‐specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano‐DESI MSI) for the proteoform‐selective imaging of biological tissues. Nano‐DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof‐of‐concept experiments demonstrate that nano‐DESI MSI combined with on‐tissue top‐down proteomics is ideally suited for the proteoform‐selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.

Interactions of proteins with metal-based nanoparticles from a point of view of analytical chemistry - Challenges and opportunities

Interactions of proteins with nanomaterials draw attention of many research groups interested in fundamental phenomena. However, alongside with valuable information regarding physicochemical aspects of such processes and their mechanisms, they more and more often prove to be useful from a point of view of bioanalytics. Deliberate use of processes based on adsorption of proteins on nanoparticles (or vice versa) allows for a development of new analytical methods and improvement of the existing ones. It also leads to obtaining of nanoparticles of desired properties and functionalities, which can be used as elements of analytical tools for various applications. Due to interactions with nanoparticles, proteins can also gain new functionalities or lose their interfering potential, which from perspective of bioanalytics seems to be very inviting and attractive. In the framework of this article we will discuss the bioanalytical potential of interactions of proteins with a chosen group of nanoparticles, and implementation of so driven processes for biosensing. Moreover, we will show both positive and negative (opportunities and challenges) aspects resulting from the presence of proteins in media/samples containing metal-based nanoparticles or their precursors.

iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions

Among all the PTMs, the protein phosphorylation is pivotal for various pathological and physiological processes. About 30 percent of eukaryotic proteins undergo the phosphorylation modification, leading to various changes in conformation, function, stability, localization, and so forth. In eukaryotic proteins, phosphorylation occurs on serine (S), Threonine (T) and Tyrosine (Y) residues. Among these all, serine phosphorylation has its own importance as it is associated with various importance biological processes, including energy metabolism, signal transduction pathways, cell cycling, and apoptosis. Thus, its identification is important, however, the in vitro, ex vivo and in vivo identification can be laborious, time-taking and costly. There is a dire need of an efficient and accurate computational model to help researchers and biologists identifying these sites, in an easy manner. Herein, we propose a novel predictor for identification of Phosphoserine sites (PhosS) in proteins, by integrating the Chou's Pseudo Amino Acid Composition (PseAAC) with deep features. We used well-known DNNs for both the tasks of learning a feature representation of peptide sequences and performing classifications. Among different DNNs, the best score is shown by Covolutional Neural Network based model which renders CNN based prediction model the best for Phosphoserine prediction. Based on these results, it is concluded that the proposed model can help to identify PhosS sites in a very efficient and accurate manner which can help scientists understand the mechanism of this modification in proteins.

The critical role of collagen VI in lung development and chronic lung disease

Type VI collagen (collagen VI) is an obligate extracellular matrix component found mainly in the basement membrane region of many mammalian tissues and organs, including skeletal muscle and throughout the respiratory system. Collagen VI is probably most recognized in medicine as the genetic cause of a spectrum of muscular dystrophies, including Ullrich Congenital Myopathy and Bethlem Myopathy. Collagen VI is thought to contribute to myopathy, at least in part, by mediating muscle fiber integrity by anchoring myoblasts to the muscle basement membrane. Interestingly, collagen VI myopathies present with restrictive respiratory insufficiency, thought to be due primarily to thoracic muscular weakening. Although it was recently recognized as one of the (if not the) most abundant collagens in the mammalian lung, there is a substantive knowledge gap concerning its role in respiratory system development and function. A few studies have suggested that collagen VI insufficiency is associated with airway epithelial cell survival and altered lung function. Our recent work suggested collagen VI may be a genomic risk factor for chronic lung disease in premature infants. Using this as motivation, we thoroughly assessed the role of collagen VI in lung development and in lung epithelial cell biology. Here, we describe the state-of-the-art for collagen VI cell and developmental biology within the respiratory system, and reveal its essential roles in normal developmental processes and airway epithelial cell phenotype and intracellular signaling.

Comprehending the Proteomic Landscape of Ovarian Cancer: A Road to the Discovery of Disease Biomarkers

Despite recent technological advancements allowing the characterization of cancers at a molecular level along with biomarkers for cancer diagnosis, the management of ovarian cancers (OC) remains challenging. Proteins assume functions encoded by the genome and the complete set of proteins, termed the proteome, reflects the health state. Comprehending the circulatory proteomic profiles for OC subtypes, therefore, has the potential to reveal biomarkers with clinical utility concerning early diagnosis or to predict response to specific therapies. Furthermore, characterization of the proteomic landscape of tumor-derived tissue, cell lines, and PDX models has led to the molecular stratification of patient groups, with implications for personalized therapy and management of drug resistance. Here, we review single and multiple marker panels that have been identified through proteomic investigations of patient sera, effusions, and other biospecimens. We discuss their clinical utility and implementation into clinical practice.

Optimization of serine phosphorylation prediction in proteins by comparing human engineered features and deep representations

Deep representations can be used to replace human-engineered representations, as such features are constrained by certain limitations. For the prediction of protein post-translation modifications (PTMs) sites, research community uses different feature extraction techniques applied on Pseudo amino acid compositions (PseAAC). Serine phosphorylation is one of the most important PTM as it is the most occurring, and is important for various biological functions. Creating efficient representations from large protein sequences, to predict PTM sites, is a time and resource intensive task. In this study we propose, implement and evaluate use of Deep learning to learn effective protein data representations from PseAAC to develop data driven PTM detection systems and compare the same with two human representations.. The comparisons are performed by training an xgboost based classifier using each representation. The best scores were achieved by RNN-LSTM based deep representation and CNN based representation with an accuracy score of 81.1% and 78.3% respectively. Human engineered representations scored 77.3% and 74.9% respectively. Based on these results, it is concluded that the deep features are promising feature engineering replacement to identify PhosS sites in a very efficient and accurate manner which can help scientists understand the mechanism of this modification in proteins.

Oxidative, Reductive, and Nitrosative Stress Effects on Epigenetics and on Posttranslational Modification of Enzymes in Cardiometabolic Diseases

Oxidative (OS), reductive (RS), and nitrosative (NSS) stresses produce carbonylation, glycation, glutathionylation, sulfhydration, nitration, and nitrosylation reactions. OS, RS, and NSS are interrelated since RS results from an overactivation of antioxidant systems and NSS is the result of the overactivation of the oxidation of nitric oxide (NO). Here, we discuss the general characteristics of the three types of stress and the way by which the reactions they induce (a) damage the DNA structure causing strand breaks or inducing the formation of 8-oxo-d guanosine; (b) modify histones; (c) modify the activities of the enzymes that determine the establishment of epigenetic cues such as DNA methyl transferases, histone methyl transferases, acetyltransferases, and deacetylases; (d) alter DNA reparation enzymes by posttranslational mechanisms; and (e) regulate the activities of intracellular enzymes participating in metabolic reactions and in signaling pathways through posttranslational modifications. Furthermore, the three types of stress may establish new epigenetic marks through these reactions. The development of cardiometabolic disorders in adult life may be programed since early stages of development by epigenetic cues which may be established or modified by OS, RS, and NSS. Therefore, the three types of stress participate importantly in mediating the impact of the early life environment on later health and heritability. Here, we discuss their impact on cardiometabolic diseases. The epigenetic modifications induced by these stresses depend on union and release of chemical residues on a DNA sequence and/or on amino acid residues in proteins, and therefore, they are reversible and potentially treatable.

Insights into Machine Learning-based Approaches for Virtual Screening in Drug Discovery: Existing Strategies and Streamlining Through FP-CADD

BACKGROUND

Machine learning is an active area of research in computer science by the availability of big data collection of all sorts prompting interest in the development of novel tools for data mining. Machine learning methods have wide applications in computer-aided drug discovery methods. Most incredible approaches to machine learning are used in drug designing, which further aid the process of biological modelling in drug discovery. Mainly, two main categories are present which are Ligand-Based Virtual Screening (LBVS) and Structure-Based Virtual Screening (SBVS), however, the machine learning approaches fall mostly in the category of LBVS.

OBJECTIVES

This study exposits the major machine learning approaches being used in LBVS. Moreover, we have introduced a protocol named FP-CADD which depicts a 4-steps rule of thumb for drug discovery, the four protocols of computer-aided drug discovery (FP-CADD). Various important aspects along with SWOT analysis of FP-CADD are also discussed in this article.

CONCLUSION

By this thorough study, we have observed that in LBVS algorithms, Support Vector Machines (SVM) and Random Forest (RF) are those which are widely used due to high accuracy and efficiency. These virtual screening approaches have the potential to revolutionize the drug designing field. Also, we believe that the process flow presented in this study, named FP-CADD, can streamline the whole process of computer-aided drug discovery. By adopting this rule, the studies related to drug discovery can be made homogeneous and this protocol can also be considered as an evaluation criterion in the peer-review process of research articles.

Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity

Protein composition is restricted by the genetic code to a relatively small number of natural amino acids. Similarly, the known three-dimensional structures adopt a limited number of protein folds. However, proteins exert a large variety of functions and show a remarkable ability for regulation and immediate response to intracellular and extracellular stimuli. To some degree, the wide variability of protein function can be attributed to the post-translational modifications. Post-translational modifications have been observed in all kingdoms of life and give to proteins a significant degree of chemical and consequently functional and structural diversity. Their importance is partly reflected in the large number of genes dedicated to their regulation. So far, hundreds of post-translational modifications have been observed while it is believed that many more are to be discovered along with the technological advances in sequencing, proteomics, mass spectrometry and structural biology. Indeed, the number of studies which report novel post translational modifications is getting larger supporting the notion that their space is still largely unexplored. In this review we explore the impact of post-translational modifications on protein structure and function with emphasis on catalytic activity regulation. We present examples of proteins and protein families whose catalytic activity is substantially affected by the presence of post translational modifications and we describe the molecular basis which underlies the regulation of the protein function through these modifications. When available, we also summarize the current state of knowledge on the mechanisms which introduce these modifications to protein sites.

Posttranslational Modifications of PD-L1 and Their Applications in Cancer Therapy

Posttranslational modifications (PTM) of PD-L1 have emerged as important regulatory mechanisms that modulate immunosuppression in patients with cancer. In exposure to inflammatory cytokines, cancer cells and antigen-presenting cells, such as macrophages and dendritic cells, express PD-L1 to inhibit the activity of effector T cells through PD-1 engagement. Recent studies suggested that glycosylation, phosphorylation, ubiquitination, sumoylation, and acetylation play important roles in the regulation of PD-L1 protein stability and translocation and protein-protein interactions. Aberrant alterations of PTMs directly influence PD-L1-mediated immune resistance. On the basis of the newly identified regulatory signaling pathways of PD-L1 PTMs, researchers have investigated the cancer therapeutic potential of natural food compounds, small-molecule inhibitors, and mAbs by targeting PD-L1 PTMs. Results of these preclinical studies demonstrated that targeting PTMs of PD-L1 yields promising antitumor effects and that clinical translation of these therapeutic strategies is warranted. Cancer Res; 78(22); 6349-53. ©2018 AACR.

Biochemical Characterization of the Lysine Acetylation of Tyrosyl-tRNA Synthetase in Escherichia coli

Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic-code-expansion strategy to site-specifically incorporate Nϵ -acetyl-l-lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5-related N-acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl-CoA or acetyl-phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.

Characterization of in vivo phosphorylation modification of differentially accumulated proteins in cotton fiber-initiation process

Initiation of cotton fiber from ovule epidermal cells determines the ultimate number of fibers per cotton ovule, making it one of the restriction factors of cotton fiber yield. Previous comparative proteomics studies have collectively revealed 162 important differentially accumulated proteins (DAPs) in cotton fiber-initiation process, however, whether and how post-translational modifications, especially phosphorylation modification, regulate the expression and function of the DAPs are still unclear. Here we reported the successful identification of 17 phosphopeptides from 16 phosphoproteins out of the 162 DAPs using the integrated bioinformatics analyses of peptide mass fingerprinting data and targeted MS/MS identification method. In-depth analyses indicated that 15 of the 17 phosphorylation sites were novel phosphorylation sites first identified in plants, whereas 6 of the 16 phosphoproteins were found to be the phosphorylated isoforms of 6 proteins. The phosphorylation-regulated dynamic protein network derived from this study not only expanded our understanding of the cotton fiber-initiation process, but also provided a valuable resource for future functional studies of the phosphoproteins.

New Insights into the Role of Histone Deacetylases as Coactivators of Inflammatory Gene Expression

SIGNIFICANCE

The expression and/or activity of histone deacetylases (HDACs) can be regulated by a variety of environmental conditions, including inflammation and oxidative stress. These events result in diminished or exaggerated protein acetylation, both of which can be causative for many ailments. While the anti-inflammatory activity of HDAC inhibitors (HDACis) is well known, recent studies started unraveling details of the molecular mechanisms underlying the pro-inflammatory function of HDACs.

RECENT ADVANCES

Recent evidence shows that HDACs are found in association with transcribed regions and ensure proper transcription by maintaining acetylation homeostasis. We also discuss current insights in the molecular mechanisms mediating acetylation-dependent inhibition of pro-inflammatory transcription factors of the NF-κB, HIF-1, IRF, and STAT families.

CRITICAL ISSUES

The high number of acetylations and the complexity of the regulatory consequences make it difficult to assign biological effects directly to a single acetylation event. The vast majority of acetylated proteins are nonhistone proteins, and it remains to be shown whether the therapeutic effects of HDACis are attributable to altered histone acetylation.

FUTURE DIRECTIONS

In the traditional view, only exaggerated acetylation is harmful and causative for diseases. Recent data show the relevance of acetylation homeostasis and suggest that both diminished and inflated acetylation can enable the development of ailments. Since acetylation of nonhistone proteins is essential for the induction of a substantial part of the inflammatory gene expression program, HDACis are more than "epigenetic drugs." The identification of substrates for individual HDACs will be the prerequisite for the adequate use of highly specific HDACis.

Drug target central

BACKGROUND

One of the primary pillars of drug discovery is the drug target, its relationship to both the drugs designed against it and the biological processes in which it is involved. Here we review the informatics approaches required to build a complete catalogue of known drug targets.

OBJECTIVE

Using Pfizer's internal target database as a narrative, we review the steps involved in the construction of an integrated, enterprise target-informatics system. We consider how compiling the drug target universe requires integration across several resources such as competitor intelligence and pharmacological activity databases, as well as input from techniques such as text-mining. In particular, we address data standards and the complexities of representing targets in a structured ontology as well as opportunities for future development.

CONCLUSION

Drug target-orientated databases address important areas of drug discovery such as chemogenomics, drug/candidate repurposing and business intelligence. As research in industry and academia drives continued expansion of the druggable genome, it is crucial that such systems be maintained to provide an accurate picture of the landscape. This power of this information stretches beyond drug discovery and into the wider scientific community where small molecule tool compounds can enable the dissection of complex cellular pathways.

The 2010 ESPEN Sir David Cuthbertson Lecture: new and old proteins: clinical implications

The past century had witnessed vast advances in biomedical research, particularly in the fields of genomics and proteomics, yet the translation of these discoveries into clinical practice has been hindered by gaps in mechanistic understanding of variability governing disease susceptibility and pathogenesis. Among the greatest challenges are the dynamic nature of the proteome and the imperfect methodologies currently available to study it. Here, we review key recently developed proteomic techniques that have allowed for dynamic characterization of protein quality, as well as quantity, and discuss their potential applications in understanding aging and metabolic disorders including diabetes. These methodologies revealed that senescence is characterized, in part, by decreased rates of de novo protein synthesis and potentially also degradation, in addition to concomitantly increased levels of oxidative stress, ultimately resulting in excessive accumulation of damaged and dysfunctional proteins. Insulin may be a key mediator in these pathologies, as hyperinsulinemia has been shown to hinder protein degradation while transient insulin deficiency may accelerate oxidative damage. We also discuss two interventions that have been proposed to delay, and possibly reverse, senescence by augmenting protein degradation: chronic caloric restriction and aerobic exercise.

Histo-proteomic profiling of formalin-fixed, paraffin-embedded tissue

In the functional proteome era, the proteomic profiling of clinicopathologic-annotated tissues is an essential step for mining and evaluating candidate biomarkers for disease. For many diseases, but especially cancer, the development of predictive biomarkers requires performing assays directly on the diseased tissue. The last decade has seen the explosion of both prognostic and predictive biomarkers in the research setting but few of these biomarkers have entered widespread clinical use. Previously, application of routine proteomic methodologies to clinical formalin-fixed and paraffin-embedded tissue specimens has provided unsatisfactory results. In this paper, we will discuss recent advancements in proteomic profiling technology for clinical applications. These approaches focus on the retention of histomorphologic information as an element of the proteomic analysis.

Identification and characterization of molecular targets of natural products by mass spectrometry

Natural products, and their derivatives and mimics, have contributed to the development of important therapeutics to combat diseases such as infections and cancers over the past decades. The value of natural products to modern drug discovery is still considerable. However, its development is hampered by a lack of a mechanistic understanding of their molecular action, as opposed to the emerging molecule-targeted therapeutics that are tailored to a specific protein target(s). Recent advances in the mass spectrometry-based proteomic approaches have the potential to offer unprecedented insights into the molecular action of natural products. Chemical proteomics is established as an invaluable tool for the identification of protein targets of natural products. Small-molecule affinity selection combined with mass spectrometry is a successful strategy to "fish" cellular targets from the entire proteome. Mass spectrometry-based profiling of protein expression is also routinely employed to elucidate molecular pathways involved in the therapeutic and possible toxicological responses upon treatment with natural products. In addition, mass spectrometry is increasingly utilized to probe structural aspects of natural products-protein interactions. Limited proteolysis, photoaffinity labeling, and hydrogen/deuterium exchange in conjunction with mass spectrometry are sensitive and high-throughput strategies that provide low-resolution structural information of non-covalent natural product-protein complexes. In this review, we provide an overview on the applications of mass spectrometry-based techniques in the identification and characterization of natural product-protein interactions, and we describe how these applications might revolutionize natural product-based drug discovery.

A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue

Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue offers significant diagnostic utility but is complicated due to the high level of covalently crosslinked proteins arising from formalin fixation. To address these challenges, we developed a reliable protein extraction method for FFPE tissue, based on heat-induced antigen retrieval within a pressure cooker. The protein extraction yield from archival FFPE tissue section is approximately 90% of that recovered from frozen tissue. This method demonstrates preservation of immunoreactivity and recovery of full-length proteins by Western blotting. Additionally, we developed a well-based RP protein array platform utilizing an electrochemiluminescence detection system. Protein samples derived from FFPE tissue by means of laser capture dissection, with as few as 500 shots demonstrate measurable signal differences for different proteins. The lysates coated to the array plate, remain stable over 1 month at room temperature. Theses data suggest that this new protein-profiling platform coupled with the protein extraction method can be used for molecular profiling analysis in FFPE tissue, and contribute to the validation and development of biomarkers in clinical studies.

Photocaged Agonist for an Analogue-Specific form of the Vitamin D Receptor

Nuclear hormone receptors (NHRs) represent a diverse class of ligand-dependent transcriptional regulators. NHRs that have been rendered functionally inactive due to mutations that abrogate proper ligand binding can often be rescued by appropriately designed hormone analogues. The analogue-specific receptor-ligand pairs provide an ideal platform from which to develop new chemogenomic tools for the spatial and temporal control of gene expression. Here, we describe the synthesis and in vitro assessment of a photocaged VDR agonist specific to a mutant NHR that is associated with vitamin D-resistant rickets. The results provide insight into the utility of the agonist as a potential tool for photoinduced gene patterning.

An aptamer-based protein biochip

The establishment of an aptamer-based biochip for protein detection is described. Using a model system comprising human IgE as the analyte and single-stranded DNA aptamers specific for IgE or anti-IgE antibodies as immobilized ligands on chips, we could demonstrate that aptamers were equivalent or superior to antibodies in terms of specificity and sensitivity, respectively. Aptamer-based analyte detection on glass slides could clearly be demonstrated at minimum concentrations of 10 ng/mL IgE. In addition, we successfully showed specific analyte recognition in complex protein samples by the aptamer-based biochip system. Using DNA aptamers specific for human thrombin as an additional model receptor/ligand system, dual protein detection on a single slide could be proven. In conclusion, we could show the suitability of nucleic acid aptamers as low molecular weight receptors on biochips for sensitive and specific protein detection, representing an innovative tool for future proteomics.

msmsEval: tandem mass spectral quality assignment for high-throughput proteomics

Background

In proteomics experiments, database-search programs are the method of choice for protein identification from tandem mass spectra. As amino acid sequence databases grow however, computing resources required for these programs have become prohibitive, particularly in searches for modified proteins. Recently, methods to limit the number of spectra to be searched based on spectral quality have been proposed by different research groups, but rankings of spectral quality have thus far been based on arbitrary cut-off values. In this work, we develop a more readily interpretable spectral quality statistic by providing probability values for the likelihood that spectra will be identifiable.

Results

We describe an application, msmsEval, that builds on previous work by statistically modeling the spectral quality discriminant function using a Gaussian mixture model. This allows a researcher to filter spectra based on the probability that a spectrum will ultimately be identified by database searching. We show that spectra that are predicted by msmsEval to be of high quality, yet remain unidentified in standard database searches, are candidates for more intensive search strategies. Using a well studied public dataset we also show that a high proportion (83.9%) of the spectra predicted by msmsEval to be of high quality but that elude standard search strategies, are in fact interpretable.

Conclusion

msmsEval will be useful for high-throughput proteomics projects and is freely available for download from . Supports Windows, Mac OS X and Linux/Unix operating systems.

Mapping of two O-GlcNAc modification sites in the capsid protein of the potyvirus Plum pox virus

A large number of O-linked N-acetylglucosamine (O-GlcNAc) residues have been mapped in vertebrate proteins, however targets of O-GlcNAcylation in plants still have not been characterized. We show here that O-GlcNAcylation of the N-terminal region of the capsid protein of Plum pox virus resembles that of animal proteins in introducing O-GlcNAc monomers. Thr-19 and Thr-24 were specifically O-GlcNAcylated. These residues are surrounded by amino acids typical of animal O-GlcNAc acceptor sites, suggesting that the specificity of O-GlcNAc transferases is conserved among plants and animals. In laboratory conditions, mutations preventing O-GlcNAcylation of Thr-19 and Thr-24 did not have noticeable effects on PPV competence to infect Prunus persicae or Nicotiana clevelandii. However, the fact that Thr-19 and Thr-24 are highly conserved among different PPV strains suggests that their O-GlcNAc modification could be relevant for efficient competitiveness in natural conditions.

Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome

Metabolic enzymes control cellular metabolite concentrations dynamically in response to changing environmental and intracellular conditions. Such real-time feedback regulation suggests the global metabolome may sample distinct dynamic steady states, forming "basins of stability" in the energy landscape of possible metabolite concentrations and enzymatic activities. Using metabolite, protein and transcriptional profiling, we characterize three dynamic steady states of the yeast metabolome that form by perturbing synthesis of the universal methyl donor S-adenosylmethionine (AdoMet). Conversion between these states is driven by replacement of serine with glycine+formate in the media, loss of feedback inhibition control by the metabolic enzyme Met13, or both. The latter causes hyperaccumulation of methionine and AdoMet, and dramatic global compensatory changes in the metabolome, including differences in amino acid and sugar metabolism, and possibly in the global nitrogen balance, ultimately leading to a G1/S phase cell cycle delay. Global metabolic changes are not necessarily accompanied by global transcriptional changes, and metabolite-controlled post-transcriptional regulation of metabolic enzymes is clearly evident.

Null Mutations in Drosophila N-Acetylglucosaminyltransferase I Produce Defects in Locomotion and a Reduced Life Span

UDP-GlcNAc:alpha3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I (encoded by Mgat1) controls the synthesis of hybrid, complex, and paucimannose N-glycans. Mice make hybrid and complex N-glycans but little or no paucimannose N-glycans. In contrast, Drosophila melanogaster and Caenorhabditis elegans make paucimannose N-glycans but little or no hybrid or complex N-glycans. To determine the functional requirement for beta1,2-N-acetylglucosaminyltransferase I in Drosophila, we generated null mutations by imprecise excision of a nearby transposable element. Extracts from Mgat1(1)/Mgat1(1) null mutants showed no beta1,2-N-acetylglucosaminyltransferase I enzyme activity. Moreover, mass spectrometric analysis of these extracts showed dramatic changes in N-glycans compatible with lack of beta1,2-N-acetylglucosaminyltransferase I activity. Interestingly, Mgat1(1)/Mgat1(1) null mutants are viable but exhibit pronounced defects in adult locomotory activity when compared with Mgat1(1)/CyO-GFP heterozygotes or wild type flies. In addition, in null mutants males are sterile and have a severely reduced mean and maximum life span. Microscopic examination of mutant adult fly brains showed the presence of fused beta lobes. The removal of both maternal and zygotic Mgat1 also gave rise to embryos that no longer express the horseradish peroxidase antigen within the central nervous system. Taken together, the data indicate that beta1,2-N-acetylglucosaminyltransferase I-dependent N-glycans are required for locomotory activity, life span, and brain development in Drosophila.

Global Analysis of the Hortaea werneckii Proteome: Studying Steroid Response in Yeast

The response of the halophilic black yeast Hortaea werneckii to the steroid hormone progesterone has been studied at the protein level using fluorescent two-dimensional differential gel electrophoresis (2D-DIGE) technology in combination with mass spectrometry. Data on protein identification from this study reveal molecular mechanisms of the response to progesterone. In particular, the overexpression of Pck2 and Pac2 in the stimulated cells indicates the interactions of progesterone with the cell growth and reproduction signaling pathways.

Development of a Disposable Infusion System for the Delivery of Protein Therapeutics

This paper describes the development and optimization of a low flow open-loop infusion device for continuous delivery of protein therapeutics. Specifically, a non-electronic polymer device is actuated with responsive hydrogels to infuse at 2 microL/hr for 12 hours. Hydrogel actuators transduce a chemical signal (change in pH of the local environment) into a mechanical response (swelling) generating the pressure to drive the infusion. The hydrogel actuators are separated from the drug reservoir by an elastomeric impermeable membrane. As the hydrogel actuators expand, the expansion deflects the flexible membrane down and reduces the volume of the drug reservoir causing the infusion of drug through the needle that is the only outlet for the reservoir.

Applying proteomics to drug discovery

Proteomics is a technology that has come to prominence over the last few years largely as a result of the advances that have been made in the equipment and software associated with the performance and analysis of two dimensional (2D) gel electrophoresis. With this technique it is now possible to resolve and identify proteins on 2D gels with a high degree of reproducibility and sensitivity. This facilitates the detection and quantification of thousands of proteins from complex biological samples in a single analysis and, more significantly, the comparison of these data accurately and reproducibly between samples. Thus, qualitative and quantitative assessments of changes are possible between the healthy and diseased state, in the presence and absence of drug, or between responders and non-responders. The added ability of carrying out such analysis at a high throughput opens up the possibilities for using proteomics to great effect throughout the drug discovery process. This review outlines the proteomic process and indicates areas where its potential has begun to be realised.

N-glycosylation is required for efficient secretion of a novel human secreted glycoprotein, hPAP21

The present study reported the isolation and characterization of a novel human secreted protein, named as hPAP21 (human protease-associated domain-containing protein, 21 kDa), encoded by the hypothetical gene chromosome 2 open reading frame 7 (C2orf7) that contains signal peptide in its N-terminus, without transmembrane domain, except for PA domain in its middle. Western blotting assay indicated that the c-Myc tagged hPAP21 could be secreted into culture medium in the transfected Chinese hamster ovary cells. However, the molecular weights, whatever intracellular (28 kDa) or extracellular (30 kDa) forms, are larger than that of the prediction. To define whether the glycosylation was important process for its secretion, endoglycosidase H (Endo H) and PNGase F (PNG F) were employed to evaluate the effect of glycosylation types on secretion of hPAP21. Interestingly, the extracellular forms were primarily sensitive to PNG F, not Endo H, implying that complex N-glycosylation could be required for the secretion of hPAP21. Furthermore, N-glycosylation of Asn171 was confirmed as potential crucial process for the secretory protein via site-directed mutagenesis assay. All data will be contributed to the understanding of molecular functions of hPAP21.

O-GlcNAc transferase is in a functional complex with protein phosphatase 1 catalytic subunits

A hallmark of signal transduction is the dynamic and inducible post-translational modification of proteins. In addition to the well characterized phosphorylation of proteins, other modifications have been shown to be regulatory, including O-linked beta-N-acetylglucosamine (O-GlcNAc). O-GlcNAc modifies serine and threonine residues on a myriad of nuclear and cytosolic proteins, and for several proteins there appears to be a reciprocal relationship between phosphorylation and O-GlcNAc modification. Here we report further evidence of this yin-yang relationship by demonstrating that O-GlcNAc transferase, the enzyme that adds O-GlcNAc to proteins, exists in stable and active complexes with the serine/threonine phosphatases PP1beta and PP1gamma, enzymes that remove phosphate from proteins. The existence of this complex highlights the importance of understanding the dynamic relationship between O-GlcNAc and phosphate in modulating protein function in many cellular processes and disease states such as Alzheimer's disease and type II diabetes.

The coactivator of transcription CREB-binding protein interacts preferentially with the glycosylated form of Stat5

The signal transducer and activator of transcription (Stat) gene family comprises seven members with similarities in their domain structure and a common mode of activation. Members of this gene family mediate interferon induction of gene transcription and the response to a large number of growth factors and hormones. Extracellular ligand binding to transmembrane receptors causes the intracellular activation of associated tyrosine kinases, phosphorylation of Stat molecules, dimerization, and translocation to the nucleus. Prolactin-induced phosphorylation of Stat5 is a key event in the development and differentiation of mammary epithelial cells. In addition to the crucial phosphorylation at tyrosine 694, we have identified an O-linked N-acetylglucosamine (O-GlcNAc) as another secondary modification essential for the transcriptional induction by Stat5. This modification was only found on nuclear Stat5 after cytokine activation. Similar observations were made with Stat1, Stat3, and Stat6. Glycosylation of Stat5, however, does not seem to be a prerequisite for nuclear translocation. Mass spectrometric analysis revealed a glycosylated peptide in the N-terminal region of Stat5. Replacement of threonine 92 by an alanine residue (Stat5a-T92A) strongly reduced the prolactin induction of Stat5a glycosylation and abolished transactivation of a target gene promoter. Only the glycosylated form of Stat5 was able to bind the coactivator of transcription CBP, an essential interaction for Stat5-mediated gene transcription.

A Proteomic Approach for Quantitation of Phosphorylation Using Stable Isotope Labeling in Cell Culture

Posttranslational modifications are major mechanisms of regulating protein activity and function in vertebrate cells. It is essential to obtain qualitative information about posttranslational modification patterns of proteins to understand signal transduction mechanisms in greater detail. However, it is equally important to measure the dynamics of posttranslational modifications such as phosphorylation to approach signaling networks from a systems biology perspective. Despite a number of advances, methods to quantitate posttranslational modifications remain difficult to implement due to a number of factors including lack of a generic method, elaborate chemical steps, and requirement for large amounts of sample. We have previously shown that stable isotope-containing amino acids in cell culture (SILAC) can be used to differentially label growing cell populations for quantitation of protein levels. In this report, we extend the use of SILAC as a novel proteomic approach for the relative quantitation of posttranslational modifications such as phosphorylation. We have used SILAC to quantitate the extent of known phosphorylation sites as well as to identify and quantitate novel phosphorylation sites.

Sumoylation of Smad4, the common Smad mediator of transforming growth factor-beta family signaling

Transforming growth factor-beta (TGF-beta) and TGF-beta-related factors regulate cell growth, differentiation, and apoptosis, and play key roles in normal development and tumorigenesis. TGF-beta family-induced changes in gene expression are mediated by serine/threonine kinase receptors at the cell surface and Smads as intracellular effectors. Receptor-activated Smads combine with a common Smad4 to translocate into the nucleus where they cooperate with other transcription factors to activate or repress transcription. The activities of the receptor-activated Smads are controlled by post-translational modifications such as phosphorylation and ubiquitylation. Here we show that Smad4 is modified by sumoylation. Sumoylation of Smad4 was enhanced by the conjugating enzyme Ubc9 and members of the PIAS family of SUMO ligases. A major sumoylation site in Smad4 was localized to Lys-159 in its linker segment with an additional site at Lys-113 in the MH-1 domain. Increased sumoylation in the presence of the PIASy E3 ligase correlated with targeting of Smad4 to subnuclear speckles that contain SUMO-1 and PIASy. Replacement of lysines 159 and 113 by arginines or increased sumoylation enhanced the stability of Smad4, and transcription in mammalian cells and Xenopus embryos. These observations suggest a role for Smad4 sumoylation in the regulation of TGF-beta signaling through Smads.

Solid supports for microarray immunoassays

Stimulated by the achievements of the first phase in genomics and the resulting need of assigning functions to the acquired sequence information, novel formats of immunoassays are being developed for high-throughput multi-analyte studies. In principle, they are similar in nature to the microarray assays already established at the level of nucleic acids. However, the biochemical diversity and the sheer number of proteins are such that an equivalent analysis is much more complex and thus difficult to accomplish. The wide range of protein concentration complicates matters further. Performing microarray immunoassays already represents a challenge at the level of preparing a working chip surface. Arrays have been produced on filter supports, in microtiter plate wells and on glass slides, the last two usually coated with one-, two- or three-dimensionally structured surface modifications. The usefulness and suitability of all these support media for the construction and application of antibody microarrays are reviewed in this manuscript in terms of the different kinds of immunoassay and the various detection procedures. Additionally, the employment of microarrays containing alternative sensor molecules is discussed in this context. The sensitivity of microspot immunoassays predicted by the current analyte theory is not yet a reality, indicating the extent of both the technology's potential and the size of the task still ahead.

Immunisation of channel catfish, Ictalurus punctatus, with Ichthyophthirius multifiliis immobilisation antigens elicits serotype-specific protection

Surface immobilisation antigens (i-antigens) were purified from two strains of Ichthyophthirius multifiliis (NY1 and G5) that represent different i-antigen serotypes, namely A and D, respectively. The efficacy of the purified antigens as subunit vaccines was then tested in challenge studies using parasites of the homologous or heterologous serotype. Three groups of juvenile channel catfish (70 animals per group) were immunised with i-antigens from either the G5 or NY1 isolates, or with bovine serum albumin (BSA) as a control. Proteins were injected intraperitoneally (i.p.) at a dose of 10 microg/fish with complete Freund's adjuvant on day 1, followed by a second injection in incomplete Freund's adjuvant on day 15. Fish immunised with the purified i-antigens developed high titres of serum immobilising antibodies whereas sera from BSA-injected control fish did not. Fish antisera immobilised parasites of the homologous, but not the heterologous strain, and recognised the corresponding i-antigens on Western blots run under non-reducing conditions. On day 36, each group was divided into two subgroups (n=30). One subgroup was challenged with G5 parasites, and the other was challenged with NY1 parasites. When challenged with G5 parasites, 70% of fish immunised with the G5 i-antigens survived. When challenged with NY1 parasites, 33.3% of fish immunised with the NY1 i-antigens survived. All BSA-injected control fish died, as did all fish injected with the purified antigens and challenged with the non-homologous parasite strain. Statistical analyses indicated significant differences among test and control groups with regard to the mean days to death (MDD). While the results of these studies clearly support a role for i-antigens in protection, active immunity in response to natural infection is not serotype-specific. The utility of i-antigens, as well as the existence of other potential vaccine candidates for the prevention of 'white-spot' disease, are discussed.

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

Using an integrated genomic and proteomic approach, we have investigated the effects of carbon source perturbation on steady-state gene expression in the yeast Saccharomyces cerevisiae growing on either galactose or ethanol. For many genes, significant differences between the abundance ratio of the messenger RNA transcript and the corresponding protein product were observed. Insights into the perturbative effects on genes involved in respiration, energy generation, and protein synthesis were obtained that would not have been apparent from measurements made at either the messenger RNA or protein level alone, illustrating the power of integrating different types of data obtained from the same sample for the comprehensive characterization of biological systems and processes.

Protein therapeutics: promises and challenges for the 21st century

Recent advances in massively parallel experimental and computational technologies are leading to radically new approaches to the early phases of the drug production pipeline. The revolution in DNA microarray technologies and the imminent emergence of its analogue for proteins, along with machine learning algorithms, promise rapid acceleration in the identification of potential drug targets, and in high-throughput screens for subpopulation-specific toxicity. Similarly, advances in structural genomics in conjunction with in vitro and in silico evolutionary methods will rapidly accelerate the number of lead drug candidates and substantially augment their target specificity. Taken collectively, these advances will usher in an era of predictive medicine, which will move medical practice from reactive therapy after disease onset, to proactive prevention.

Glycosylation of nucleocytoplasmic proteins: signal transduction and O-GlcNAc

The dynamic glycosylation of serine or threonine residues on nuclear and cytosolic proteins by O-linked beta-N-acetylglucosamine (O-GlcNAc) is abundant in all multicellular eukaryotes. On several proteins, O-GlcNAc and O-phosphate alternatively occupy the same or adjacent sites, leading to the hypothesis that one function of this saccharide is to transiently block phosphorylation. The diversity of proteins modified by O-GlcNAc implies its importance in many basic cellular and disease processes. Here we systematically examine the current data implicating O-GlcNAc as a regulatory modification important to signal transduction cascades.

Parasite proteomics

Proteomics offers a new set of tools for investigating parasites and parasite-associated disease. In this article, John Barrett, Jim Jefferies and Peter Brophy describe the key technologies involved, including two-dimensional gel electrophoresis, image analysis, biological mass spectroscopy and database searching. The potential applications of proteomics in drug and vaccine discovery are reviewed, as are possible future developments.

Differential expression of the Ca2+ binding S100A6 protein in normal, preneoplastic and neoplastic colon mucosa

The expression of calcium-binding protein S100A6 was investigated in normal colon tissue, in colon adenomas and in colorectal carcinomas. Using an immunoblotting approach we detected four S100A6 variants with Mwt of 10 kDa and pI of 5.05 (isoform I), 5.15 (isoform II), 5.23 (isoform III) and 5.32 (isoform IV) that were differentially expressed in the analysed samples. The quantitative examination of S100A6 variant expression in 25 pairs of colorectal carcinoma and matched control mucosa proved a statistically significant increased abundance of S100A6 isoforms I (P = 0.004) and III (P = 0.025) in malignant tissue, and conversely, an increased level of S100A6 isoform IV in healthy tissue (P = 0.022). The expression of isoforms I and III and the loss of isoform IV were also observed in colon cancer cell lines. In addition, the immunohistochemical study of 16 primary colorectal carcinomas revealed both in the non-paired Student t-test and in the Mann Whitney test the statistically significant accumulation of S100A6 protein (P < 0.001) in the invasive margin of the tumour. The immunohistochemical analysis of S100A6 protein in polyps differing in clinical severity gave a strong staining that was maximal in dysplastic lesions. Thus, our results indicate a possible, statistically significant correlation (non-paired Student t-test P = 0.036) between S100A6 expression and colon carcinoma progression.

Mass spectrometric analysis of catechol-histidine adducts from insect cuticle

Adducts of catechols and histidine, which are produced by reactions of 1,2-quinones and p-quinone methides with histidyl residues in proteins incorporated into the insect exoskeleton, were characterized using electrospray ionization mass spectrometry (ESMS), tandem electrospray mass spectrometry (ESMS-MS, collision-induced dissociation), and ion trap mass spectrometry (ITMS). Compounds examined included adducts obtained from acid hydrolysates of Manduca sexta (tobacco hornworm) pupal cuticle exuviae and products obtained from model reactions under defined conditions. The ESMS and ITMS spectra of 6-(N-3')-histidyldopamine [6-(N-3')-His-DA, pi isomer] isolated from M. sexta cuticle were dominated by a [M + H]+ ion at m/z 308, rather than the expected m/z 307. High-resolution fast atom bombardment MS yielded an empirical formula of C14H18N3O5, which was consistent with this compound being 6-(N-1')-histidyl-2-(3, 4-dihydroxyphenyl)ethanol [6-(N-1')-His-DOPET] instead of a DA adduct. Similar results were obtained when histidyl-catechol compounds linked at C-7 of the catechol were examined; the (N-1') isomer was confirmed as a DA adduct, and the (N-3') isomer identified as an (N-1')-DOPET derivative. Direct MS analysis of unfractionated cuticle hydrolysate revealed intense parent and product ions characteristic of 6- and 7-linked adducts of histidine and DOPET. Mass spectrometric analysis of model adducts synthesized by electrochemical oxidative coupling of N-acetyldopamine (NADA) quinone and N-acetylhistidine (NAcH) identified the point of attachment in the two isomers. A prominent product ion corresponding to loss of CO2 from [M + H]+ of 2-NAcH-NADA confirmed this as being the (N-3') isomer. Loss of (H2O + CO) from 6-NAcH-NADA suggested that this adduct was the (N-1') isomer. The results support the hypothesis that insect cuticle sclerotization involves the formation of C-N cross-links between histidine residues in cuticular proteins, and both ring and side-chain carbons of three catechols: NADA, N-beta-alanyldopamine, and DOPET.

Proteomics: a major new technology for the drug discovery process

Proteomics is a new enabling technology that is being integrated into the drug discovery process. This will facilitate the systematic analysis of proteins across any biological system or disease, forwarding new targets and information on mode of action, toxicology and surrogate markers. Proteomics is highly complementary to genomic approaches in the drug discovery process and, for the first time, offers scientists the ability to integrate information from the genome, expressed mRNAs, their respective proteins and subcellular localization. It is expected that this will lead to important new insights into disease mechanisms and improved drug discovery strategies to produce novel therapeutics.