Download or read book Development and Application of Mass Spectrometry based Strategies for Structural Elucidation of Heparin Isomers and Metabolic Investigations of Nutrition and Pluripotent Stem Cells written by John Kenji Meissen and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) is a powerful analytical tool applied in modern biological sciences research. Its capacity for accurate quantitation of molecular structures, ability to determine molecular mass with millidalton accuracy, and capability to fragment ions into constituent structures provide scientists with the means necessary to effectively explore complex biological systems. The goals of my dissertation work were to develop and apply new MS-based strategies to enhance knowledge and understanding of biochemical phenotypes; in particular, my novel mass spectrometry methods were applied to differentiate pluripotent stem cell types, to understand the metabolic effects of fructose consumption, and to study the role of rare heparin and heparan sulfate structural features in mediating protein binding. Chapter 1 covers the development and application of methodology employing collision induced dissociation (CID) to effectively identify heparin and heparan sulfate disaccharide sulfation patterns, including forms containing the rare 3-O-sulfate moiety. Heparin and heparin sulfate possess a large number of structural isomers due to variable sulfation patterns spanning numerous positions within a repeating disaccharide subunit, and a single CID event was inadequate to generate fragment ions differentiating 3-O-sulfated species from other structural isomers. However, application of two successive CID events enabled cross-ring dissociation generating unique fragment ions for 3-O-sulfated structures. A method employing two successive CID events was developed and applied to an 11-sulfated heparin octasaccharide structure displaying affinity for chemokine ligand 2 (CCL2) revealing that, in contrast to several other heparin and heparan sulfate binding proteins, CCL2 does not preferentially bind a structure containing 3-O-sulfation. Following completion of the heparin/heparan sulfate project, the focus of the dissertation work shifted toward metabolomics. Metabolomics, the identification and quantification of all metabolites in a system under a given set of conditions, is a growing discipline in biological research and can enhance our understanding of biochemical response in complex biological systems to disease state, environmental stress, nutrition, and many other factors. Chapter 2 explores characterization of currently available instrumentation, chromatography methods, and software tools for construction of a liquid chromatography mass spectrometry (LCMS)-based metabolite profiling method maximizing the capabilities of current technologies. Six different chromatography columns with twelve different mobile phase combinations were evaluated with a series of standards to elucidate an effective chromatography method. The mass accuracy and isotope abundance error of the Agilent 6530 quadrupole time of flight (QTOF) and Leco Citius liquid chromatography high resolution time of flight mass spectrometers were determined with known plasma sample metabolites to identify the limitations of each platform. The capabilities and limitations of four untargeted data processing tools, including MZmine and Genedata Refiner MS, were evaluated based on their ability to accurately report intensity of known metabolites in plasma samples with data sets from both instruments. This series of characterization and evaluation experiments enabled selection and integration of individual components to construct a hydrophilic interaction chromatography (HILIC)-QTOF MS metabolite profiling workflow which maximizes the capabilities of tested technologies and possesses the potential to expand understanding of biological systems across many research projects. Chapter 3 investigates the metabolic relationships of induced pluripotent stem cells (iPSCs), iPSC parental embryonic fibroblasts, and embryonic stem cells (ESC). The HILIC-QTOF workflow developed in chapter 2 and an established gas chromatography time of flight (GC-TOF) method were used for metabolite profiling of all three cell types. GC-TOF data processing provided 111 identified metabolites including glycolysis, pentose phosphate pathway, and citric acid cycle metabolites as well as amino acids, free fatty acids, and sugar alcohols. HILIC-QTOF data processing yielded 55 annotated metabolites including many complex lipids, acylcarnitines, amino acids, and purine structures. Annotated structures were integrated into MetaMapp metabolite networks to facilitate identification of compound classes and metabolite pathways displaying statistically significant differences between cell lines. Results indicate that iPSCs display greater metabolic similarity to genuine ESCs than the iPSC parental embryonic fibroblasts. However, iPSCs possess clear differences from ESCs in complex lipid structures, essential and non-essential amino acids, and metabolites involved in polyamine biosynthesis. Chapter 4 explores the metabolic effects of fructose with a human HepG2 liver cell model. Targeted methodologies were applied to test the hypothesis that high fructose exposure would increase hexosamine generation, and that the increase in hexosamine generation would be associated with greater lipogenic gene expression in the HepG2 model system. Lipogenic enzyme abundance and expression levels were determined for HepG2 cells incubated in media containing 5.5 mM glucose, 5.5 mM glucose + 5.0 mM fructose, and 10.5 mM glucose. Hexosamine biosynthesis pathway (HBP) metabolite levels were determined with targeted LC-QTOF and GC-TOF strategies for each hexose condition. Application of the targeted metabolite analysis strategies in combination with lipogenic gene expression and enzyme abundance analysis revealed that fructose exposure does not result in increased levels of hexosamine biosynthesis pathway metabolites or, contrary to rodent models, cause increased expression of lipogenic enzymes in the HepG2 model system. Should this effect translate to the human liver in vivo, it would suggest that increased lipogenesis caused by high fructose consumption occurs primarily through means other than lipogenic gene expression. Similar to chapter 4, chapter 5 explores the metabolic effects of fructose with a human HepG2 liver cell model. However, untargeted metabolite profiling methods were applied to generate a more broad investigation of fructose effects on liver cell metabolism. The HILIC-QTOF workflow developed in chapter 2 and an established GC-TOF method were used for metabolite profiling of HepG2 metabolite extracts from cells incubated in media conditions identical to the previous targeted analysis. Analysis of cell extracts with the GC-TOF system enabled identification of 112 different metabolites, and analysis with the HILIC-QTOF system enabled annotation of 54 different metabolites. Integration of GC-TOF and HILIC-QTOF data sets yielded 156 unique annotations representing a wide array of structural classes and enzymatic pathways. Results indicate that metabolite profiles of HepG2 liver cells grown in all three media conditions are greatly similar. However, several distinct changes in metabolite abundance were observed based on both fructose addition and hexose concentration. Fructose dependent effects were observed in long-chain acylcarnitine structures and amino acids involved in folate metabolism. Carbohydrate concentration dependent effects were observed with acylcarnitine and complex lipid structures.

Download or read book Mass Spectrometry based Strategies for Protein Footprinting written by Jing Li and published by . This book was released on 2016 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) has emerged as a powerful tool for epitope mapping, protein-ligand interaction, protein-protein interaction, aggregation, and effect of solution environment on protein conformation because they provide high-throughput data with relatively high structural resolution. Two popular MS-based approaches are hydrogen deuterium exchange-mass spectrometry (HDX-MS) and fast photochemical oxidation of proteins (FPOP), which complement classical biophysical and biochemical techniques in achieving higher structural resolution. The research presented in this dissertation is focused on the application of mass spectrometry-based footprinting techniques in characterizing the biophysical properties of Part I: pH-dependent conformation change of diphtheria toxin T domain (Chapters 2-4)); Part II: Ca2+ binding proteins and the role of Ca2+ regulation (Chapters 5-6); and Part III: protein-protein interaction including epitope mapping of IL-23 (Chapter 7) and Marburg virus protein VP24 (Chapter 8). Chapter 1 serves as an introduction to mass spectrometry instrumentation and standard LC-MS workflow. Two mass spectrometry based-footprinting techniques are introduced: (1) hydrogen deuterium exchange (HDX), and (2) fast photochemical oxidation of proteins (FPOP). Part I focuses on the development of pH-dependent HDX-MS for the conformation study of diphtheria toxin T domain. In Chapter 2, we describe the use pH-dependent HDX to study the pH-dependent conformation change of wild-type diphtheria toxin T domain monomer along its translocation pathway. In Chapter 3, we study the pH-dependent dissociation and reformation of T domain dimer. In Chapter 4, we apply the same method to a T domain mutant H223Q to further investigate the role of key histidine residues in triggering the conformation change. Part II focuses on the application of HDX mass spectrometry for the study of calcium binding proteins. Chapter 5 describes the Ca2+-binding property of ACaM and its Ca2+-regulated interaction with myosin VI. In chapter 6, HDX is also applied to an EF-hand Ca2+ binding protein, DREAM, for the study of its Ca2+ binding sites and stoichiometry. Part III of the dissertation focuses on the development and application of MS-based footprinting methods to investigate protein-protein interaction. Chapter 7 describes the methodology of fast photochemical oxidation of proteins (FPOP) for epitope mapping of IL-23 interacting a therapeutic antibody from Bristol-Myers Squibb. Chapter 8 discusses the use of HDX, FPOP, and NEM chemical labeling for the study of Marburg virus protein VP24 and its interaction with the host protein Keap1 Kelch domain. These seven studies on characterization of protein conformation dynamics, Ca2+ binding protein, and protein-protein interaction show the successful application of mass spectrometry in the structural study of large biomolecules.

Download or read book Mass Spectrometry based Strategies for Protein Characterization written by Ke Li (Chemist) and published by . This book was released on 2018 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS)-based protein footprinting characterizes protein structure and protein-ligand interactions by interrogating protein solvent-accessible surfaces by using chemical reagents as probes. The method is highly applicable to protein or protein-ligand complexes that are difficult to study by conventional means such as X-ray crystallography and nuclear magnetic resonance. In this dissertation, we describe the development and application of MS-based protein footprinting from three perspectives, including I) protein aggregation and amyloid formation (Chapter 2-3), II) protein-ligand interactions (Chapter 4-5), and III) in-cellulo structures and dynamic motion of membrane proteins (Chapter 6). Fast Photochemical Oxidation of Proteins (FPOP) is the main methodology implemented in the work presented in this dissertation. Chapter 1 provides an overview of FPOP and discusses its fundamentals as well as its important applications in both academic research and biotechnology drug development. In Part I, Chapter 2 covers the early method development of FPOP for monitoring amyloid beta (A[beta]) aggregation. In this work, we demonstrated the high sensitivity and spatial resolution of the method in probing the solvent accessibility of A[beta] at global, sub-regional, and some amino-acid residue levels as a function of its aggregation, and revealed A[beta] species at various oligomeric states identified by their characteristic modification levels. In Chapter 3, we extended the application of the platform to assess the effect of a putative polyphenol inhibitor on amyloid formation and to provide insights into the mechanism of action of the inhibitor in remodeling A[beta] aggregation pathways. In Part II, we evaluated different protein footprinting techniques, including FPOP, hydrogen-deuterium exchange (HDX), and carboxyl group footprinting, for probing protein-ligand (drug candidates) interaction in the context of a therapeutic development. Chapter 4 focused on protein-protein interaction by investigating the epitope of IL-6 receptor for two adnectins that have similar apparent biophysical properties. In Chapter 5, we probed the hydrophobic binding cavity of bromodomain protein for a small molecule inhibitor. This study serves as an example of interrogating protein-small molecule interactions. The two studies in Part II demonstrate the unique capabilities and limitations of protein footprinting methods in protein structural characterization. In Part III, we pushed the boundary of MS-based protein footprinting by applying the method to footprint live cells and investigate the dynamic structures/motion of membrane-transport proteins in their native cellular environment. We employed protein engineering, suspension cell expression and isotopic-encoded carboxyl group footprinting to identify salt bridges in two proteins, GLUT1 and GLUT5, that control their alternating access motions for substrate translocation. With functional analysis and mutagenesis, live-cell footprinting provides new insights into the transport mechanism of proteins in the major facilitator superfamily. The five studies in the dissertation demonstrate the powerful capability of MS-based protein footprinting in protein structural biology and biophysics research. The method also holds great potential in studying more complicated biological systems and solving demanding problems related to protein structure and properties.

Download or read book Development and Application of Mass Spectrometry based Biophysical Approaches written by Ying Zhang and published by . This book was released on 2015 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher order structures. One of the emerging biophysical approaches is MS-based protein footprinting. Protein surface regions can be covalently labeled by chemical reagents in a biologically relevant environment. These chemical labels can be read out by MS through either bottom-up or top-down MS proteomics analysis. The outcome provides protein conformational information. Among various chemical labeling strategies, hydrogen deuterium exchange (HDX) is one of the most commonly used approaches in MS-based protein biophysical studies. HDX-MS is introduced in Chapter 1 by covering the early developments and new applications especially in measuring interaction affinities. Although HDX-MS has been developed for decades, there are still many challenges in protein characterization that require new or improved HDX method development. One such challenge is characterization of protein aggregation. Protein aggregation leads to loss of protein function, and protein aggregates are implicated in several neurodegenerative diseases like Alzheimer's and Parkinson's diseases. A key issue in studies of protein aggregation is real-time monitoring under biologically relevant condition. We developed an HDX-MS-based approach by studying Alzheimer's disease related A[beta] aggregation, and we described this development in Chapter 2. A[beta] proteins are labeled by deuterium in a pulsed way during A[beta] aggregation. The extents of aggregations are monitored by MS as deuterium uptake. This pulsed HDX platform provides peptide-level information about A[beta] aggregation. Ligands (drug candidates) were also evaluated with this platform to determine how the drug candidates affect oligomerization (Chapter 3). Ligand interactions can induce protein conformational changes, which are required in various protein functions like signaling, enzyme activity. Such interactions are fundamental to all biological processes. One of the often used ligands in cells is calcium. Calcium interacts with a variety of calcium-binding proteins, most of which have conserved sequence that form EF-hand motifs to bind calcium. MS-HDX has been an important tool in studies of these typical calcium-binding proteins. Many proteins without an EF-hand motif also require calcium for their function. For example, protein-arginine deiminase (PAD) is an enzyme for arginine citrullination and binds calcium without EF-hand motif. We conducted differential HDX studies on PAD2 protein (Chapter 4). Multiple and cooperative calcium binding of PAD2 are detected by HDX. HDX was further extended by applying protein-ligand titration in an HDX experiment (i.e., Protein-ligand interactions by mass spectrometry, titration and H/D exchange, PLIMSTEX). The calcium binding affinity of each binding site can be elucidated by PLIMSTEX (Chapter 5). Protein aggregation or ligand-binding induced conformational changes can also be detected by MS-HDX. One significant question in MS-based biophysical studies is how to generate structural information for proteins in the absence of a high resolution structure. In a newly developed platform, we combined a traditional structural biology approach, homology modeling, and MS-HDX to generate a structural model for diheme cytochrome c (DHCC) from Heliobacterium (Chapter 6), a protein for which solvent accessibility information from HDX experiment was used as the guide for homology modeling and used to generate a refined structural model of DHCC by using various computational approaches. In summary, we describe in this thesis development and application of several new, refined approaches of HDX and analyze protein aggregation, protein-ligand binding and unknown protein structures. We hope other scientists can apply these approaches to solve complicated and demanding biological problems that are difficult to investigate using traditional biophysical methods.

Download or read book Mass Spectrometry based Strategies for Biomolecular Structure Analysis written by Yuetian Yan and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry is an important method for studying the structure of both small molecules and large biomolecules (e.g., proteins). The majority of the applications prior to 1970 were focused on small molecules, owing to the limited ionization methods which posed difficulties in producing gas-phase ions for large biomolecules then. Beginning in the 1980's, with the introduction of new ionization methods (ESI and MALDI), the applications have gradually switched to biological science measuring large bioorganic molecules. Today, with the developing interest in metabolomics and proteomics, and ongoing improvement in MS-based techniques, mass spectrometry is extensively applied in the study of both small and large molecules. The research presented in this thesis falls into two main parts, which focus on the application of MS in (1) structural analysis of steroid metabolites and (2) characterization of protein-protein interactions. In the first part, combinations of different MS methods are adopted and used to solve the structures of unknown steroid metabolites, which are the pheromones responsible for mouse communication in mouse urine. This part includes three chapters, the first two of which discuss the method development of using MS to study the structure of steroid metabolites; and the third chapter presents the application of the MS methods in solving a newly discovered steroid pheromone, which is determined as a sex-specific hormone. In the second part, two MS-based strategies, namely, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), are applied in two studies of protein-protein interactions, including: (1) dimerization of SecA, which is a motor protein in bacteria translocation pathway; and (2) interface mapping of EGFR binding to Adnectin1. In the first chapter in Part 2, we used HDX MS to characterize the dimer interface of SecA, and, meanwhile, detected a conformational change from open to closed forms at the pre-protein binding domain upon dimerization. This conformational change provided leads for the active form of SecA. In the second chapter in Part 2, we applied FPOP, which is modified to suit therapeutic protein formulation conditions, to map the epitope of Adnectin1-EGFR interaction at amino acid residue level. The epitope identified agrees with that from both HDX study and crystallography results, presenting more evidence of the capability of FPOP in epitope mapping. These five studies on characterization of steroid metabolites and protein-protein interactions show the successful application of mass spectrometry in the structural study of both small molecules and large proteins. Furthermore, there's a great potential for study of more complex systems.

Download or read book Developing Liquid Chromatography mass Spectrometry Strategies for Investigating Energy Metabolism with Application to Isocitrate Dehydrogenase Mutations in Cancer written by Khalid Mohammad Al-Qahtani and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Mass Spectrometry Based Method Development for Elucidation of Protein Sequences Structures and Post Translational Modifications written by Qingyu Sun and published by . This book was released on 2011 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advanced development of mass spectrometry (MS) makes MS a powerful technique for proteomics study. The increasing demands for proteomics study stimulate creation of more applicable MS-based methods. This dissertation focuses on development of novel MS-based methods to characterize three different aspects of proteins: primary sequence, post-translational modifications (PTMs) and three-dimensional (3D) structure.

Download or read book Development and Application of Mass Spectrometry based Protein Footprinting in Structural Proteomics written by Ming Cheng (Chemist) and published by . This book was released on 2019 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integral mass spectrometry (MS) has emerged as an important tool for protein structural characterization. It readouts are a broad range of structural information, including stoichiometry, interactions, conformations and conformation change, and dynamics. Protein footprinting is a pivotal component in the intergral MS toolkit.My dissertation centers around the development and application of protein footprinting to characterize protein structure. It is divided into seven chapters. Chapter 1 serves as the introduction for integral mass spectrometry in structural proteomic. In Chapter 2, we extended the fast-photochemical oxidation of proteins (FPOP) platform by adding the trifluoromethyl radical (·CF3) as a new reagent. We discovered that ·CF3 footprint proteins in a complementary way as hydroxide radicals. The ·CF3 radical has exceptional reactivity, modifying 18 amino acids out of 20. Further studies demonstrate that it can report the conformational change between holo-myoglobin and apo-myoglobin and can define the topology of the VKOR membrane protein. This work bridges trifluoromethylation chemistry in materials and medicinal chemistry to that in structural biology. In Chapter 3, collaborated with Dr. Mark Chance's laboratory in Case Western Reserve University (CWRU) to apply ·CF3 chemistry on the synchrotron platform, which is the first platform that uses ·OH for protein footprinting. Synchrotron radiolysis generates ·CF3 in water media by ionizing water molecules to give ·OH. The ·CF3 shows complementary chemical reactivity with canonical ·OH labeling yet results in higher reactivity coverage. The ·CF3 reagent is the second footprinting reagent enabled by synchrotron since 1999. This work serves as a proof-of-concept to demonstrate that synchrotron platform is adaptable to other novel chemistries that can increase footprinting coverage. Further, taking advantage of X-ray irradiation, we achieved direct protein trifluoromethylation in the absence of metal catalysis or peroxide for the first time, with the synchrotron platform. In Chapter 4, we devloped a laser-mediated radical method for integral membrane protein (IMP) footprinting. Classical footprinting methods use hydrophilic reagents to label protein surfaces. IN so doing, we generate structural information by measuring the solvent accessibility of the backbone or side chains in aqueous media. Owing to the amphipathic nature of IMP, this new approach exploits the highly hydrophobic nature of perfluoroalkyl iodine together with tip sonication to ensure efficient labeling of a transmembrane domain (TM). The chemistry yields 100% reactivity coverage for tyrosine, and complete IMP labeling in a fast fashion. The resulting protein modification, which is resistant to hydrolysis, compatible with proteolysis, and amenable of tandem mass analysis, is appropriate for footprinting by bottom-up analysis. (Collaboration with Dr. Weikai Li from Wash U Medical School). In Chapter 5, we investigated an array of digestion conditions by using different combination of protease and additives to optimize the coverage of IMP digestion. IMPs are under-represented in conventional bottom-up proteomic analysis that generally favors soluble, abundant and easy-to-digest proteins. The new protrocol of IMP digestion significantly decreases our workload for sample preparation, allows us to avoid common contaminants that impair LC-MS, and generally yields >90% sequence coverage by generating peptides suitable for structural proteomic studies. Further, the deep analysis enable us to identify a "sweet spot" in the digestion protocol that may provide guidance to choose a suitable protease in structural proteomics in future. In Chapter 6, apart from methodology development, we used hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize the binding interface for Mxra8-immune complex and Mxra8-chikungunya virus protein complex. The cell adhesion molecule Mxra8 is identified as a receptor for multiple arthritogenic alphaviruses such as chikungunya virus. We identified putative binding sites for eight anti-Mxra8 monoclonal antibodies (mAbs). HDX-MS enables us to classify the novel mAbs, predict their competing binding interface with chikungunya virus, and provide a molecular level explanation for the observation that mAbs can block the Chikungunya virus infection. From the HDX kinetic curves, we also observe that the mAbs have higher affinity than do Chikungunya virus proteins when binding with Mxa8. Finally, the HDX data help to assign the orientation of Mxra8 on the Cryo-EM structure of Chikungunya virus complex (Collaboration with Dr. Daved H. Fremont and Dr. Michael s Diamond, Wash U School of Medicine). In Chapter 7, we provide a conclusion for my dissertation. We will discuss challenges and opportunities for protein footprinting, and its role in the expanding toolkit of structural proteomics.

Download or read book General Methods in Biomarker Research and their Applications written by Victor R. Preedy and published by Springer. This book was released on 2015-08-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past decade there has been a major sea change in the way disease is diagnosed and investigated due to the advent of high throughput technologies, such as microarrays, lab on a chip, proteomics, genomics, lipomics, metabolomics etc. These advances have enabled the discovery of new and novel markers of disease relating to autoimmune disorders, cancers, endocrine diseases, genetic disorders, sensory damage, intestinal diseases etc. In many instances these developments have gone hand in hand with the discovery of biomarkers elucidated via traditional or conventional methods, such as histopathology or clinical biochemistry. Together with microprocessor-based data analysis, advanced statistics and bioinformatics these markers have been used to identify individuals with active disease or pathology as well as those who are refractory or have distinguishing pathologies. New analytical methods that have been used to identify markers of disease and is suggested that there may be as many as 40 different platforms. Unfortunately techniques and methods have not been readily transferable to other disease states and sometimes diagnosis still relies on single analytes rather than a cohort of markers. There is thus a demand for a comprehensive and focused evidenced-based text and scientific literature that addresses these issues. Hence the formulation of Biomarkers in Disease. The series covers a wide number of areas including for example, nutrition, cancer, endocrinology, cardiology, addictions, immunology, birth defects, genetics and so on. The chapters are written by national or international experts and specialists.

Download or read book Bioinformatics for Glycobiology and Glycomics written by Claus-Wilhelm von der Lieth and published by John Wiley & Sons. This book was released on 2009-10-01 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first to be dedicated to the bioinformatics of carbohydrates and glycoproteins. It provides an introduction to this emerging field of science both for the experimentalist working in glycobiology and glycomics, and also for the computer scientist looking for background information for the development of highly sophisticated algorithmic approaches. The book provides an overview of the state-of-the-art in the field, with reviews on databases, and the tools in use for analysis, interpretation, and prediction of the structures of complex carbohydrates, and demonstrates the value of bioinformatics for glycobiology. The availability of comprehensive databases and corresponding bioinformatics tools, to access and analyse the large amounts of experimental data relating to the structure of carbohydrates, will be a prerequisite for the success of the large-scale glycomics projects that aim to decipher new, so far unknown, biological functions of glycans. Efficient bioinformatics descriptions and tools can considerably enhance the efficiency of glycomics research, in terms of data quality, analysis and experimental costs. For a complete understanding of the molecular processes in which carbohydrates are involved, such as protein–carbohydrate interactions and the impact of glycosylation on protein function, knowledge of the 3D structure of the carbohydrate, the protein–carbohydrate complex, or the glycoprotein is often indispensable. This book provides a thorough introduction into methods used for conformational analysis of carbohydrates. Key features: Describes bioinformatic approaches to handle carbohydrate-active enzymes and glycosylation. Provides an overview on bioinformatics tools that facilitate analysis of carbohydrate structures. Gives introduction into molecular modelling of carbohydrate 3D structure and carbohydrates contained in the Protein Databank. Assumes only a basic knowledge of biology and bioinformatics.

Download or read book Capillary Gel Electrophoresis written by Andras Guttman and published by Newnes. This book was released on 2021-12-04 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Capillary Gel Electrophoresis and Related Microseparation Techniques covers all theoretical and practical aspects of capillary gel electrophoresis. It also provides an excellent overview of the key application areas of nucleic acid, protein and complex carbohydrate analysis, affinity-based methodologies, micropreparative aspects and related microseparation methods. It not only gives readers a better understanding of how to utilize this technology, but also provides insights into how to determine which method will provide the best technical solutions to particular problems. This book can also serve as a textbook for undergraduate and graduate courses in analytical chemistry, analytical biochemistry, molecular biology and biotechnology courses. Covers all theoretical and practical aspects of capillary gel electrophoresis Excellent overview of the key applications of nucleic acid, protein and complex carbohydrate analysis, affinity-based methodologies, micropreparative aspects and related microseparation methods Teaches readers how to use the technology and select methods that are ideal for fundamental problems Can serve as a textbook for undergraduate and graduate courses in analytical chemistry, analytical biochemistry, molecular biology and biotechnology courses

Download or read book Handbook of Anticancer Drugs from Marine Origin written by Se-Kwon Kim and published by Springer. This book was released on 2014-11-27 with total page 801 pages. Available in PDF, EPUB and Kindle. Book excerpt: This timely desk reference focuses on marine-derived bioactive substances which have biological, medical and industrial applications. The medicinal value of these marine natural products are assessed and discussed. Their function as a new and important resource in novel, anticancer drug discovery research is also presented in international contributions from several research groups. For example, the potential role of Spongistatin, Apratoxin A, Eribulin mesylate, phlorotannins, fucoidan, as anticancer agents is explained. The mechanism of action of bioactive compounds present in marine algae, bacteria, fungus, sponges, seaweeds and other marine animals and plants are illustrated via several mechanisms. In addition, this handbook lists various compounds that are active candidates in chemoprevention and their target actions. The handbook also places into context the demand for anticancer nutraceuticals and their use as potential anti-cancer pharmaceuticals and medicines. This study of advanced and future types of natural compounds from marine sources is written to facilitate the understanding of Biotechnology and its application to marine natural product drug discovery research.

Download or read book The Glycome written by Adeel Malik and published by CRC Press. This book was released on 2021-07-07 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a comprehensive understanding of the enigmatic identity of the glycome, a complex but important area of research that has been largely ignored due to its complexity. The authors thoroughly deal with almost all aspects of the glycome, i.e., elucidation of the glycan identity enigma and its role in regulation of the cellular process, and in disease etiology. The book bridges the knowledge gap in understanding the glycome, from being a cell signature to its applications in disease etiology. In addition, it details many of the major insights regarding the possible role of the glycome in various diseases as a therapeutic marker. The book systematically covers the major aspects of the glycome, including the significance of substituting the diverse monosaccharide units to glycoproteins, the role of glycans in disease pathologies, and the challenges and advances in glycobiology. The authors stress the significance and huge encoding power of carbohydrates as well as provide helpful insights in framing the bigger picture. The Glycome: Understanding the Diversity and Complexity of Glycobiology details state-of-the-art developments and emerging challenges of glycome biology, which are going to be key areas of future research, not only in the glycobiology field but also in pharmaceutics.

Download or read book Drug Transport Across the Blood brain Barrier written by A.G. de Boer and published by CRC Press. This book was released on 1997-04-08 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: The availability of various in vitro and in vivo techniques has considerably advanced the research on drug transport and metabolism across the blood-brain barrier (BBB). These specialized and sophisticated experimental strategies are of fundamental importance if one is to gain a greater understanding of enhanced and selective drug delivery to the brain. The reader will find in this book methods for in vitro endothelial/astrocyte cell culture models, and for in vivo intracerebral microdialysis to study drug tranport across the BBB. This book, however, is not merely a laboratory manual consisting of recipes for BBB research; it permits the presentation of the different methods in fine detail, revealing tricks and short cuts that frequently do not appear in the literature. The researcher is well aware that differences (subtle or otherwise) in experimental steps used in different laboratories may influence the outcome of any particular procedure. The book also illustrates the accessibility and the application of the different methods in different species. Background information of the protocol is given in every chapter, which also contains a literature list that the reader may wish to refer to for further information. This volume will be invaluable to basic researchers as well as to those involved in the search for agents suitable for pharmaceutic intervention in the central nervous system.

Download or read book Industrial Pharmaceutical Biotechnology written by Heinrich Klefenz and published by Wiley-VCH. This book was released on 2002-04-22 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on pharmaceutical biotechnology as a key area of life sciences. The complete range of concepts, processes and technologies of biotechnology is applied in modern industrial pharmaceutical research, development and production. The results of genome sequencing and studies of biological-genetic function are combined with chemical, micro-electronic and microsystem technology to produce medical devices and diagnostic biochips. A multitude of biologically active molecules is expanded by additional novel structures created with newly arranged gene clusters and bio-catalytic chemical processes. New organisational structures in the co-operation of institutes, companies and networks enable faster knowledge and product development and immediate application of the results of research and process development. This book is the ideal source of information for scientists and engineers in research and development, for decision-makers in biotech, pharma and chemical corporations, as well as for research institutes, but also for founders of biotech companies and people working for venture capital corporations.

Download or read book Encyclopedia of Biology written by Don Rittner and published by Infobase Publishing. This book was released on 2004-08 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contains approximately 800 alphabetical entries, prose essays on important topics, line illustrations, and black-and-white photographs.

Download or read book Inherited Metabolic Diseases written by Georg F. Hoffmann and published by Springer Science & Business Media. This book was released on 2009-11-21 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: The explosion of insights in the field of metabolic disease has shed new light on diagnostic as well as treatment options. ‘Inherited Metabolic Disease – A Clinical Approach’ is written with a reader-friendly consistent structure. It helps the reader to find the information in an easily accessible and rapid way when needed. Starting with an overview of the major groups of metabolic disorders it includes algorithms with questions and answers as well as numerous graphs, metabolic pathways, and an expanded index. Clinical and diagnostic details with a system and symptom based are given to facilitate an efficient and yet complete diagnostic work-up of individual patients. Further, it offers helpful advice for emergency situations, such as hypoglycemia, hyperammonemia, lactic acidosis or acute encephalopathy. Five different indices allow a quick but complete orientation for common important constellations. Last but not least, it has an appendix with a guide to rapid differential diagnosis of signs and symptoms and when not to suspect metabolic disease. It will help physicians to diagnose patients they may otherwise fail to diagnose and to reduce unnecessary referrals. For metabolic and genetic specialists especially the indices will be helpful as a quick look when being called for advice. It has all it needs to become a gold standard defining the clinical practice in this field.