This book provides glycoscientists with a handbook of useful databases that can be applied to glycoscience research. Although many databases are now publicly available, one of the hurdles for their users is the learning curve required to effectively utilize those databases. Therefore, this book not only describes the existing databases, but also provides tips on how to obtain the target data. That is, because many databases provide a variety of data that could be obtained from different perspectives, each chapter provides users with potential biological questions that can be answered by a particular database and step-by-step instructions, with figures, on how to obtain that data. Troubleshooting tips are also provided to aid users encountering problems that can be predicted when using these databases. Moreover, contact information for each database is provided in case unexpected issues arise.

This book provides the latest information of life science databases that center in the life science research and drive the development of the field. It introduces the fundamental principles, rationales and methodologies of creating and updating life science databases. The book brings together expertise and renowned researchers in the field of life science databases and brings their experience and tools at the fingertips of the researcher. The book takes bottom-up approach to explain the structure, content and the usability of life science database. Detailed explanation of the content, structure, query and data retrieval are discussed to provide practical use of life science database and to enable the reader to use database and provided tools in practice. The readers will learn the necessary knowledge about the untapped opportunities available in life science databases and how it could be used so as to advance basic research and applied research findings and transforming them to the benefit of human life. Chapter 2 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

The growing importance of glycobiology and carbohydrate chemistry in modern biotechnology and the pharmaceutical industry makes accurate carbohydrate analysis indispensable. This book provides the principles and protocols of various fundamental carbohydrate analysis methods. Choice of method is entirely dependent upon the type of material being investigated (biological samples, food products, etc.), and the level of structural detail required, i.e. sugar content, compositional analysis, linkages between the sugar components, or the total chemical structure of a given molecule. Full structural characterization of carbohydrate chains requires significant time, resources, and skill in several methods of analysis; no single technique can address all glycan analysis needs. This book summarizes several existing analytical techniques (both chemical and physical) in an introductory volume designed for the non-expert researcher or novice scientist. While background in carbohydrate chemistry is assumed, all information necessary to understanding the described techniques is addressed in the text.

This volume describes computational approaches to predict multitudes of PTM sites. Chapters describe in depth approaches on algorithms, state-of-the-art Deep Learning based approaches, hand-crafted features, physico-chemical based features, issues related to obtaining negative training, sequence-based features, and structure-based features. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Authoritative and cutting-edge, Computational Methods for Predicting Post-Translational Modification Sites aims to be a useful guide for researchers who are interested in the field of PTM site prediction.

Aerobic organisms have evolved to utilise the intrinsic oxidising power of oxygen from the atmosphere. This so-called 'activation' of oxygen is often catalysed by a heme-containing enzyme. This book highlights the many and varied catalytic activities of O2-dependent heme–iron enzymes, including monoxygenases and cytochrome P450, dioxygenases, oxidases and model heme systems. Dioxygen-dependent Heme Enzymes will be a useful resource for postgraduate students and researchers in biochemistry and metallobiology working in, or moving into, research areas involving heme proteins.

Carbohydrate-active enzymes are responsible for both biosynthesis and the breakdown of carbohydrates and glycoconjugates. They are involved in many metabolic pathways; in the biosynthesis and degradation of various biomolecules, such as bacterial exopolysaccharides, starch, cellulose and lignin; and in the glycosylation of proteins and lipids. Carbohydrate-active enzymes are classified into glycoside hydrolases, glycosyltransferases, polysaccharide lyases, carbohydrate esterases, and enzymes with auxiliary activities (CAZy database, www.cazy.org). Glycosyltransferases synthesize a huge variety of complex carbohydrates with different degrees of polymerization, moieties and branching. On the other hand, complex carbohydrate breakdown is carried out by glycoside hydrolases, polysaccharide lyases and carbohydrate esterases. Their interesting reactions have attracted the attention of researchers across scientific fields, ranging from basic research to biotechnology. Interest in carbohydrate-active enzymes is due not only to their ability to build and degrade biopolymers—which is highly relevant in biotechnology—but also because they are involved in bacterial biofilm formation, and in glycosylation of proteins and lipids, with important health implications. This book gathers new research results and reviews to broaden our understanding of carbohydrate-active enzymes, their mutants and their reaction products at the molecular level.

Glycoproteins are central to numerous cellular processes and are among the most structurally complex biomolecules in nature. This unique complexity stems from variability in complex oligosaccharides that are located throughout the protein, a feature that is profoundly important for regulating biomolecular interactions but also makes glycoproteins difficult to study. As such, glycoprotein analysis entails a range of techniques to bridge the knowledge gap between glycoprotein structure and biological function. This book serves as an authoritative guide to glycoprotein analysis, written by internationally recognised experts in the field and discussed in the context of real-world applications across the life sciences. It provides a wide-ranging assessment of the modern methods, from those used to characterise glycoprotein structure, to approaches proficient in uncovering the molecular mechanisms by which they function as well as those capable of measuring structural dynamics and macromolecular assembly. These methods differ to a large extent and include mass spectrometry, glycan/lectin arrays, nuclear magnetic resonance, infrared spectroscopy, scanning probe microscopy and high-performance liquid chromatography. Equally important are computational techniques, including molecular dynamics and bioinformatics, which are also covered and discussed in the wider context of glycoprotein analysis. Glycobiology is indeed a rapidly growing field and the development of advanced tools for glycoproteins analysis has been enabled by researchers from different backgrounds working to overcome long-standing analytical challenges and biological questions involving glycosylation. This book is intended to aid academic and professional researchers at various levels of their career to gain a deeper appreciation of cutting-edge methods in glycoprotein analysis and their applications in biomolecular research, biotherapeutic development, structural biology and biophysical chemistry.