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 0 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 in Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2005-05-06 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first systematic summary of biophysical mass spectrometrytechniques Recent advances in mass spectrometry (MS) have pushed the frontiersof analytical chemistry into the biophysical laboratory. As aresult, the biophysical community's acceptance of MS-based methods,used to study protein higher-order structure and dynamics, hasaccelerated the expansion of biophysical MS. Despite this growing trend, until now no single text has presentedthe full array of MS-based experimental techniques and strategiesfor biophysics. Mass Spectrometry in Biophysics expertly closesthis gap in the literature. Covering the theoretical background and technical aspects of eachmethod, this much-needed reference offers an unparalleled overviewof the current state of biophysical MS. Mass Spectrometry inBiophysics begins with a helpful discussion of general biophysicalconcepts and MS-related techniques. Subsequent chaptersaddress: * Modern spectrometric hardware * High-order structure and dynamics as probed by various MS-basedmethods * Techniques used to study structure and behavior of non-nativeprotein states that become populated under denaturingconditions * Kinetic aspects of protein folding and enzyme catalysis * MS-based methods used to extract quantitative information onprotein-ligand interactions * Relation of MS-based techniques to other experimental tools * Biomolecular properties in the gas phase Fully referenced and containing a helpful appendix on the physicsof electrospray mass spectrometry, Mass Spectrometry in Biophysicsalso offers a compelling look at the current challenges facingbiomolecular MS and the potential applications that will likelyshape its future.

Download or read book Mass Spectrometry in Structural Biology and Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2012-04-03 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.

Download or read book Applications of Mass Spectrometry in Life Safety written by Crisan Popescu and published by Springer Science & Business Media. This book was released on 2008-09-02 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) along with its hyphenated techniques is capable of high throughput, sensitivity, accuracy and selectivity for the analysis of structure and composition of almost any product. Like in electrophoresis, MS separates mo- cules based on the mass-to-charge ratio. In case of gel electrophoresis (SDS- PAGE), a well-known and efficient bioanalytical technique, proteins bear negative charges but have the same charge density, so proteins are separated according to their size. Similarly, in case of MS analysis, proteins carry the same charge, and are separated by their molecular weight. Unlike SDS-PAGE, however, modern ultra high resolution MS discerns very small mass differences and can resolve and completely identify in a single experiment species of the same nominal mass in complex biological mixtures. Consequently, MS can be used for the structural characterization, identification and sensitive detection of mixtures of biomolecules or for assessing the quality of isolated proteins (purity, integrity, or post-translational modifications, for example), carbohydrates, nucleic acids, drugs, metabolites, pollutants etc. In the post-genome era, MS is continuously developing as one of the most re- able analytical method for elucidating the structure of molecules originating from various biological matrices. The potential of MS for high-sensitive structural a- lyses became unsurpassable after the introduction of electrospray (ESI) and matrix assisted laser/desorption ionization (MALDI) methods, on one hand, and the pos- bility to deduce in detail unknown biopolymer structures by highly accurate mo- cular mass measurement followed by sequencing using dissociation techniques based on multiple stage MS, on the other.

Download or read book Biophysics for Therapeutic Protein Development written by Linda O. Narhi and published by Springer Science & Business Media. This book was released on 2013-02-26 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book can be used to provide insight into this important application of biophysics for those who are planning a career in protein therapeutic development, and for those outside this area who are interested in understanding it better. The initial chapters describe the underlying theory, and strengths and weaknesses of the different techniques commonly used during therapeutic development. The majority of the chapters discuss the applications of these techniques, including case studies, across the product lifecycle from early discovery, where the focus is on identifying targets, and screening for potential drug product candidates, through expression and purification, large scale production, formulation development, lot-to-lot comparability studies, and commercial support including investigations.

Download or read book Medical Applications of Mass Spectrometry written by Karoly Vekey and published by Elsevier. This book was released on 2011-08-11 with total page 607 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry is fast becoming an indispensable field for medical professionals. The mass spectrometric analysis of metabolites and proteins promises to revolutionize medical research and clinical diagnostics. As this technology rapidly enters the medical field, practicing professionals and students need to prepare to take full advantage of its capabilities. Medical Applications of Mass Spectrometry addresses the key issues in the medical applications of mass spectrometry at the level appropriate for the intended readership. It will go a long way to help the utilization of mass spectrometry in medicine.The book comprises five parts. A general overview is followed by a description of the basic sampling and separation methods in analytical chemistry. In the second part a solid foundation in mass spectrometry and modern techniques of data analysis is presented. The third part explains how mass spectrometry is used in exploring various classes of biomolecules, including proteins and lipids. In the fourth section mass spectrometry is introduced as a diagnostic tool in clinical treatment, infectious pathogen research, neonatal diagnostics, cancer, brain and allergy research, as well as in various fields of medicine: cardiology, pulmonology, neurology, psychiatric diseases, hemato-oncology, urologic diseases, gastrointestinal diseases, gynecology and pediatrics. The fifth part covers emerging applications in biomarker discovery and in mass spectrometric imaging. * Provides a broad look at how the medical field is benefiting from advances in mass spectrometry.* Guides the reader from basic principles and methods to cutting edge applications.* There is NO comparable book on the market to fill this fast growing field.

Download or read book Mass Spectrometry Developmental Approaches to Answer Biological Questions written by Gwenael Pottiez and published by Springer. This book was released on 2015-02-05 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt: The understanding of the events taking place in a cell, a biological fluid or in any biological system is the main goal of biology research. Many fields of research use different technology to assess those events. Mass spectrometry is one of those techniques and this undergoes constant evolution and adaptation to always enhance the accuracy of the information provided. Proteomics provides a large panel of data on protein identity and protein expression that were made possible by mass spectrometry. For several years now mass spectrometry has become central to performing proteomic research, however this powerful tool is under constant evolution to be more sensitive and more resolute. More importantly mass spectrometry became a field of research focusing on new applications. Indeed, the complexity in biological systems relies on the changes of expression of transcription of proteins but also on the post-translational modification of proteins, the structure of proteins and the interaction between proteins, amongst others. As of now, several investigations tried to improve the quantification of proteins by mass spectrometry, the determination of post-translational modifications, the protein-protein and protein-nucleic acids interaction or the proteins structures. This book is structured as follows: after a brief introduction of the usual and most popular applications for mass spectrometry in proteomics, the most recent research and developments in mass spectrometry-based methodologies will be explored.

Download or read book Applied Biophysics for Drug Discovery written by Donald Huddler and published by John Wiley & Sons. This book was released on 2017-10-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: Applied Biophysics for Drug Discovery is a guide to new techniques and approaches to identifying and characterizing small molecules in early drug discovery. Biophysical methods are reasserting their utility in drug discovery and through a combination of the rise of fragment-based drug discovery and an increased focus on more nuanced characterisation of small molecule binding, these methods are playing an increasing role in discovery campaigns. This text emphasizes practical considerations for selecting and deploying core biophysical method, including but not limited to ITC, SPR, and both ligand-detected and protein-detected NMR. Topics covered include: • Design considerations in biophysical-based lead screening • Thermodynamic characterization of protein-compound interactions • Characterizing targets and screening reagents with HDX-MS • Microscale thermophoresis methods (MST) • Screening with Weak Affinity Chromatography • Methods to assess compound residence time • 1D-NMR methods for hit identification • Protein-based NMR methods for SAR development • Industry case studies integrating multiple biophysical methods This text is ideal for academic investigators and industry scientists planning hit characterization campaigns or designing and optimizing screening strategies.

Download or read book Biophysical Methods for Biotherapeutics written by Tapan K. Das and published by John Wiley & Sons. This book was released on 2014-04-28 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: With a focus on practical applications of biophysical techniques, this book links fundamental biophysics to the process of biopharmaceutical development. • Helps formulation and analytical scientists in pharma and biotech better understand and use biophysical methods • Chapters organized according to the sequential nature of the drug development process • Helps formulation, analytical, and bioanalytical scientists in pharma and biotech better understand and usestrengths and limitations of biophysical methods • Explains how to use biophysical methods, the information obtained, and what needs to be presented in a regulatory filing, assess impact on quality and immunogenicity • With a focus on practical applications of biophysical techniques, this book links fundamental biophysics to the process of biopharmaceutical development.

Download or read book Biophysical Approaches Determining Ligand Binding to Biomolecular Targets written by Alberto Podjarny and published by Royal Society of Chemistry. This book was released on 2011-04-01 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: The binding of small ligands to biological molecules is central to most aspects of biological function. The past twenty years has seen the development of an increasing armoury of biophysical methods that not only detect such binding, but also provide varying degrees of information about the kinetics, thermodynamics and structural aspects of the process. These methods have received increasing attention with the growth in more rational approaches to drug discovery and design. This book reviews the latest advances in the application of biophysics to the study of ligand binding. It provides a complete overview of current techniques to identify ligands, characterise their binding sites and understand their binding mechanisms. Particular emphasis is given to the combined use of different techniques and their relative strengths and weaknesses. Consistency in the way each technique is described makes it easy for readers to select the most suitable protocol for their research. The introduction explains why some techniques are more suitable than others and emphasizes the possible synergies between them. The following chapters, all written by a specialist in the particular technique, focus on each method individually. The book finishes by describing how several complimentary techniques can be used together for maximum effectiveness. This book is suitable for biomolecular scientists at graduate or post-doctoral level in academia and industry. Biologists and chemists will also find it a useful introduction to the techniques available.

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 Sample Preparation in Biological Mass Spectrometry written by Alexander R. Ivanov and published by Springer Science & Business Media. This book was released on 2011-06-15 with total page 1081 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point. In this volume we have compiled the contributions from several laboratories which are employing mass spectrometry for biological analysis. With the latest inventions and introduction of highly sophisticated mass spectrometry equipment sample preparation becomes an extremely important bottleneck of biomedical analysis. We have a goal of giving the reader several successful examples of sample preparation, development and optimization, leading to the success in analytical steps and proper conclusions made at the end of the day. This book is structured as a compilation of contributed chapters ranging from protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

Download or read book Aggregation of Therapeutic Proteins written by Wei Wang and published by John Wiley & Sons. This book was released on 2010-12-28 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives pharmaceutical scientists an up-to-date resource on protein aggregation and its consequences, and available methods to control or slow down the aggregation process. While significant progress has been made in the past decade, the current understanding of protein aggregation and its consequences is still immature. Prevention or even moderate inhibition of protein aggregation has been mostly experimental. The knowledge in this book can greatly help pharmaceutical scientists in the development of therapeutic proteins, and also instigate further scientific investigations in this area. This book fills such a need by providing an overview on the causes, consequences, characterization, and control of the aggregation of therapeutic proteins.

Download or read book Mass Spectrometry Based Approaches for Treating Human Diseases and Diagnostics written by Thiago Verano-Braga and published by Springer Nature. This book was released on with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Development and Application of Mass Spectrometry Based Approaches to Study Chemical Modifications of Nucleic Acids and Proteins written by Peiyuan Zheng and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Biophysical Characterization of Proteins in Developing Biopharmaceuticals written by Damian J. Houde and published by Elsevier. This book was released on 2019-11-13 with total page 586 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysical Characterization of Proteins in Developing Biopharmaceuticals, Second Edition, presents the latest on the analysis and characterization of the higher-order structure (HOS) or conformation of protein based drugs. Starting from the very basics of protein structure, this book explains the best way to achieve this goal using key methods commonly employed in the biopharmaceutical industry. This book will help today’s industrial scientists plan a career in this industry and successfully implement these biophysical methodologies. This updated edition has been fully revised, with new chapters focusing on the use of chromatography and electrophoresis and the biophysical characterization of very large biopharmaceuticals. In addition, best practices of applying statistical analysis to biophysical characterization data is included, along with practical issues associated with the concept of a biopharmaceutical’s developability and the technical decision-making process needed when dealing with biophysical characterization data. Presents basic protein characterization methods and tools applicable to (bio)pharmaceutical research and development Highlights the capabilities and limitations of each technique Discusses the underlining science of each tool Empowers industrial biophysical chemists by providing a roadmap for applying biophysical tools Outlines the needs for new characterization and analytical tools in the biopharmaceutical industry

Download or read book Molecular Biophysics for the Life Sciences written by Norma Allewell and published by Springer Science & Business Media. This book was released on 2013-09-28 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides an overview of the development and scope of molecular biophysics and in-depth discussions of the major experimental methods that enable biological macromolecules to be studied at atomic resolution. It also reviews the physical chemical concepts that are needed to interpret the experimental results and to understand how the structure, dynamics, and physical properties of biological macromolecules enable them to perform their biological functions. Reviews of research on three disparate biomolecular machines—DNA helicases, ATP synthases, and myosin--illustrate how the combination of theory and experiment leads to new insights and new questions.