June 15, 2021

Download Ebook Free Biophysical Mass Spectrometry

Mass Spectrometry in Biophysics

Mass Spectrometry in Biophysics
Author : Igor A. Kaltashov,Stephen J. Eyles
Publisher : John Wiley & Sons
Release Date : 2005-05-06
Category : Science
Total pages :320
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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.

Mass Spectrometry in Structural Biology and Biophysics

Mass Spectrometry in Structural Biology and Biophysics
Author : Igor A. Kaltashov,Stephen J. Eyles
Publisher : John Wiley & Sons
Release Date : 2012-04-03
Category : Medical
Total pages :289
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With its detailed and systematic coverage of the current state of biophysical mass spectrometry (MS), here is one of the first systematic presentations of the full experimental array of MS-based techniques used in biophysics, covering both fundamental and practical issues. The book presents a discussion of general biophysical concepts and a brief overview of traditional biophysical techniques before outlining the more advanced concepts of mass spectrometry. The new edition gives an up-to-date and expanded coverage of experimental methodologies and a clear look at MS-based methods for studying higher order structures and biopolymers. A must for researchers in the field of biophysics, structural biology, and protein chemistry.

Mass Spectrometry in Structural Biology and Biophysics

Mass Spectrometry in Structural Biology and Biophysics
Author : Stephen J. Eyles
Publisher : Unknown
Release Date : 2021
Category :
Total pages :312
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Biophysical Characterization of Proteins in Developing Biopharmaceuticals

Biophysical Characterization of Proteins in Developing Biopharmaceuticals
Author : Damian J. Houde,Steven A. Berkowitz
Publisher : Elsevier
Release Date : 2019-11-13
Category : Medical
Total pages :586
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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

Development and Application of Mass Spectrometry-based Biophysical Approaches

Development and Application of Mass Spectrometry-based Biophysical Approaches
Author : Ying Zhang
Publisher : Unknown
Release Date : 2015
Category :
Total pages :492
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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.

Hydrogen Exchange Mass Spectrometry of Proteins

Hydrogen Exchange Mass Spectrometry of Proteins
Author : David D. Weis
Publisher : John Wiley & Sons
Release Date : 2016-03-21
Category : SCIENCE
Total pages :376
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Hydrogen exchange mass spectrometry is widely recognized for its ability to probe the structure and dynamics of proteins. The application of this technique is becoming widespread due to its versatility for providing structural information about challenging biological macromolecules such as antibodies, flexible proteins and glycoproteins. Although the technique has been around for 25 years, this is the first definitive book devoted entirely to the topic. Hydrogen Exchange Mass Spectrometry of Proteins: Fundamentals, Methods and Applications brings into one comprehensive volume the theory, instrumentation and applications of Hydrogen Exchange Mass Spectrometry (HX-MS) - a technique relevant to bioanalytical chemistry, protein science and pharmaceuticals. The book provides a solid foundation in the basics of the technique and data interpretation to inform readers of current research in the method, and provides illustrative examples of its use in bio- and pharmaceutical chemistry and biophysics In-depth chapters on the fundamental theory of hydrogen exchange, and tutorial chapters on measurement and data analysis provide the essential background for those ready to adopt HX-MS. Expert users may advance their current understanding through chapters on methods including membrane protein analysis, alternative proteases, millisecond hydrogen exchange, top-down mass spectrometry, histidine exchange and method validation. All readers can explore the diversity of HX-MS applications in areas such as ligand binding, membrane proteins, drug discovery, therapeutic protein formulation, biocomparability, and intrinsically disordered proteins.

Methods in Modern Biophysics

Methods in Modern Biophysics
Author : Bengt Nölting
Publisher : Springer Science & Business Media
Release Date : 2013-03-09
Category : Science
Total pages :254
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Incorporating dramatic recent advances, "Methods in Modern Biophysics" presents a fresh and timely introduction to modern biophysical methods. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, and proteomics. Containing much information previously unavailable in tutorial form, "Methods in Modern Biophysics" employs worked examples and more than 260 illustrations to fully detail the techniques and their underlying mechanisms. The book was written for advanced undergraduate and graduate students, postdocs, researchers, lecturers and professors in biophysics, biochemistry, general biology and related fields.

Biophysical Applications of Amide Protein Hydrogen Exchange and MALDI Mass Spectrometry to Protein Folding

Biophysical Applications of Amide Protein Hydrogen Exchange and MALDI Mass Spectrometry to Protein Folding
Author : Yuan Dai
Publisher : Unknown
Release Date : 2006
Category : Amides
Total pages :268
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Introduction to Biomolecular Structure and Biophysics

Introduction to Biomolecular Structure and Biophysics
Author : Gauri Misra
Publisher : Springer
Release Date : 2017-09-07
Category : Medical
Total pages :274
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This comprehensive book presents a modern concept in biophysics based on recently published research. It highlights various aspects of the biophysical fundamentals and techniques that are currently used to study different physical properties of biomolecules, and relates the biological phenomenon with the underlying physical concepts. The content is divided into nine chapters summarizing the structural details of proteins, including recently discovered novel folds, higher order structures of nucleic acids, as well as lipids and the physical forces governing the macromolecular interactions which are essential for the various biological processes. It also provides insights into the recent advances in biophysical techniques including Hydrogen Deuterium Exchange with Mass Spectrometry (HDX-MS), Small angle X-ray scattering (SAXS) and Cryo Electron Microscopy (cryo EM), supplemented with interesting experimental data. It is a valuable reference resource for anyone with a desire to gain a better understanding of the fundamentals of biophysical concepts and techniques of important biomolecules.

Biophysical Mass Spectrometry Techniques for Probing the Higher-Order Structure of Proteins and Complexes

Biophysical Mass Spectrometry Techniques for Probing the Higher-Order Structure of Proteins and Complexes
Author : Sterling, Jr. (Harry John)
Publisher : Unknown
Release Date : 2012
Category :
Total pages :366
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Electrospray ionization mass spectrometry (ESI-MS) is a powerful analytical platform for answering a wide variety of questions about the identity, quantity, structure, function, dynamics and energetics of biological molecules. Key advantages of ESI-MS include unrivaled specificity, attomole sensitivity, and the capacity for simultaneous analysis of complex mixtures with analyte masses that differ by less than 1 ppm. The low flow rates and sub-micron sized droplets formed with "nano" ESI allows biomolecular ions to be readily formed from purely aqueous or buffered aqueous solutions, and these ions have been shown to retain a "memory" of their solution-phase structures so that higher-order structural information can be obtained directly from a gas-phase measurement. All of the work described in this dissertation was undertaken in an effort to develop new nanoESI-based techniques that augment the existing array of biophysical mass spectrometry techniques for probing the structure/function relationships of biological molecules in their native environments. In part one, a hypothesis for the origin of nanoESI "supercharging" is developed and exhaustively tested utilizing a variety of solution- and gas-phase techniques with a range of different proteins and protein complexes. The results of all of these studies support the hypothesis that the origin of aqueous solution supercharging is the rapid chemical and/or thermal denaturation of a protein or protein complex analyte in an evaporating ESI droplet due to enrichment of the reagent caused by its high boiling point relative to that of water. Aqueous solution supercharging has recently been used in a variety of new applications and an understanding of its underlying mechanism is therefore essential. In part two, two new biophysical mass spectrometry applications are described. The first is a tandem-MS application of aqueous solution supercharging for obtaining hydrogen/deuterium exchange (HDX) rate constants in real-time with nearly single amino acid spatial resolution, and the second describes an MS method to obtain the quaternary structure of protein complexes that require high concentrations of essential salts. Finally, two ideas for new HDX-MS methods that capitalize on the mechanism of aqueous solution supercharging are outlined.

Novel Mass Spectrometry-based Strategies for Biophysical Analysis of Proteins and Protein-ligand Complexes

Novel Mass Spectrometry-based Strategies for Biophysical Analysis of Proteins and Protein-ligand Complexes
Author : Liangjie Tang
Publisher : ProQuest
Release Date : 2007
Category : Ligands (Biochemistry)
Total pages :308
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The third protocol developed here is a SUPREX-like protocol that employs a chemical modification reaction (i.e., oxidation reaction) in place of the amide H/D exchange reaction in SUPREX. This SUPREX-like protocol, termed SPROX (Stability of Proteins from Rates of Oxidation) was developed and tested to detect and quantify protein-ligand binding using cyclophilin A and BCAII as model systems.

Mass spectrometry in chemical physics, biophysics and environmental sciences

Mass spectrometry in chemical physics, biophysics and environmental sciences
Author : Международный Семинар-Школа Масс-Спектрометрия в Химической Физике, Биофизике и Экологии
Publisher : Unknown
Release Date : 2004
Category :
Total pages :284
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Applied Biophysics for Drug Discovery

Applied Biophysics for Drug Discovery
Author : Donald Huddler,Edward R. Zartler
Publisher : John Wiley & Sons
Release Date : 2017-10-02
Category : Medical
Total pages :312
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13.2.1 Protein Dynamics of SA WT and S1 Mutant DHFR in Apo and Bound States

Molecular Biophysics for the Life Sciences

Molecular Biophysics for the Life Sciences
Author : Norma Allewell,Linda O. Narhi,Ivan Rayment
Publisher : Springer Science & Business Media
Release Date : 2013-09-28
Category : Science
Total pages :397
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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.

Introduction to Biomolecular Structure and Biophysics

Introduction to Biomolecular Structure and Biophysics
Author : Gauri Misra
Publisher : Unknown
Release Date : 2017
Category : Biomedical engineering
Total pages :274
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This comprehensive book presents a modern concept in biophysics based on recently published research. It highlights various aspects of the biophysical fundamentals and techniques that are currently used to study different physical properties of biomolecules, and relates the biological phenomenon with the underlying physical concepts. The content is divided into nine chapters summarizing the structural details of proteins, including recently discovered novel folds, higher order structures of nucleic acids, as well as lipids and the physical forces governing the macromolecular interactions which are essential for the various biological processes. It also provides insights into recent advances in biophysical techniques including Hydrogen Deuterium Exchange with Mass Spectrometry (HDX-MS), Small Angle X-ray Scattering (SAXS) and cryo Electron Microscopy (cryo EM), supplemented with interesting experimental data. It is a valuable reference resource for anyone with a desire to gain a better understanding of the fundamentals of biophysical concepts and techniques used to study important biomolecules.