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Mass Spectrometry in Biophysics

Mass Spectrometry in Biophysics Book
Author : Igor A. Kaltashov,Stephen J. Eyles
Publisher : John Wiley & Sons
Release : 2005-05-06
ISBN : 0471705160
Language : En, Es, Fr & De

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Book Description :

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 Book
Author : Igor A. Kaltashov,Stephen J. Eyles
Publisher : John Wiley & Sons
Release : 2012-04-03
ISBN : 0470937793
Language : En, Es, Fr & De

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Book Description :

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.

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 Book
Author : Sterling, Jr. (Harry John)
Publisher : Unknown
Release : 2012
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

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.

Methods in Modern Biophysics

Methods in Modern Biophysics Book
Author : Bengt Nölting
Publisher : Springer Science & Business Media
Release : 2013-03-09
ISBN : 3662053675
Language : En, Es, Fr & De

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Book Description :

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.

Development and Application of Mass Spectrometry based Biophysical Approaches

Development and Application of Mass Spectrometry based Biophysical Approaches Book
Author : Ying Zhang
Publisher : Unknown
Release : 2015
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

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.

Biophysical Characterization of Proteins in Developing Biopharmaceuticals

Biophysical Characterization of Proteins in Developing Biopharmaceuticals Book
Author : Damian J. Houde,Steven A. Berkowitz
Publisher : Elsevier
Release : 2019-11-13
ISBN : 0444641742
Language : En, Es, Fr & De

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Book Description :

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

Mass Spectrometry based Strategies for Protein Biophysics

Mass Spectrometry based Strategies for Protein Biophysics Book
Author : Richard Yu-Cheng Huang
Publisher : Unknown
Release : 2012
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Two important biophysical characteristics of proteins, their interaction with ligands and their post-translational modifications, modulate various biological processes including signal transduction, chemical synthesis, and cell function. Protein-ligand interactions include the interactions with protein, peptide, DNA, and metal. Characterization of the physical properties of these interactions (binding interfaces, binding affinities, and the protein conformational changes due to the binding) is essential in understanding the mechanism of related diseases and, more importantly, in future drug design. Mass spectrometry, with its own revolution and improvement, becomes a powerful tool in protein and peptide analysis. In this thesis, we applied two mass spectrometry-based strategies, proteomics and protein footprinting, to characterize these biophysical properties of three disease-related proteins, connexin 43 (Cx43), troponin, and apolipoprotein E (ApoE), and Fenna-Matthews-Olson protein (FMO), which is the key factor in energy transfer of the photosynthetic system of green sulfur bacteria. By the combination of standard proteomics workflow and two fragmentation methods, collision-induced dissociation (CID) and electron transfer dissociation (ETD), we successfully identified 15 serine residues, including one novel site, in the Cx43-CT that are phosphorylated by CaMKII, the activity of which may be important in regulating Cx43 in normal and diseased hearts. We further utilized hydrogen/deuterium exchange (H/DX), one mass spectrometry-based protein footprinting strategy, to examine the binding affinities of troponin C (TnC), a cardiac disease-related protein, with its four metal binding ligands (Ca2+), and their binding order. We then expanded this approach to elucidate the dynamics of TnC within the complex and its interactions with other subunits (TnT and TnI) at peptide-level resolution. This same approach was also applied to two protein-ligand complexes: (1) the interaction of FMO and its binding partner, CsmA baseplate protein, in which the orientation of FMO between chlorosome and membrane can be confirmed, and (2) the interaction of ApoE and Abeta 40, which are both key factors in Alzheimer's disease. Moreover, we improved the spatial resolution of H/DX to residue-level by conducting ETD fragmentation in the study of ApoE oligomerization. Our results reveal, for the first time, the amino acid residues involved in its self-oligomerization. These six applications of mass spectrometry-based approaches show their potential in the characterization of different protein biophysical properties. The investigation of a more complex protein system can then be pursued.

Molecular Biophysics for the Life Sciences

Molecular Biophysics for the Life Sciences Book
Author : Norma Allewell,Linda O. Narhi,Ivan Rayment
Publisher : Springer Science & Business Media
Release : 2013-09-28
ISBN : 1461485487
Language : En, Es, Fr & De

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Book Description :

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 Biophysical Methods for Protein and Nucleic Acid Research

Introduction to Biophysical Methods for Protein and Nucleic Acid Research Book
Author : Jay A. Glasel,Murray P. Deutscher
Publisher : Academic Press
Release : 1995-11-20
ISBN : 9780080534985
Language : En, Es, Fr & De

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Book Description :

The first of its kind, Introduction to Biophysical Methods for Protein and Nucleic Acid Research serves as a text for the experienced researcher and student requiring an introduction to the field. Each chapter presents a description of the physical basis of the method, the type of information that may be obtained with the method, how data should be analyzed and interpreted and, where appropriate, practical tips about procedures and equipment. Key Features * Modern Use of Mass Spectroscopy * NMR Spectroscopy * Molecular Modeling and Graphics * Macintosh and DOS/Windows 3.x disks

Biophysical Chemistry

Biophysical Chemistry Book
Author : Alan Cooper
Publisher : Royal Society of Chemistry
Release : 2015-11-09
ISBN : 1782625100
Language : En, Es, Fr & De

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Book Description :

Biophysical Chemistry covers the physical chemistry of biological macromolecules and the experimental techniques used to study them. Topics covered include: an introduction to biological molecules; spectroscopy, mass spectrometry and hydrodynamics of macromolecules; a ""bluffer's guide"" to molecular thermodynamics; biomolecular kinetics; chromatography and electrophoresis; and single-molecule methods. The easily digestible, pragmatic approach captures the reader with the fascinating challenges the subject poses for theoretical and experimental scientists. This book will be ideal for early undergraduates studying chemical or physical sciences and will act as a basis for more advanced study. Students in other areas of biological sciences will appreciate the less intimidating approach to physical chemistry as demonstrated here. Ideal for the needs of undergraduate chemistry students, Tutorial Chemistry Texts is a major series consisting of short, single topic or modular texts concentrating on the fundamental areas of chemistry taught in undergraduate science courses. Each book provides a concise account of the basic principles underlying a given subject, embodying an independent-learning philosophy and including worked examples.

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 Book
Author : Liangjie Tang
Publisher : ProQuest
Release : 2007
ISBN : 9780549685463
Language : En, Es, Fr & De

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Book Description :

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.

Hydrogen Exchange Mass Spectrometry of Proteins

Hydrogen Exchange Mass Spectrometry of Proteins Book
Author : David D. Weis
Publisher : John Wiley & Sons
Release : 2016-01-12
ISBN : 1118703731
Language : En, Es, Fr & De

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Book Description :

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.

Mass spectrometry in chemical physics biophysics and environmental sciences

Mass spectrometry in chemical physics  biophysics and environmental sciences Book
Author : Международный Семинар-Школа Масс-Спектрометрия в Химической Физике, Биофизике и Экологии
Publisher : Unknown
Release : 2004
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Mass spectrometry in chemical physics biophysics and environmental sciences book written by Международный Семинар-Школа Масс-Спектрометрия в Химической Физике, Биофизике и Экологии, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Applied Biophysics for Drug Discovery

Applied Biophysics for Drug Discovery Book
Author : Donald Huddler,Edward R. Zartler
Publisher : John Wiley & Sons
Release : 2017-10-02
ISBN : 111909948X
Language : En, Es, Fr & De

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Book Description :

13.2.1 Protein Dynamics of SA WT and S1 Mutant DHFR in Apo and Bound States

Biophysical Methods for Biotherapeutics

Biophysical Methods for Biotherapeutics Book
Author : Tapan K. Das
Publisher : John Wiley & Sons
Release : 2014-02-27
ISBN : 1118354680
Language : En, Es, Fr & De

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Book Description :

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.

Introduction to Biomolecular Structure and Biophysics

Introduction to Biomolecular Structure and Biophysics Book
Author : Gauri Misra
Publisher : Unknown
Release : 2017
ISBN : 9789811049699
Language : En, Es, Fr & De

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Book Description :

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.

Mass Spectrometry in Structural Biology and Biophysics

Mass Spectrometry in Structural Biology and Biophysics Book
Author : Stephen J. Eyles
Publisher : Unknown
Release : 2021-10-22
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Mass Spectrometry in Structural Biology and Biophysics book written by Stephen J. Eyles, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Peptide level Biophysical Characterization of Protein ligand Interactions by H D Exchange Mass Spectrometry

Peptide level Biophysical Characterization of Protein ligand Interactions by H D Exchange Mass Spectrometry Book
Author : Justin Baxter Sperry
Publisher : Unknown
Release : 2008
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Peptide level Biophysical Characterization of Protein ligand Interactions by H D Exchange Mass Spectrometry book written by Justin Baxter Sperry, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Biophysical Techniques in Photosynthesis

Biophysical Techniques in Photosynthesis Book
Author : Thijs Aartsma,Jörg Matysik
Publisher : Springer Science & Business Media
Release : 2008-02-01
ISBN : 1402082509
Language : En, Es, Fr & De

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Book Description :

Since the first volume on Biophysical Techniques in Photosynthesis Research, published in 1996, new experimental techniques and methods have been devised at a rapid pace. The present book is a sequel which complements the publication of the first volume by providing a comprehensive overview of the most important new techniques developed over the past ten years, especially those that are relevant for research on the mechanism and fundamental aspects of photosynthesis.