Mass Spectrometry in Biophysics

Mass Spectrometry in Biophysics
Author: Igor A. Kaltashov,Stephen J. Eyles
Publsiher: John Wiley & Sons
Total Pages: 320
Release: 2005-05-06
ISBN 10: 0471705160
ISBN 13: 9780471705161
Language: EN, FR, DE, ES & NL

Mass Spectrometry in Biophysics Book Review:

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
Publsiher: John Wiley & Sons
Total Pages: 289
Release: 2012-04-03
ISBN 10: 0470937793
ISBN 13: 9780470937792
Language: EN, FR, DE, ES & NL

Mass Spectrometry in Structural Biology and Biophysics Book Review:

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 Characterization of Proteins in Developing Biopharmaceuticals

Biophysical Characterization of Proteins in Developing Biopharmaceuticals
Author: Damian J. Houde,Steven A. Berkowitz
Publsiher: Elsevier
Total Pages: 586
Release: 2019-11-13
ISBN 10: 0444641742
ISBN 13: 9780444641748
Language: EN, FR, DE, ES & NL

Biophysical Characterization of Proteins in Developing Biopharmaceuticals Book Review:

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

Introduction to Biophysical Methods for Protein and Nucleic Acid Research

Introduction to Biophysical Methods for Protein and Nucleic Acid Research
Author: Jay A. Glasel,Murray P. Deutscher
Publsiher: Academic Press
Total Pages: 510
Release: 1995-11-20
ISBN 10: 9780080534985
ISBN 13: 0080534988
Language: EN, FR, DE, ES & NL

Introduction to Biophysical Methods for Protein and Nucleic Acid Research Book Review:

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 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)
Publsiher: Unknown
Total Pages: 366
Release: 2012
ISBN 10: 1928374650XXX
ISBN 13: OCLC:810064697
Language: EN, FR, DE, ES & NL

Biophysical Mass Spectrometry Techniques for Probing the Higher Order Structure of Proteins and Complexes Book Review:

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.

Development and Application of Mass Spectrometry based Biophysical Approaches

Development and Application of Mass Spectrometry based Biophysical Approaches
Author: Ying Zhang
Publsiher: Unknown
Total Pages: 492
Release: 2015
ISBN 10: 1928374650XXX
ISBN 13: OCLC:920875376
Language: EN, FR, DE, ES & NL

Development and Application of Mass Spectrometry based Biophysical Approaches Book Review:

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 Techniques in Photosynthesis

Biophysical Techniques in Photosynthesis
Author: Thijs Aartsma,Jörg Matysik
Publsiher: Springer Science & Business Media
Total Pages: 520
Release: 2008-02-01
ISBN 10: 1402082509
ISBN 13: 9781402082504
Language: EN, FR, DE, ES & NL

Biophysical Techniques in Photosynthesis Book Review:

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.

Methods in Modern Biophysics

Methods in Modern Biophysics
Author: Bengt Nölting
Publsiher: Springer Science & Business Media
Total Pages: 254
Release: 2013-03-09
ISBN 10: 3662053675
ISBN 13: 9783662053676
Language: EN, FR, DE, ES & NL

Methods in Modern Biophysics Book Review:

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 Techniques in Drug Discovery

Biophysical Techniques in Drug Discovery
Author: Angeles Canales
Publsiher: Royal Society of Chemistry
Total Pages: 320
Release: 2017-11-14
ISBN 10: 1788012860
ISBN 13: 9781788012867
Language: EN, FR, DE, ES & NL

Biophysical Techniques in Drug Discovery Book Review:

Biophysical techniques are used in many key stages of the drug discovery process including in screening for new receptor ligands, in characterising drug mechanisms, and in validating data from biochemical and cellular assays. This book provides an overview of the biophysical methods applied in drug discovery today, including traditional techniques and newer developments. Perspectives from academia and industry across a spectrum of techniques are brought together in a single volume. Small and biotherapeutic approaches are covered and strengths and limitations of each technique are presented. Case studies illustrate the application of each technique in real applied examples. Finally, the book covers recent developments in areas such as electron microscopy with discussions of their possible impact on future drug discovery. This is a go-to volume for biophysicists, analytical chemists and medicinal chemists providing a broad overview of techniques of contemporary interest in drug discovery.

Applied Biophysics for Drug Discovery

Applied Biophysics for Drug Discovery
Author: Donald Huddler,Edward R. Zartler
Publsiher: John Wiley & Sons
Total Pages: 312
Release: 2017-10-02
ISBN 10: 111909948X
ISBN 13: 9781119099482
Language: EN, FR, DE, ES & NL

Applied Biophysics for Drug Discovery Book Review:

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

Biophysical Chemistry

Biophysical Chemistry
Author: Alan Cooper
Publsiher: Royal Society of Chemistry
Total Pages: 196
Release: 2004
ISBN 10: 9780854044801
ISBN 13: 0854044809
Language: EN, FR, DE, ES & NL

Biophysical Chemistry Book Review:

This book will be ideal for early undergraduates studying chemical or physical sciences and will act as a basis for more advanced study.

Biophysics

Biophysics
Author: Mark C. Leake
Publsiher: CRC Press
Total Pages: 390
Release: 2016-09-15
ISBN 10: 1498702511
ISBN 13: 9781498702515
Language: EN, FR, DE, ES & NL

Biophysics Book Review:

An Up-to-Date Toolbox for Probing Biology Biophysics: Tools and Techniques covers the experimental and theoretical tools and techniques of biophysics. It addresses the purpose, science, and application of all physical science instrumentation and analysis methods used in current research labs. The book first presents the historical background, concepts, and motivation for using a physical science toolbox to understand biology. It then familiarizes students from the physical sciences with essential biological knowledge. The text subsequently focuses on experimental biophysical techniques that primarily detect biological components or measure/control biological forces. The author describes the science and application of key tools used in imaging, detection, general quantitation, and biomolecular interaction studies, which span multiple length and time scales of biological processes both in the test tube and in the living organism. Moving on to theoretical biophysics tools, the book presents computational and analytical mathematical methods for tackling challenging biological questions. It concludes with a discussion of the future of this exciting field. Future innovators will need to be trained in multidisciplinary science to be successful in industry, academia, and government support agencies. Addressing this challenge, this textbook educates future leaders on the development and application of novel physical science approaches to solve complex problems linked to biological questions.

Methods in Molecular Biophysics

Methods in Molecular Biophysics
Author: Igor N. Serdyuk,Nathan R. Zaccai,Joseph Zaccai,Giuseppe Zaccai
Publsiher: Cambridge University Press
Total Pages: 709
Release: 2017-05-18
ISBN 10: 1107056373
ISBN 13: 9781107056374
Language: EN, FR, DE, ES & NL

Methods in Molecular Biophysics Book Review:

A comprehensive graduate textbook explaining key physical methods in biology, reflecting the very latest research in this fast-moving field.

Ion Mobility Mass Spectrometry

Ion Mobility Mass Spectrometry
Author: Alison E Ashcroft,Frank Sobott
Publsiher: Royal Society of Chemistry
Total Pages: 476
Release: 2021-11-26
ISBN 10: 1839162899
ISBN 13: 9781839162893
Language: EN, FR, DE, ES & NL

Ion Mobility Mass Spectrometry Book Review:

Over the last decade, the use of ion mobility separation in combination with mass spectrometry analysis has developed significantly. This technique adds a unique extra dimension enabling the in-depth analysis of a wide range of complex samples in the areas of the chemical and biological sciences. Providing a comprehensive guide to the technique, each chapter is written by an internationally recognised expert and with numerous different commercial platforms to choose from, this book will help the end users understand the practicalities of using different instruments for different ion mobility purposes. The first section provides a detailed account of the fundamentals behind the technique and the current range of available instrumentation. The second section focusses on the wide range of applications that have benefitted from ion mobility – mass spectrometry and includes topics taken from current research in the pharmaceutical, metabolomics, glycomics, and structural molecular biology fields. The book is primarily aimed at researchers, appealing to practising chemists and biochemists, as well as those in the pharmaceutical and medical fields.

Mass Spectrometry based Strategies for Protein Biophysics

Mass Spectrometry based Strategies for Protein Biophysics
Author: Richard Yu-Cheng Huang
Publsiher: Unknown
Total Pages: 548
Release: 2012
ISBN 10: 1928374650XXX
ISBN 13: OCLC:812463249
Language: EN, FR, DE, ES & NL

Mass Spectrometry based Strategies for Protein Biophysics Book Review:

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.

Proteomics for Biological Discovery

Proteomics for Biological Discovery
Author: Timothy D. Veenstra,John R. Yates, III
Publsiher: John Wiley & Sons
Total Pages: 361
Release: 2006-06-12
ISBN 10: 0470007737
ISBN 13: 9780470007730
Language: EN, FR, DE, ES & NL

Proteomics for Biological Discovery Book Review:

Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.

Biophysical Approaches Determining Ligand Binding to Biomolecular Targets

Biophysical Approaches Determining Ligand Binding to Biomolecular Targets
Author: Alberto Podjarny,Annick Dejaegere,Bruno Kieffer
Publsiher: Royal Society of Chemistry
Total Pages: 356
Release: 2011
ISBN 10: 1849730091
ISBN 13: 9781849730099
Language: EN, FR, DE, ES & NL

Biophysical Approaches Determining Ligand Binding to Biomolecular Targets Book Review:

This book provides a complete overview of current techniques to identify ligands, characterise their binding sites and understand binding mechanisms. 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.

Biophysical Techniques in Drug Discovery

Biophysical Techniques in Drug Discovery
Author: Angeles Canales
Publsiher: Royal Society of Chemistry
Total Pages: 320
Release: 2017-11-20
ISBN 10: 1782627332
ISBN 13: 9781782627333
Language: EN, FR, DE, ES & NL

Biophysical Techniques in Drug Discovery Book Review:

Biophysical techniques are used in many key stages of the drug discovery process including in screening for new receptor ligands, in characterising drug mechanisms, and in validating data from biochemical and cellular assays. This book provides an overview of the biophysical methods applied in drug discovery today, including traditional techniques and newer developments. Perspectives from academia and industry across a spectrum of techniques are brought together in a single volume. Small and biotherapeutic approaches are covered and strengths and limitations of each technique are presented. Case studies illustrate the application of each technique in real applied examples. Finally, the book covers recent developments in areas such as electron microscopy with discussions of their possible impact on future drug discovery. This is a go-to volume for biophysicists, analytical chemists and medicinal chemists providing a broad overview of techniques of contemporary interest in drug discovery.

Hydrogen Exchange Mass Spectrometry of Proteins

Hydrogen Exchange Mass Spectrometry of Proteins
Author: David D. Weis
Publsiher: John Wiley & Sons
Total Pages: 376
Release: 2016-01-11
ISBN 10: 1118703693
ISBN 13: 9781118703694
Language: EN, FR, DE, ES & NL

Hydrogen Exchange Mass Spectrometry of Proteins Book Review:

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.

Proteomics and Protein Protein Interactions

Proteomics and Protein Protein Interactions
Author: Gabriel Waksman
Publsiher: Springer Science & Business Media
Total Pages: 348
Release: 2005-12-21
ISBN 10: 9780387245317
ISBN 13: 0387245316
Language: EN, FR, DE, ES & NL

Proteomics and Protein Protein Interactions Book Review:

The rapidly evolving field of protein science has now come to realize the ubiquity and importance of protein-protein interactions. It had been known for some time that proteins may interact with each other to form functional complexes, but it was thought to be the property of only a handful of key proteins. However, with the advent of high throughput proteomics to monitor protein-protein interactions at an organism level, we can now safely state that protein-protein interactions are the norm and not the exception. Thus, protein function must be understood in the larger context of the various binding complexes that each protein may form with interacting partners at a given time in the life cycle of a cell. Proteins are now seen as forming sophisticated interaction networks subject to remarkable regulation. The study of these interaction networks and regulatory mechanism, which I would like to term "systems proteomics," is one of the thriving fields of proteomics. The bird-eye view that systems proteomics offers should not however mask the fact that proteins are each characterized by a unique set of physical and chemical properties. In other words, no protein looks and behaves like another. This complicates enormously the design of high-throughput proteomics methods. Unlike genes, which, by and large, display similar physico-chemical behaviors and thus can be easily used in a high throughput mode, proteins are not easily amenable to the same treatment. It is thus important to remind researchers active in the proteomics field the fundamental basis of protein chemistry. This book attempts to bridge the two extreme ends of protein science: on one end, systems proteomics, which describes, at a system level, the intricate connection network that proteins form in a cell, and on the other end, protein chemistry and biophysics, which describe the molecular properties of individual proteins and the structural and thermodynamic basis of their interactions within the network. Bridging the two ends of the spectrum is bioinformatics and computational chemistry. Large data sets created by systems proteomics need to be mined for meaningful information, methods need to be designed and implemented to improve experimental designs, extract signal over noise, and reject artifacts, and predictive methods need to be worked out and put to the test. Computational chemistry faces similar challenges. The prediction of binding thermodynamics of protein-protein interaction is still in its infancy. Proteins are large objects, and simplifying assumptions and shortcuts still need to be applied to make simulations manageable, and this despite exponential progress in computer technology. Finally, the study of proteins impacts directly on human health. It is an obvious statement to say that, for decades, enzymes, receptors, and key regulator proteins have been targeted for drug discovery. However, a recent and exciting development is the exploitation of our knowledge of protein-protein interaction for the design of new pharmaceuticals. This presents particular challenges because protein-protein interfaces are generally shallow and interactions are weak. However, progress is clearly being made and the book seeks to provide examples of successes in this area.