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Author : Xudong Huang
Publisher :
ISBN 13 :
Total Pages : 196 pages
Book Rating : 4.:/5 (23 download)
Download or read book Probing Protein Conformation by Chemical Cross-linking and Mass Spectrometry written by Xudong Huang and published by . This book was released on 2004 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Bingqing Zhao (Bioanalytical chemist)
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.5/5 (16 download)
Download or read book Advancing Chemical Cross-linking Mass Spectrometry for Protein Structure and Interaction Analysis written by Bingqing Zhao (Bioanalytical chemist) and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking mass spectrometry elucidates protein structures and protein-protein interactions by establishing distance constraints between residues pairs. Interpreting the mass spectra of covalently linked peptide pairs is more challenging than identifying peptides in proteomics. This dissertation presents improvements in methodology for identifying cross-linked peptides and their application to probing protein interacting surfaces.
Author : Kevin Downard
Publisher : John Wiley & Sons
ISBN 13 : 047014632X
Total Pages : 153 pages
Book Rating : 4.4/5 (71 download)
Download or read book Mass Spectrometry of Protein Interactions written by Kevin Downard and published by John Wiley & Sons. This book was released on 2007-08-24 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authoritative guide to analyzing protein interactions by mass spectrometry Mass spectrometry (MS) is playing an increasingly important role in the study of protein interactions. Mass Spectrometry of Protein Interactionspresents timely and definitive discussions of the diverse range of approaches for studying protein interactions by mass spectrometry with an extensive set of references to the primary literature. Each chapter is written by authors or teams of authors who are international authorities in their fields. This leading reference text: * Discusses the direct detection of protein interactions through electrospray ionization (ESI-MS); ion mobility analysis; and matrix-assisted laser desorption/ionization (MALDI-MS) * Covers the indirect analysis of protein interactions through hydrogen-deuterium exchange (HX-MS); limited proteolysis; cross-linking; and radial probe (RP-MS) * Guides researchers in the use of mass spectrometry in structural biology, biochemistry, and protein science to map and define the huge number and diversity of protein interactions * Reviews the latest discoveries and applications and addresses new and ongoing challenges This is a comprehensive reference for researchers in academia and industry engaged in studies of protein interactions and an excellent text for graduate and postgraduate students.
Author : Eugen Netz
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (14 download)
Download or read book Improved Cross-linking Mass Spectrometry Algorithms for Probing Protein Structures and Interactions written by Eugen Netz and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the most active molecules in living bodies. They catalyze chemical reactions, provide structural support for cells and allow organisms to move. Their function is intrinsically linked to their folded structure. Resolving the structures of proteins and protein complexes is crucial for our understanding of basic biological processes and diseases. Cross-Linking Mass Spectrometry (XL-MS) is a method to gain structural insights into protein complexes. The field of XL-MS data analysis software is not yet as established as many other methods in proteomics. XL-MS analysis software has significant room for improvement in terms of sensitivity, efficiency and standardization of file formats and workflows to facilitate interoperability and reproducibility. In this thesis we present a new XL-MS search engine, OpenPepXL. We develop an algorithm that scores all candidate cross-linked peptide pairs and is efficient enough to be used on a standard desktop PC for most applications. OpenPepXL supports the standardized XL-MS identification file format defined as a part of the MzIdentML 1.2 specifications that were developed in collaboration with the Proteomics Standards Initiative. We benchmark OpenPepXL against other state-of-the-art XL-MS identification tools on multiple datasets that allow cross-link validation through structures or other means. We show that our exhaustive approach, although not the quickest one, is superior in sensitivity to other tools. We suggest this is due to some tools improving their processing time by discarding too many candidates in early steps of the data analysis. We apply XL-MS analysis with OpenPepXL to multiple protein complexes related to meiosis and the type III secretion system. The first project involved several proteins with unknown structures, some of which are expected to be at least partially intrinsically disordered and therefore difficult to investigate using most traditional structural research methods. Unfortunately, we could not find cross-links between the interaction sites we were interested in the most, but we were able to identify many others in these complexes and gained some structural insights. In the second project we used the photo-cross-linking amino acid pBpa to test very specific hypotheses about interactions within the type III secretion system. We were not able to gain any new structural information yet. However, we could confirm that this is a viable approach. It is possible to identify cross-links between a pBpa residue incorporated into a protein sequence and a residue it cross-links to on a residue level resolution.
Author : David D. Weis
Publisher : John Wiley & Sons
ISBN 13 : 1118703731
Total Pages : 376 pages
Book Rating : 4.1/5 (187 download)
Download or read book Hydrogen Exchange Mass Spectrometry of Proteins written by David D. Weis and published by John Wiley & Sons. This book was released on 2016-01-12 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Andreas Kukol
Publisher : Humana Press
ISBN 13 : 9781493954919
Total Pages : 474 pages
Book Rating : 4.9/5 (549 download)
Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Author : W. Andy Tao
Publisher : John Wiley & Sons
ISBN 13 : 1118970217
Total Pages : 448 pages
Book Rating : 4.1/5 (189 download)
Download or read book Mass Spectrometry-Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-10 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.
Author : Chhabil Dass
Publisher : John Wiley & Sons
ISBN 13 : 0470118482
Total Pages : 512 pages
Book Rating : 4.4/5 (71 download)
Download or read book Fundamentals of Contemporary Mass Spectrometry written by Chhabil Dass and published by John Wiley & Sons. This book was released on 2007-05-11 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern mass spectrometry - the instrumentation and applications in diverse fields Mass spectrometry has played a pivotal role in a variety of scientific disciplines. Today it is an integral part of proteomics and drug discovery process. Fundamentals of Contemporary Mass Spectrometry gives readers a concise and authoritative overview of modern mass spectrometry instrumentation, techniques, and applications, including the latest developments. After an introduction to the history of mass spectrometry and the basic underlying concepts, it covers: Instrumentation, including modes of ionization, condensed phase ionization techniques, mass analysis and ion detection, tandem mass spectrometry, and hyphenated separation techniques Organic and inorganic mass spectrometry Biological mass spectrometry, including the analysis of proteins and peptides, oligosaccharides, lipids, oligonucleotides, and other biological materials Applications to quantitative analysis Based on proven teaching principles, each chapter is complete with a concise overview, highlighted key points, practice exercises, and references to additional resources. Hints and solutions to the exercises are provided in an appendix. To facilitate learning and improve problem-solving skills, several worked-out examples are included. This is a great textbook for graduate students in chemistry, and a robust, practical resource for researchers and scientists, professors, laboratory managers, technicians, and others. It gives scientists in diverse disciplines a practical foundation in modern mass spectrometry.
Author : Haruki Nakamura
Publisher : Springer
ISBN 13 : 9811322007
Total Pages : 272 pages
Book Rating : 4.8/5 (113 download)
Download or read book Integrative Structural Biology with Hybrid Methods written by Haruki Nakamura and published by Springer. This book was released on 2019-01-08 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.
Author : Joseph S. Schoeniger
Publisher :
ISBN 13 :
Total Pages : 60 pages
Book Rating : 4.:/5 (316 download)
Download or read book Chemical Crosslinking and Mass Spectrometry Studies of the Structure and Dynamics of Membrane Proteins and Receptors written by Joseph S. Schoeniger and published by . This book was released on 2005 with total page 60 pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.
Author : Timothy D. Veenstra
Publisher : John Wiley & Sons
ISBN 13 : 0470007737
Total Pages : 361 pages
Book Rating : 4.4/5 (7 download)
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Greg T. Hermanson
Publisher : Academic Press
ISBN 13 : 0080568726
Total Pages : 1233 pages
Book Rating : 4.0/5 (85 download)
Download or read book Bioconjugate Techniques written by Greg T. Hermanson and published by Academic Press. This book was released on 2010-07-26 with total page 1233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioconjugate Techniques, 2nd Edition, is the essential guide to the modification and cross linking of biomolecules for use in research, diagnostics, and therapeutics. It provides highly detailed information on the chemistry, reagent systems, and practical applications for creating labeled or conjugate molecules. It also describes dozens of reactions with details on hundreds of commercially available reagents and the use of these reagents for modifying or cross linking peptides and proteins, sugars and polysaccharides, nucleic acids and oligonucleotides, lipids, and synthetic polymers. A one-stop source for proven methods and protocols for synthesizing bioconjugates in the lab Step-by-step presentation makes the book an ideal source for researchers who are less familiar with the synthesis of bioconjugates More than 600 figures that visually describe the complex reactions associated with the synthesis of bioconjugates Includes entirely new chapters on the latest areas in the field of bioconjugation as follows: Microparticles and nanoparticlesSilane coupling agentsDendrimers and dendronsChemoselective ligationQuantum dotsLanthanide chelatesCyanine dyesDiscrete PEG compoundsBuckyballs,fullerenes, and carbon nanotubesMass tags and isotope tagsBioconjugation in the study of protein interactions
Author : Katrin Marcus
Publisher : Humana Press
ISBN 13 : 9781617798849
Total Pages : 539 pages
Book Rating : 4.7/5 (988 download)
Download or read book Quantitative Methods in Proteomics written by Katrin Marcus and published by Humana Press. This book was released on 2012-06-08 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the “hot” topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.
Author : Shan S. Wong
Publisher : CRC Press
ISBN 13 : 9780849358869
Total Pages : 360 pages
Book Rating : 4.3/5 (588 download)
Download or read book Chemistry of Protein Conjugation and Cross-Linking written by Shan S. Wong and published by CRC Press. This book was released on 1991-06-18 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking reagents have attained great practical use in industry as well as in basic research, and an understanding of their fundamental principles of reaction is paramount to their applications. With broad coverage of the development and application of these reagents, Chemistry of Protein Conjugation and Cross-Linking discusses the mechanism of reaction and allows you to put the theory into practice. The book offers an explanation of the underlying mechanism of chemical modification, surveys all the bifunctional reagents used in bioconjugation and cross-linking, and provides a review of practical applications of these reagents in various areas of biochemistry, molecular biology, biotechnology, nucleic acid chemistry, immunochemistry, and diagnostic and biomedical disciplines. It contains numerous examples and illustrations, plus step-by-step explanations to reaction procedures. It is an excellent introduction and a comprehensive reference about chemical modification.
Author : Roland F. Rivera-Santiago
Publisher :
ISBN 13 :
Total Pages : 226 pages
Book Rating : 4.:/5 (951 download)
Download or read book Application and Refinement of a Zero-length Chemical Cross-linking and Mass Spectrometry Method to Examine Native Protein Structures written by Roland F. Rivera-Santiago and published by . This book was released on 2015 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical cross-linking and mass spectrometry (CX-MS) is a structural technique that has been gaining in popularity with the advent of instruments that provide increased access to high-resolution MS/MS data. The Speicher laboratory is interested in zero-length cross-links, which provide the highest-quality data, but are the most difficult to identify and analyze. A MS sample preparation and data analysis pipeline, including a software package called ZXMiner, has been developed to collect and analyze zero-length CX-MS data to use in molecular modeling experiments. I used this pipeline to examine the peroxiredoxin-6 (PRDX6) enzyme, which prevents oxidative damage in the lung. I found the identified cross-links did not fit the published crystal structure of a catalytic intermediate, which suggests PRDX6 undergoes conformational changes as part of catalysis. A solution structure of PRDX6 was created using this CX-MS data. Next, I performed optimization experiments in order to adapt the ZXMiner data analysis pipeline from the LTQ Orbitrap XL instrument it was created for to a more state-of-the-art Q Exactive Plus instrument in order to expand its ability to probe complex samples. Combined with a new version of ZXMiner, I was able to determine several parameters that improved the quality of cross-link data for erythrocyte membrane white ghost (WG) samples. I combined the cross-links identified in those samples with immunoprecipitation experiments and review of the pertinent literature to determine a topology model for the anion exchanger 1 (AE1) protein, which plays critical roles in CO2 transport and the erythrocyte membrane skeleton. Using this topology model and published crystal structures for the N-terminal domain of AE1, I was able to perform combinatorial modeling experiments which resulted in a model of the full-length protein that resolved several controversies in the field. These results show that zero-length CX-MS is a powerful technique to determine structural information of proteins difficult to interrogate through conventional means.
Author : Harald Tschesche
Publisher : Walter de Gruyter
ISBN 13 : 3110252368
Total Pages : 379 pages
Book Rating : 4.1/5 (12 download)
Download or read book Methods in Protein Biochemistry written by Harald Tschesche and published by Walter de Gruyter. This book was released on 2011-12-23 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a survey of recent developments in protein biochemistry. Top researchers in the field of protein biochemistry describe modern methods to address the challenges of protein purification by three-phase partitioning, and their folding and degradation by the functions of chaperones. The significance of peptide purity for fibril formation is addressed as well as the use of target oriented peptide arrays in palliative approaches in mucoviszidose. The design and application of protein epitope mimetics just as the structural resolving of the misfolding of various mutant proteins in serpinopathies enlarge our tools in resolving pathophysiological imbalances.
Author : Igor A. Kaltashov
Publisher : John Wiley & Sons
ISBN 13 : 0471705160
Total Pages : 320 pages
Book Rating : 4.4/5 (717 download)
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.
