Insights Into the Structure, Dynamics and Interactions of Large Protein Complexes Using Structural Mass Spectrometry PDF Download

Author: Zainab Ahdash
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Author: M. Chance
Publisher: John Wiley & Sons
ISBN: 0470258861
Category : Science
Languages : en
Pages : 325

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Book Description
Presents a wide variety of mass spectrometry methods used to explore structural mechanisms, protein dynamics and interactions between proteins. Preliminary chapters cover mass spectrometry methods for examining proteins and are then followed by chapters devoted to presenting very practical, how-to methods in a detailed way. Includes footprinting and plistex specifically, setting this book apart from the competition.

Author: Igor A. Kaltashov
Publisher: John Wiley & Sons
ISBN: 0470937793
Category : Science
Languages : en
Pages : 312

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

Author: Eugen Netz
Publisher:
ISBN:
Category :
Languages : en
Pages : 0

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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: James Garrett Bonner
Publisher:
ISBN: 9780438897878
Category : Mass spectrometry
Languages : en
Pages : 107

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Specific factors scrutinized herein include a detailed understanding of participating electrostatic interactions within gas-phase peptides and proteins, as these are the most influential factors for the structures in the absence of intermolecular interactions. The exquisite precision afforded by action excitation energy transfer paired with molecular dynamics is used to probe local ion-dipole and ion-ion behavior in the absence of solvent versus partial solvation. Utilizing a newly developed technique termed photoelectron transfer dissociation, the prevalence of gaseous zwitterions are investigated. This particular coulombic interaction was chosen due to important structural implications being tied to their existence and the fact that little is currently known about their propensity to exist in the gas-phase. Efforts are also made to facilitate crosslinking analysis used for structural elucidation by incorporating 213 nm UVPD into the MS/MS workflow. Crosslink-specific fragmentation produces reporter ions able to drastically reduce search space allowing for confident identification and further insights into molecular structure. These and other experiments serve to better our understanding of protein structure and its stability outside of a native context.

Author: Hao Zhang
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages : 189

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Converting gene-sequence information into functional information about a protein is a major challenge of post-genomic biology. Proteins have a variety of functions from serving as catalysts to acting as structural components; all these functions are closely related to protein structure. The first step to understand protein function is often a structural study of that protein. Two major approaches, NMR spectroscopy and X-ray crystallography, can provide an atomic-level, 3D structural model of a protein. The applications of these high resolution approaches, however, are limited by protein size, conformational flexibility, and aggregation propensity. To obtain complementary structural information about proteins, a variety of approaches from traditional structural biology (e.g., circular dichroism, fluorescence spectroscopy) to new advances (e.g., computational prediction, protein footprinting) are required. Mass spectrometry (MS) has become an important tool for studying protein structure, dynamics, interactions, and function. In particular, detailed characterization of protein-ligand interactions is now possible, a critical step toward understanding biological function. Mass spectrometric analysis of protein structure can take two approaches. First, protein-ligand interactions can be probed by chemical labeling followed by MS analysis to determine the resulting mass shift (extent of labeling) and the location of the labeling. This approach in a titration format gives protein-ligand affinities. The labeling takes place in solution, where biochemistry occurs, and can be under physiological conditions, whereas the mass spectrometer is used for analysis typically by bottom-up proteomic strategies. In the other approach, protein assemblies can also be transferred directly into the gas phase and interrogated by MS to afford structural insights. One can view this is a top-down approach. The measurements refer to a gas-phase species, and that raises the question of whether the outcomes of the measurements have relevance to the structure and properties of proteins in solution or in a living system. Although there are differences in experimental format, results, and sensitivity between the two approaches of MS-based protein structural analysis, the similarity of those approaches must not be overlooked. All MS-based structural analyses rely heavily on the identification of peptides, purified protein species, or protein complexes. This analysis has been accelerated by the developments of MS instrumentation and methodology in protein analysis; the structural information provided by MS-based analysis is greatly facilitated by having a structural model of the protein. The integrated results from MS approaches, traditional structural biology approaches (e.g., NMR and X-ray), and computational modeling give more complete structural information of proteins than that from any one of the approaches alone. In the first part of thesis, we focus on the development and application of chemical-labeling methods (protein footprinting) in studies of protein conformation. In the second part, a combined top-down approach of native ESI and electron-capture dissociation (ECD) in FTICR MSis presented for structural studies of protein assemblies in the gas phase.

Author: Euan Pyle
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Author: Joseph A. Marsh
Publisher: Humana
ISBN: 9781493992775
Category : Science
Languages : en
Pages : 506

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This volume details the importance of multiple experimental techniques and computational methods needed to obtain the comprehensive picture of protein complex structure, dynamics and assembly afforded by the emerging field of integrative structural biology. Chapters guide readers through the broad spectrum of approaches required for a complete representation of protein complexes, including expression and purification, experimental characterization of structure and assembly, and computational methods for identifying protein complexes and modelling their assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein Complex Assembly: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Author: Nikolaos E. Labrou
Publisher: Humana
ISBN: 9781071601655
Category : Medical
Languages : en
Pages : 290

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This volume explores detailed methods and experimental protocols evaluating the effect of a compound or a mixture of compounds on the action of enzymes that are significant targets in pharmaceuticals. Consisting of three sections, the book delves into recent biocomputing and bioinformatics protocols, state-of-the art modern biophysical, electrophoretic, and chromatographic methods and high-throughput screening approaches, as well as detailed protocols and examples of the inhibition analysis and evaluation of selected enzymes. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Targeting Enzymes for Pharmaceutical Development: Methods and Protocols serves as a vital reference for academics and industry professionals working on expanding our understanding of the wide range of important enzyme targets.

Author: Bruce Alberts
Publisher:
ISBN: 9780815332183
Category : Cytology
Languages : en
Pages : 0

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