Structural Analysis Of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches

Download Structural Analysis Of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches full books in PDF, epub, and Kindle. Read online Structural Analysis Of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!

Structural Analysis of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches

Author : Jingshu Guo
Publisher :
ISBN 13 :
Total Pages : 405 pages
Book Rating : 4.:/5 (867 download)

DOWNLOAD NOW!

Book Synopsis Structural Analysis of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches by : Jingshu Guo

Download or read book Structural Analysis of Macromolecular Complexes Using Electrospray Ionization Mass Spectrometry Based Approaches written by Jingshu Guo and published by . This book was released on 2013 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) has become one of the most robust, reliable and widely used analytical techniques in scientific research due to factors like its speed of analysis, ease of operation, high sensitivity, and applicability to a broad range of analytes. The development of the so-called "soft" ionization methods electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) played a pivotal role in the application of MS to biochemical and biophysical fields enabling comprehensive studies of biomolecules, macromolecules and their complexes. This dissertation presents method development and the application of MS-based strategies for complete sequence and structure determination of hemoglobin (Hb); investigation of the interaction between human Hb and Band 3; characterization of the interaction between Alanyl-tRNA synthetase with tRNA and various ligands; and characterization of various thiol-protected silver nanoclusters. First, the complete primary amino acid sequences of hemoglobin from the endangered species snow leopard (Uncia uncia), Amur tiger (Panthera tigris altaica), Cheetah (Acinonyx jubatus) and Francois' Langur (Trachypithecus francoisi) were determined using a combination of the bottom-up approach to proteomics in combination with single crystal X-ray diffraction. In this approach, MS was used to provide on average 70% coverage of the sequences, which was used in refinement of the diffraction data. The electron density maps from the diffraction data were used to determine the parts of the sequences not covered by MS as well as differentiate between isomeric residues. During the refinement of the X-ray diffraction data, a unique conformational state, the Bform, for naturally occurring ligated hemoglobin was discovered in two feline Hbs. Structural comparisons and possible biological relevance for the B-form will be presented. The binding of human hemoglobin to synthetic peptides corresponding to the Hb-binding sites of human erythrocyte Band 3 is also presented. The effects on binding of ligation and oxidation state of normal human HbA; human sickle HbS; Hb-binding site and peptide length; and Band 3 N-terminal acetylation were investigated. The optimization of MS instrumental parameters and solution conditions for stabilizing and protecting labile thiol-protected silver nanoclusters through ionization, mass analysis and detection is presented. The relatively much more stable and well characterized gold-glutathione cluster Au25(SG)18 was used as a model for instrumental optimization (SG, glutathione). The most crucial instrumental parameters to protecting the clusters were cone gas flow rate, trap/transfer collision energy, and source temperature. Using these optimized parameters and adjustment of solution conditions led to the formula assignment for Ag32(SG)19, the species isolated from band 6 of a polyacrylamide gel electrophoretic separation. Using a similar approach the formula assignment for Ag44L30-4 (L, p-mercaptobenzoic acid) was confirmed. Collision induced dissociation (CID) studies were used to demonstrate that Ag43L28-3, another abundant species in the mass spectra was in fact a fragment of the intact cluster from the facile loss of AgL2-. CID and ion mobility mass spectrometry (IMMS) of Au25(SG)18, Ag32(SG)19, and Ag44L30-4 were used to gain insight into the surface structure and stability of the fragile silver clusters. Finally, the 3'-tRNA binding site on E. coli Alanyl-tRNA synthetase was identified by first crosslinking the 3'-periodate-oxidized tRNAala to the enzyme followed by the bottom-up MS sequencing. Modified lysine residues identified were 74, 526 585, 637, 739 and 648. Lys 74 was in the aminoacylation domain while 526 585, 637, 739 and 648 were in the editing domain. These results highlight an alteration of the 3'-terminal of tRNAala interaction with the enzyme. To study the stability ARS with various ligands, non-hydrolysable adenylate analogs, ASAd and GSAd, were used. Data shows that complete binding of ASAd and GSAd was achieved and that binding occurred in a 1:1 stoichiometry. Binding of ASAd, the analog of the cognate ligand, stabilizes the enzyme against changes in solution pH relative to the apo-enzyme and the enzyme with GSAd bound.

Protein Structures and Interactions Studied by Electrospray Mass Spectrometry

Author : Jiangjiang Liu
Publisher :
ISBN 13 :
Total Pages : 352 pages
Book Rating : 4.:/5 (16 download)

DOWNLOAD NOW!

Book Synopsis Protein Structures and Interactions Studied by Electrospray Mass Spectrometry by : Jiangjiang Liu

Download or read book Protein Structures and Interactions Studied by Electrospray Mass Spectrometry written by Jiangjiang Liu and published by . This book was released on 2013 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the emergence of electrospray ionization (ESI) mass spectrometry (MS) as a tool for protein structural studies, this area has experienced tremendous growth. ESI-MS is highly sensitive, and it allows the analysis of biological systems ranging in size from a few atoms to large multi-protein complexes. This work aims to solve questions in protein structural biology by using ESI-MS in conjunction with other techniques. We initially apply ESI-MS for studying the monomeric protein cytochrome c (Chapter 2). The physical reasons underlying the irreversible thermal denaturation of this protein remain controversial. By utilizing deconvoluted charge state distributions, oxidative modifications were found to be the major reason underlying the observed behavior. The positions of individual oxidation sites were identified by LC-MS/MS-based tryptic peptide mapping. Chapter 3 and 4 focus on noncovalent protein complexes. ESI allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these assemblies by MS. It remains somewhat unclear, however, in how far this approach is suitable for measuring binding affinities. We demonstrate that the settings used for rf-only quadrupoles in the ion path are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful Kd measurements. Overall, our data support the viability of the direct ESI-MS approach for determining binding affinities of protein-protein complexes in solution. Having established suitable conditions for the analysis of noncovalent protein complexes, ESI-MS is applied for monitoring the folding and assembly of hemoglobin (Hb). The native structure of this protein comprises four heme-bound subunits. Hb represents an important model system for exploring coupled folding/binding reactions, an area that remains difficult to tackle experimentally. We demonstrate that efficient Hb refolding depends on the heme ligation status. Only under properly optimized conditions is it possible to return denatured Hb to its tetrameric native state with high yield. ESI-MS allows the observation of on-pathway and off-pathway intermediates that become populated during this highly complex self-assembly process. In summary, this work demonstrates that ESI-MS is a highly versatile tool for addressing questions at the interface of chemistry and structural biology.

Differential Ion Mobility Spectrometry

Author : Alexandre A. Shvartsburg
Publisher : CRC Press
ISBN 13 : 9781420051070
Total Pages : 322 pages
Book Rating : 4.0/5 (51 download)

DOWNLOAD NOW!

Book Synopsis Differential Ion Mobility Spectrometry by : Alexandre A. Shvartsburg

Download or read book Differential Ion Mobility Spectrometry written by Alexandre A. Shvartsburg and published by CRC Press. This book was released on 2008-12-24 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last decade, scientific and engineering interests have been shifting from conventional ion mobility spectrometry (IMS) to field asymmetric waveform ion mobility spectrometry (FAIMS). Differential Ion Mobility Spectrometry: Nonlinear Ion Transport and Fundamentals of FAIMS explores this new analytical technology that separates and characterizes ions by the difference between their mobility in gases at high and low electric fields. It also covers the novel topics of higher-order differential IMS and IMS with alignment of dipole direction. The book relates the fundamentals of FAIMS and other nonlinear IMS methods to the physics of gas-phase ion transport. It begins with the basics of ion diffusion and mobility in gases, covering the main attributes of conventional IMS that are relevant to all IMS approaches. Building on this foundation, the author reviews diverse high-field transport phenomena that underlie differential IMS. He discusses the conceptual implementation and first-principles optimization of FAIMS as a filtering technique, emphasizing the dependence of FAIMS performance metrics on instrumental parameters and properties of ion species. He also explores ion reactions in FAIMS caused by field heating and the effects of inhomogeneous electric field in curved FAIMS gaps. Written by an accomplished scientist in the field, this state-of-the-art book supplies the foundation to understand the new technology of nonlinear IMS methods.

Development of Electrospray Ionization‐Mass Spectrometry for Analysis of Water Soluble and Membrane Proteins and Educational Protocols for an Analytical Chemistry Class

Download Development of Electrospray Ionization‐Mass Spectrometry for Analysis of Water Soluble and Membrane Proteins and Educational Protocols for an Analytical Chemistry Class PDF Online Free

Author : Wonhyeuk Jung
Publisher :
ISBN 13 :
Total Pages : 160 pages
Book Rating : 4.:/5 (128 download)

DOWNLOAD NOW!

Book Synopsis Development of Electrospray Ionization‐Mass Spectrometry for Analysis of Water Soluble and Membrane Proteins and Educational Protocols for an Analytical Chemistry Class by : Wonhyeuk Jung

Download or read book Development of Electrospray Ionization‐Mass Spectrometry for Analysis of Water Soluble and Membrane Proteins and Educational Protocols for an Analytical Chemistry Class written by Wonhyeuk Jung and published by . This book was released on 2021 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: Native mass spectrometry (MS) is a branch of MS analysis in which the structure of the target analytes of interest are kept intact and remaining in their "native" functional structure (as much as possible). This approach was made possible by the development of electrospray ionization (ESI), a soft ionization technique that does not fragment the target analyte during the ionization process while inducing multiple charging. The multiply charged biomolecules, in turn, can be subjected to fragmentation via collisional activation with a non-reactive gas such as nitrogen. This approach of combining native MS with fragmentation-based analysis, termed native topdown MS analysis, can be applied to large biomolecules such as membrane proteins to gain structural insights. Membrane proteins present unique challenges to conventional high-resolution structural techniques due to their hydrophobic nature. However, they are responsible for various physiological phenomena and account for 60% of known druggable targets in the cell. Thus, there is a need for an approach that can overcome issues with membrane protein analysis while complementing other biophysical techniques used to probe protein structure. Here, how native top-down MS can play this role is presented. The effects of non-ionic saccharide-based detergents, a commonly used class of detergents for membrane protein solubilization, on the resulting charge states of soluble proteins is investigated to gain insights into the mechanism of ESI. The MS-fragmentation patterns from collisionally activated dissociation of membrane proteins and membrane protein-lipid complexes are compared. How new insights into the lipid binding sites can be gained by detecting lipid-bound MS-fragments is presented. The result of the study indicates that native top-down MS analysis can provide unique structural insights for membrane proteins and their non-covalent interactions. When the analytical goal is to investigate the atomic composition of the target analyte, an ionization approach in which the sample is fully atomized before MS analysis is preferred instead. Inductively coupled plasma ionization, which atomizes and ionizes the sample via a plasma, can be coupled with MS analysis (ICP-MS) to quantify heavy metal contamination in complex samples. A protocol for ICP-MS analysis of commercial fish products for mercury contamination detection developed to aid an analytical chemistry class for instruction of undergraduate chemistry students is presented.

Electrospray Ionization and Collision Induced Dissociation Mass Spectrometric Quantitative Conjunctions with the Experimental Intensity of the Analyte Ions of Metal–Organics – Stochastic Dynamics

Download Electrospray Ionization and Collision Induced Dissociation Mass Spectrometric Quantitative Conjunctions with the Experimental Intensity of the Analyte Ions of Metal–Organics – Stochastic Dynamics PDF Online Free

Author : Bojidarka Ivanova
Publisher : GRIN Verlag
ISBN 13 : 3668918546
Total Pages : 218 pages
Book Rating : 4.6/5 (689 download)

DOWNLOAD NOW!

Book Synopsis Electrospray Ionization and Collision Induced Dissociation Mass Spectrometric Quantitative Conjunctions with the Experimental Intensity of the Analyte Ions of Metal–Organics – Stochastic Dynamics by : Bojidarka Ivanova

Download or read book Electrospray Ionization and Collision Induced Dissociation Mass Spectrometric Quantitative Conjunctions with the Experimental Intensity of the Analyte Ions of Metal–Organics – Stochastic Dynamics written by Bojidarka Ivanova and published by GRIN Verlag. This book was released on 2019-04-08 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research Paper (postgraduate) from the year 2019 in the subject Chemistry - Analytical Chemistry, University of Dortmund (Institute of Environmental Research, Department of Analytical Chemistry), language: English, abstract: Throughout the chapters in this book we argue that the temporal behaviour of the experimental mass spectrometric intensity of analyte ions obeys a certain and universal law based on a stochastic dynamic approach. The content of the book evidences convincingly through a selected series of examples to molecular systems of metal–organic complexes of transition metal ions with electronic configuration d10, for instance, AgI– and ZnII–ions, the validity of our model equation reported, more recently. It needs to be underlined that, the comprehensive study that is provided, herein, is published, for first time in the literature. The book, therefore, represents monograph containing results from our research work, detailing correlatively experimental and theoretical mass spectrometric analyses of metal–organics using ultrahigh accuracy electrospray ionization and collision induced dissociation mass spectrometry. An enormous amount of effort is concentrated on a quantitative description of the relationships between experimental measurable parameter “intensity” and diffusion or kinetic parameters of analyte ions.

Mass Spectrometry in Structural Biology and Biophysics

Author : Igor A. Kaltashov
Publisher : John Wiley & Sons
ISBN 13 : 0470937793
Total Pages : 312 pages
Book Rating : 4.4/5 (79 download)

DOWNLOAD NOW!

Book Synopsis Mass Spectrometry in Structural Biology and Biophysics by : Igor A. Kaltashov

Download or read book Mass Spectrometry in Structural Biology and Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2012-04-03 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Analyzing Biomolecular Interactions by Mass Spectrometry

Author : Jeroen Kool
Publisher : John Wiley & Sons
ISBN 13 : 3527334645
Total Pages : 402 pages
Book Rating : 4.5/5 (273 download)

DOWNLOAD NOW!

Book Synopsis Analyzing Biomolecular Interactions by Mass Spectrometry by : Jeroen Kool

Download or read book Analyzing Biomolecular Interactions by Mass Spectrometry written by Jeroen Kool and published by John Wiley & Sons. This book was released on 2015-05-04 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph reviews all relevant technologies based on mass spectrometry that are used to study or screen biological interactions in general. Arranged in three parts, the text begins by reviewing techniques nowadays almost considered classical, such as affinity chromatography and ultrafiltration, as well as the latest techniques. The second part focusses on all MS-based methods for the study of interactions of proteins with all classes of biomolecules. Besides pull down-based approaches, this section also emphasizes the use of ion mobility MS, capture-compound approaches, chemical proteomics and interactomics. The third and final part discusses other important technologies frequently employed in interaction studies, such as biosensors and microarrays. For pharmaceutical, analytical, protein, environmental and biochemists, as well as those working in pharmaceutical and analytical laboratories.

New Methods for the Study of Biomolecular Complexes

Author : W. Ens
Publisher : Springer Science & Business Media
ISBN 13 : 9780792350033
Total Pages : 376 pages
Book Rating : 4.3/5 (5 download)

DOWNLOAD NOW!

Book Synopsis New Methods for the Study of Biomolecular Complexes by : W. Ens

Download or read book New Methods for the Study of Biomolecular Complexes written by W. Ens and published by Springer Science & Business Media. This book was released on 1998-02-28 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: A NATO Advanced Research Workshop entitled New Methods for the Study of Molecular Aggregates was held at Tbe Lodge at Kananaskis Village, Alberta, Canada from 16 -20 June 1996. In fact the meeting was entirely concerned with the problem of analyzing biomolecular complexes, so the title of these proceedings has been altered to give a more precise description of the content. Tbe workshop was hosted by the time-of-flight group of the Department of Physics at the University of Manitoba, and was attended by 64 participants from around the world. '!\venty-one invited talks were given and 27 papers were presented as posters. Of the 48 contributions, 22 papers (12 orals, 10 posters) are included in these proceedings. Tbe subject of the conference was the investigation of noncovalent biomolecular complexes, with particular focus on the application of mass spectrometry to their characterization. '!\vo new ionization techniques introduced in the late 1980s, electrospray ionization (ES I) and matrix-assisted laser desorptionlionization (MALDI), resulted in a breakthrough in mass spectrometry, enabling its use in molecular weight and primary structure determination of biopolymers larger than 100 kDa. Recently it has been discovered that ESI mass spectrometry mayaiso be used to characterize complexes containing noncovalent interactions, thus opening new perspectives for supramolecular chemistry. ESI mass spectrometry has the advantage that the sampie is introduced from a homogenous solution which can be maintained at near physiological conditions of pR, concentration, and temperature.

Mass Spectrometry-based Structural Proteomics

Author : Hao Zhang
Publisher :
ISBN 13 :
Total Pages : 189 pages
Book Rating : 4.:/5 (758 download)

DOWNLOAD NOW!

Book Synopsis Mass Spectrometry-based Structural Proteomics by : Hao Zhang

Download or read book Mass Spectrometry-based Structural Proteomics written by Hao Zhang and published by . This book was released on 2011 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Development of Top-down Mass Spectrometry Methods for Structural Characterization of Protein Macromolecules Utilizing 193nm Ultraviolet Photodissociation

Download Development of Top-down Mass Spectrometry Methods for Structural Characterization of Protein Macromolecules Utilizing 193nm Ultraviolet Photodissociation PDF Online Free

Author : Michael B. Cammarata
Publisher :
ISBN 13 :
Total Pages : 322 pages
Book Rating : 4.:/5 (15 download)

DOWNLOAD NOW!

Book Synopsis Development of Top-down Mass Spectrometry Methods for Structural Characterization of Protein Macromolecules Utilizing 193nm Ultraviolet Photodissociation by : Michael B. Cammarata

Download or read book Development of Top-down Mass Spectrometry Methods for Structural Characterization of Protein Macromolecules Utilizing 193nm Ultraviolet Photodissociation written by Michael B. Cammarata and published by . This book was released on 2016 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dissertation will discuss the advancement of informative structural biology techniques utilizing a top-down centric workflow with 193nm ultraviolet photodissociation (UVPD) mass spectrometry. Native electrospray ionization is used to transport proteins to the gas phase in a native-like state, then UVPD is used for structural characterization to reveal ligand binding sites within a protein-ligand complex as well as detect conformational changes based upon the suppression or enhancement of backbone cleavages. Conformational changes induced by ligand exchange or removal and single amino acid mutations as well as combinations of the two (ligands and mutations) are investigated. The rich fragmentation patterns of UVPD are also used for structural characterization of crosslinked proteins. Typically these crosslinking experiments are performed by bottom-up mass spectrometry with has significant shortcomings. The main drawback is the need for proteolysis which cuts proteins into small peptides, thus increasing the complexity of the samples and its subsequent analysis. Additionally this proteolysis step loses the post-translation modification information or amino acid mutations that may be driving a specific protein-protein interaction. Top-down methods avoid protein digestion and thus are used to directly evaluate the protein interactions or protein complexes. These two methodologies will bring the mass spectrometry and structural biology community a step closer to the realization of high-throughput structural biology for proteins and their interactions with other proteins and small molecules.

Native Mass Spectrometry and Complementary Techniques to Characterize Biological Macromolecular Assemblies

Author : Andrew S. Norris
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (135 download)

DOWNLOAD NOW!

Book Synopsis Native Mass Spectrometry and Complementary Techniques to Characterize Biological Macromolecular Assemblies by : Andrew S. Norris

Download or read book Native Mass Spectrometry and Complementary Techniques to Characterize Biological Macromolecular Assemblies written by Andrew S. Norris and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The structures adopted by biological macromolecules and macromolecular complexes are directly tied to their function. By better understanding the relationship between structure and function of biomolecules, lifesaving and life-changing interventions can be designed such as small molecule inhibitors of viral enzymes. Characterization of macromolecules with high-resolution structural techniques has greatly improved our fundamental understanding of how structures dictate function. High-resolution structural techniques including x-ray crystallography, cryo-electron microscopy, and nuclear magnetic resonance spectroscopy, however, have many challenges and so they require complementary techniques. Native mass spectrometry is one such technique that can be used to interrogate macromolecular assemblies and accurately determine molecular weight(s), oligomeric state(s), ligand-binding, and topology of the assembly. Native mass spectrometry has the advantage of not being limited by some of the common issues encountered by high-resolution techniques like molecular flexibility and sample heterogeneity that can limit resolution attainable or prevent structure determination altogether. This attribute is particularly valuable for the characterization of protein-nucleic acid complexes that have proven to be some of the more challenging complexes for high-resolution techniques. Throughout this work, native mass spectrometry is emphasized as a clear approach for examining differences in macromolecular assemblies that highlight the structural diversity of macromolecular systems which would otherwise not be evident. Chapter 3 describes identification of the physiological protein interface of a plant protein, BX1.This approach demonstrates the use of native mass spectrometry and covalent cross-linking mass spectrometry to solve a common issue with X-ray crystallography, namely artificial protein contacts formed during the crystallization process. Chapter 4 describes the investigation of the assembly pathway for RNase P, a multi-subunit archaeal ribonucleoprotein. Additionally, native mass spectrometry addresses the absence of a protein subunit in the cryo-EM structure of the same RNase P. Chapter 5 describes the investigation of the different assembly states of DNA annealing proteins. A cryo-EM reconstruction of a section of one of the protein-DNA complexes was determined. For this protein, native mass spectrometry complemented the cryo-EM study by determining the composition of the entire complex. With the native mass spectrometry assembly data for DNA annealing proteins and the cryo-EM for one of these proteins, proposed revisions to the current model of single-strand annealing are presented. Finally, in Chapter 6, cooperative ligand binding of three cyclic homo-oligomers is reported and a cooperative binding model, the nearest-neighbor model, was used to fit the data to quantitively determine thermodynamic parameters. RNA binding was also tested, but work is still ongoing. Overall, the work presented herein demonstrates the use of native mass spectrometry to study the assembly states of macromolecular complexes and hereby gain insights not easily accessible by other structural techniques.

Ion Mobility Spectrometry

Author : G.A. Eiceman
Publisher : CRC Press
ISBN 13 : 1420038974
Total Pages : 367 pages
Book Rating : 4.4/5 (2 download)

DOWNLOAD NOW!

Book Synopsis Ion Mobility Spectrometry by : G.A. Eiceman

Download or read book Ion Mobility Spectrometry written by G.A. Eiceman and published by CRC Press. This book was released on 2005-06-23 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: Key Developments for Faster, More Precise Detection Capabilities Driven by the demand for the rapid and advanced detection of explosives, chemical and biological warfare agents, and narcotics, ion mobility spectrometry (IMS) undergone significant refinements in technology, computational capabilities, and understanding of the principles of gas phase

Applied Electrospray Mass Spectrometry

Author : Birendra N. Pramanik
Publisher : CRC Press
ISBN 13 : 0824744195
Total Pages : 407 pages
Book Rating : 4.8/5 (247 download)

DOWNLOAD NOW!

Book Synopsis Applied Electrospray Mass Spectrometry by : Birendra N. Pramanik

Download or read book Applied Electrospray Mass Spectrometry written by Birendra N. Pramanik and published by CRC Press. This book was released on 2002-02-28 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discussing strategies to determine the structure and machanisms of numerous compound classics, this book covers new chemical and elctrophoretic techniques for rapid sample preconcentration and separation. It summarizes breakthroughs in the theory and instrumentation of electrospray mass spectrometry in pharmaceutical and biomedical applications, provides practical examples for the characterization of peptides, proteins, and glycoproteins, includes applications in proteomics, combinatorial chemistry, and drug characterization. Topics include chemical and electrophoretic techniques for rapid sample preconcentration and separation, screening processes for proteins from libraries of compounds, protein folding and dynamics, and more.

Novel Analytical Methods for Examining Biomolecular Complexes Using Electrospray Ionization Mass Spectrometry

Author : Tawnya Grace Flick
Publisher :
ISBN 13 :
Total Pages : 344 pages
Book Rating : 4.:/5 (839 download)

DOWNLOAD NOW!

Book Synopsis Novel Analytical Methods for Examining Biomolecular Complexes Using Electrospray Ionization Mass Spectrometry by : Tawnya Grace Flick

Download or read book Novel Analytical Methods for Examining Biomolecular Complexes Using Electrospray Ionization Mass Spectrometry written by Tawnya Grace Flick and published by . This book was released on 2012 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Several analytical strategies and investigations are presented in this dissertation to improve the quantification, sensitivity, and structural information that can be obtained for gaseous biomolecular ions in electrospray ionization (ESI) mass spectrometry (MS) experiments. Internal or external standards are commonly employed to quantify molecules in complex mixtures because molecular ion abundances cannot be directly related to the concentration of the molecules in solution. A new standard-free quantitation method is used to obtain the relative concentrations of components in a mixture using the abundances of large, nonspecific clusters formed by ESI. Large non-covalent clusters overcome differences in ionization efficiencies between molecules, and are representative of the solution-phase mixture. The sensitivity in MS experiments can be significantly lowered by the presence of high concentrations of salts in the ESI solution because nonspecific ion adduction to biomolecules distributes ion signal into different forms with various numbers of adducts. Studies here demonstrate the extent of both sodium ion and acid molecule adduction to proteins are inversely related, and both depend significantly on the proton affinity of the anion in the ESI solution. Several solution-phase additives that contain anions with low proton affinity values are shown to effectively desalt protein ions generated by ESI, which should result in improved detection limits, more accurate mass measurements, and improved tandem MS sensitivity. Additionally, a solution-phase additive (HClO4) is discovered that can be used to count the number of basic sites accurately in peptides and proteins based on the number of HClO4 adducts to low charge states. High charge states of peptides and proteins can be readily formed by ESI of aqueous solutions that contain trivalent metal ions, and fragmentation of these trivalent metal ion-peptide or protein complexes by electron capture dissociation can be used to increase the structural information obtained from these experiments. Metal ion-biomolecule interactions are ubiquitous in nature where they play a role in many biological processes. Here, nonspecific metal ion adduction to protein cation and anions is shown to result in more compact conformations compared to the bare protein ion, likely a result of salt-bridge interactions between the metal ion and the biomolecule.

Biophysical Characterization of Proteins in Developing Biopharmaceuticals

Author : Damian J. Houde
Publisher : Elsevier
ISBN 13 : 0444641742
Total Pages : 586 pages
Book Rating : 4.4/5 (446 download)

DOWNLOAD NOW!

Book Synopsis Biophysical Characterization of Proteins in Developing Biopharmaceuticals by : Damian J. Houde

Download or read book Biophysical Characterization of Proteins in Developing Biopharmaceuticals written by Damian J. Houde and published by Elsevier. This book was released on 2019-11-13 with total page 586 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Electrospray and MALDI Mass Spectrometry

Author : Richard B. Cole
Publisher : John Wiley & Sons
ISBN 13 : 1118211553
Total Pages : 900 pages
Book Rating : 4.1/5 (182 download)

DOWNLOAD NOW!

Book Synopsis Electrospray and MALDI Mass Spectrometry by : Richard B. Cole

Download or read book Electrospray and MALDI Mass Spectrometry written by Richard B. Cole and published by John Wiley & Sons. This book was released on 2011-09-26 with total page 900 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover how advances in mass spectrometry are fueling new discoveries across a broad range of research areas Electrospray and MALDI Mass Spectrometry brings both veteran practitioners and beginning scientists up to date with the most recent trends and findings in electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. In particular, this Second Edition highlights how advances in electrospray and MALDI mass spectrometry are supporting important discoveries in new and emerging fields such as proteomics and metabolomics as well as in traditional areas of chemistry and physics research. Electrospray AND MALDI Mass Spectrometry, SECOND EDITION is divided into five parts: Part A, Fundamentals of ES, explains the fundamental phenomena underlying the electrospray process, including selectivity in ionization and inherent electrochemistry, and concludes with a chapter offering a comparative inventory of source hardware Part B, Fundamentals of MALDI, confronts ionization mechanisms, instrument development, and matrix selection, and includes a final chapter that explores the special application of MALDI to obtain two-dimensional images of spatial distributions of compounds on surfaces Part C, ES and MALDI Coupling to Mass Spectrometry Instrumentation, examines the coupling of these ionization techniques to various mass analyzers, including quadrupole ion trap, time-of-flight, Fourier transform ion cyclotron resonance, and ion mobility mass spectrometers Part D, Practical Aspects of ES and MALDI, investigates analytical issues including quantification, charge-state distributions, noncovalent interactions in solution that are preserved as gas-phase ions, and various means of ion excitation in preparation for tandem mass spectrometry, and offers a guide to the interpretation of even-electron mass spectra Part E, Biological Applications of ES and MALDI, examines the role of mass spectrometry in such areas as peptide and protein characterization, carbohydrate analysis, lipid analysis, and drug discovery Written by a team of leading experts, the book not only provides a critical review of the literature, but also presents key concepts in tutorial fashion to help readers take full advantage of the latest technological breakthroughs and applications. As a result, Electrospray and MALDI Mass Spectrometry will help researchers fully leverage the power of electrospray and MALDI mass spectrometry. The judicious compartmentalization of chapters, and the pedagogic presentation style throughout, render the book highly suitable for use as a text for graduate-level courses in advanced mass spectrometry.

Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics

Author : M. Chance
Publisher : John Wiley & Sons
ISBN 13 : 0470258861
Total Pages : 325 pages
Book Rating : 4.4/5 (72 download)

DOWNLOAD NOW!

Book Synopsis Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics by : M. Chance

Download or read book Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics written by M. Chance and published by John Wiley & Sons. This book was released on 2008-09-22 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.