Download or read book Structural Mass Spectrometry Analysis of RNA Chaperones and Protein Therapeutics written by Kerene Andrea Brown and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the advent of soft ionization techniques, most notably electrospray ionization (ESI), the application of mass spectrometry (MS) analysis has expanded to intact biomolecules. ESI-MS gave rise to the field of structural MS (a relatively new tool in structural biology) which involves different types of MS techniques such as: Native, Ion Mobility, chemical labelling and proteomics. Conventional techniques such as Nuclear Magnetic Resonance (NMR) and X-ray crystallography provide high resolution structures of proteins. Although MS cannot provide the same level of resolution, it provides important structural information such as: binding stoichiometry, mass, size, subunit composition, ligand binding sites, stability, amino acid sequence and post-translational modifications (PTMs). In this work, structural MS was employed as a tool in the characterization of a crucial RNA chaperone, human La (hLa) protein, that is implicated in the processing of various types of cellular and viral RNAs. Many RNA chaperones such as hLa have large unstructured regions which make them difficult to study on a structural basis. Work done here revealed that the C-terminal domain (CTD) of hLa plays a role in binding RNA and that it binds structured and unstructured RNA using distinct dynamic modes. In addition, work was done to support a previous hypothesis about the presence of an interdomain interaction in hLa that affects nuclear trafficking and RNA binding. Additionally, the same structural MS techniques were used to assess the biosimilarity between a biological drug, Avastin, and its biosimilar in pre-clinical development. Work was done to test the structural similarity between the two drugs and the batch-to-batch variability of the biosimilar. Structural MS proved to be an effective technique in the rapid and facile characterization of biosimilarity and in the analysis of RNA binding activity of RNA chaperones.
Download or read book Characterization of Protein Therapeutics using Mass Spectrometry written by Guodong Chen and published by Springer Science & Business Media. This book was released on 2014-07-08 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights current approaches and future trends in the use of mass spectrometry to characterize protein therapies. As one of the most frequently utilized analytical techniques in pharmaceutical research and development, mass spectrometry has been widely used in the characterization of protein therapeutics due to its analytical sensitivity, selectivity, and specificity. This book begins with an overview of mass spectrometry techniques as related to the analysis of protein therapeutics, structural identification strategies, quantitative approaches, followed by studies involving characterization of process related protein drug impurities/degradants, metabolites, higher order structures of protein therapeutics. Both general practitioners in pharmaceutical research and specialists in analytical sciences will benefit from this book that details step-by-step approaches and new strategies to solve challenging problems related to protein therapeutics research and development.
Download or read book Characterization of RNA and RNA protein Complexes by Native Mass Spectrometry written by Samantha H. Sarni and published by . This book was released on 2020 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein-nucleic acid interactions are paramount for maintaining cellular homeostasis. Characterization of protein-nucleic acid complexes by high-resolution structural biology methods remains a challenge due to intrinsic structural and chemical heterogeneity. Native mass spectrometry (nMS) is a powerful bioanalytical tool for the investigation of proteins and protein complexes; however, it has only sparingly been implemented in the analysis of protein -nucleic acid complexes. This dissertation describes the application of native mass spectrometry to the analysis of RNA and RNA-protein complexes. Chapters 2 and 3 describe the characterization of the stoichiometry of the HIV-1 viral assembly nucleation complex. Using nMS, it was revealed that Gag specifically dimerizes in the presence of RNA containing the HIV-1 packaging signal (Psi), while other RNAs are bound primarily to monomeric Gag. Further investigations focused on the effect of transcription start site heterogeneity on the dimerization of the HIV-1 genomic RNA 5′ untranslated region (5′UTR), and stoichiometry. It was observed that 5′UTRs that begin with a single guanosine preferentially dimerize and are bound by Gag. Chapter 4 focuses on the characterization of a gas-phase separation method (ion mobility) as a structural biology tool for RNA. The effect of magnesium during RNA folding, solution temperature, ionization polarity, and collisional activation on the collision cross section of tRNAPhe were probed. It was observed that magnesium is essential for the folding and stability of tRNAPhe, consistent with previous reports. The collision cross sections (CCS) of tRNAPhe were compared in both positive and negative ionization polarities. The CCS of tRNAPhe refolded in under folding conditions was lower in negative mode relative to positive mode. It was observed that the CCS of WT tRNAPhe was not affected by the solution temperatures tested, however the CCS of a mutant (MT) tRNAPhe, that has a perturbed tertiary interaction network, increased as a function of solution temperature. Furthermore, we also probed the stability of these RNAs using collision-induced unfolding and it was observed that the wild-type RNA underwent collision-induced collapse while the mutant tRNA collapsed to a lesser extent. Lastly, a small dimeric RNA-RNA complex (HJ3) was used to determine whether RNA quaternary structure is preserved upon transfer to the gas phase. The intact dimer was observed in the gas-phase, and surface-induced dissociation was identified as an effective method for probing the stoichiometry and of RNA-RNA complexes. Chapter 5 describes the characterization of Hfq-RNA complex stability and subunit connectivity by surface-induced dissociation and ion mobility. It was observed that the intrinsically disordered C-terminal domains greatly stabilize Hfq. RNA-binding to Hfq destabilizes the wild-type protein yet stabilizes a protein that lacks C-terminal domains. The dissociation products observed for RNA-bound wild-type and the mutant Hfq were remarkably similar, suggesting that the C-terminal domains do not alter the RNA binding interfaces.
Download or read book Structural Investigation of Protein RNA Assemblies by Mass Spectrometry written by Romina Hofele and published by . This book was released on 2014 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Novel Mass Spectrometry Methods for the Analysis of Covalent and Non covalent Protein Structures and Their Influence on the Functions of Therapeutic Proteins written by Jake Pawlowski and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Biotherapeutics consist of biopolymers (proteins, polysaccharides, DNA, and RNA) that are used to treat a wide range of conditions from cancer to autoimmune disease to enzyme replacement. In recent years biotherapeutics have experience tremendous growth due to advances in technology and our understanding of human biology. They are very important to modern medicine due to their ability to treat diseases which are unable to be treated with small molecule-based drugs. Unlike small molecule drugs which are synthetically produced, biotherapeutics are expressed inside cells. Produced biotherapeutics are not made up of a single homogenous population but instead a population of highly similar variants. The source of these variations are enzymatic and non-enzymatic post-translational modifications. By characterizing these modification, a profile is built that links the in vivo response of a drug to its modifications. The complexity and size of these biopolymers makes their characterization very challenging and demands the development of robust analytical techniques. Mass spectrometry- and liquid chromatography-base methods are an integral part of protein characterization. Mass spectrometry provides accurate mass measurements that are invaluable for confirming the identity of a protein and any modifications. Additionally, mass spectrometry is used to assess a protein's higher order structure. Liquid chromatography is a very powerful tool that allows for different post-translational modified populations of a biotherapeutic sample to separate by their chemical or physical properties. Separated populations can further be characterized to identify and analyze their chemical or structural composition. The presented work utilized a blend of mass spectrometry and liquid chromatography methods to characterize proteins with biotherapeutic potential.
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Chaperones written by Tilman Heise and published by . This book was released on 2020 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. 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 practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com.
Download or read book Protein Structure Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Protein Structure Analysis - Preparation and Characterization" is a compilation of practical approaches to the structural analysis of proteins and peptides. Here, about 20 authors describe and comment on techniques for sensitive protein purification and analysis. These methods are used worldwide in biochemical and biotechnical research currently being carried out in pharmaceu tical and biomedical laboratories or protein sequencing facilities. The chapters have been written by scientists with extensive ex perience in these fields, and the practical parts are well documen ted so that the reader should be able to easily reproduce the described techniques. The methods compiled in this book were demonstrated in student courses and in the EMBO Practical Course on "Microsequence Analysis of Proteins" held in Berlin September 10-15, 1995. The topics also derived from a FEBS Workshop, held in Halkidiki, Thessaloniki, Greece, in April, 1995. Most of the authors participated in these courses as lecturers and tutors and made these courses extremely lively and successful. Since polypeptides greatly vary depending on their specific structure and function, strategies for their structural analysis must for the most part be adapted to each individual protein. Therefore, advantages and limitations of the experimen tal approaches are discussed here critically, so that the reader becomes familiar with problems that might be encountered.
Download or read book RNA protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Download or read book Cryo EM Part A Sample Preparation and Data Collection written by and published by Academic Press. This book was released on 2010-09-30 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-EM Part A: Sample Preparation and Data Collection is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. Includes time-tested core methods and new innovations applicable to any researcher Methods included are useful to both established researchers and newcomers to the field Relevant background and reference information given for procedures can be used as a guide
Download or read book Advancements of Mass Spectrometry in Biomedical Research written by Alisa G. Woods and published by Springer. This book was released on 2019-07-25 with total page 813 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease, and psychiatry. Additional chapters focus on methodology, technologies and instrumentation, as well as on analysis of protein-protein interactions, protein quantitation, and protein post-translational modifications. Various omics fields such as proteomics, metabolomics, glycomics, lipidomics, and adductomics are also covered. Applications of mass spectrometry in biotechnological and pharmaceutical industry are also discussed. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research, but also to initiate and improve their own work. This book acts as a technical guide as well as a conceptual guide to the newest information in this exciting field.
Download or read book Macromolecular Protein Complexes III Structure and Function written by J. Robin Harris and published by Springer Nature. This book was released on 2020-11-30 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers important topics such as the dynamic structure and function of the 26S proteasome, the DNA replication machine: structure and dynamic function and the structural organization and protein–protein interactions in the human adenovirus capsid, to mention but a few. The 18 chapters included here, written by experts in their specific field, are at the forefront of scientific knowledge. The impressive integration of structural data from X-ray crystallography with that from cryo-electron microscopy is apparent throughout the book. In addition, functional aspects are also given a high priority. Chapter 1 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Download or read book Photoaffinity Labeling for Structural Probing Within Protein written by Yasumaru Hatanaka and published by Springer. This book was released on 2017-09-25 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the most up-to-date photoaffinity labeling method to tackle the key loop module involved in the binding process of a bioactive small molecule to its host protein. The book introduces rational points for preparing powerful photoaffinity probes, keys for the efficient analysis of labeled products, and recent successful applications for protein probing. Regarding drug design, the unique topics of the book are the special consideration of the crosslinking potential of recent probes and their application of important receptor proteins . This book presents emerging technologies of photoaffinity labeling to readers who are working in the fields of proteomics, molecular recognition, and drug discovery and development.
Download or read book The Nucleolus written by Mark O. J. Olson and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Within the past two decades, extraordinary new functions for the nucleolus have begun to appear, giving the field a new vitality and generating renewed excitement and interest. These new discoveries include both newly-discovered functions and aspects of its conventional role. The Nucleolus is divided into three parts: nucleolar structure and organization, the role of the nucleolus in ribosome biogenesis, and novel functions of the nucleolus.
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Download or read book Systems Analysis of Chromatin Related Protein Complexes in Cancer written by Andrew Emili and published by Springer Science & Business Media. This book was released on 2013-08-13 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetic modifications underlie all aspects of human physiology, including stem cell renewal, formation of cell types and tissues. They also underlie environmental impacts on human health, including aging and diseases like cancer. Consequently, cracking the epigenetic "code" is considered a key challenge in biomedical research. Chromatin structure and function are modified by protein complexes, causing genes to be turned “on” or “off” and controlling other aspects of DNA function. Yet while there has been explosive growth in the epigenetics field, human chromatin-modifying machines have only recently started to be characterized. To meet this challenge, our book explores complementary experimental tracks, pursued by expert international research groups, aimed at the physical and functional characterization of the diverse repertoire of chromatin protein machines - namely, the "readers, writers and erasers" of epigenomic marks. These studies include the identification of RNA molecules and drugs that interact selectively with components of the chromatin machinery. What makes this book distinctive is its emphasis on the systematic exploration of chromatin protein complexes in the context of human development and disease networks.
Download or read book Heat Shock Proteins in Cancer written by Stuart K. Calderwood and published by Springer Science & Business Media. This book was released on 2007-09-09 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Heat shock proteins are emerging as important molecules in the development of cancer and as key targets in cancer therapy. These proteins enhance the growth of cancer cells and protect tumors from treatments such as drugs or surgery. However, new drugs have recently been developed particularly those targeting heat shock protein 90. As heat shock protein 90 functions to stabilize many of the oncogenes and growth promoting proteins in cancer cells, such drugs have broad specificity in many types of cancer cell and offer the possibility of evading the development of resistance through point mutation or use of compensatory pathways. Heat shock proteins have a further property that makes them tempting targets in cancer immunotherapy. These proteins have the ability to induce an inflammatory response when released in tumors and to carry tumor antigens to antigen presenting cells. They have thus become important components of anticancer vaccines. Overall, heat shock proteins are important new targets in molecular cancer therapy and can be approached in a number of contrasting approaches to therapy.
