Download or read book Protein Aggregation in Bacteria written by Silvia Maria Doglia and published by John Wiley & Sons. This book was released on 2014-04-03 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodies—and on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria Physiological importance and consequences of aggregation for the bacterial cell Factors inherent to the protein sequence responsible for aggregation and evolutionary mechanisms to keep proteins soluble Structural properties of proteins expressed as soluble aggregates and as inclusion bodies within bacterial cells both from a methodological point of view and with regard to their similarity with amyloids Control of the structural and functional properties of aggregated proteins and use thereof in biotechnology and medicine Protein Aggregation in Bacteria is ideal for researchers in protein science, biochemistry, bioengineering, biophysics, microbiology, medicine, and biotechnology, particularly if they are related with the production of recombinant proteins and pharmaceutical science.
Download or read book Protein Solubility and Aggregation in Bacteria written by Salvador Ventura and published by Frontiers Media SA. This book was released on 2016-09-26 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins suffer many conformational changes and interactions through their life, from their synthesis at ribosomes to their controlled degradation. Only folded and soluble proteins are functional. Thus, protein folding and solubility are controlled genetically, transcriptionally, and at the protein sequence level. In addition, a well-conserved cellular machinery assists the folding of polypeptides to avoid misfolding and ensure the attainment of soluble and functional structures. When these redundant protective strategies are overcome, misfolded proteins are recruited into aggregates. Recombinant protein production is an essential tool for the biotechnology industry and also supports expanding areas of basic and biomedical research, including structural genomics and proteomics. Although bacteria still represent a convenient production system, many recombinant polypeptides produced in prokaryotic hosts undergo irregular or incomplete folding processes that usually result in their accumulation as insoluble aggregates, narrowing thus the spectrum of protein-based drugs that are available in the biotechnology market. In fact, the solubility of bacterially produced proteins is of major concern in production processes, and many orthogonal strategies have been exploited to try to increase soluble protein yields. Importantly, contrary to the usual assumption that the bacterial aggregates formed during protein production are totally inactive, the presence of a fraction of molecules in a native-like structure in these assemblies endorse them with a certain degree of biological activity, a property that is allowing the use of bacteria as factories to produce new functional materials and catalysts. The protein embedded in intracellular bacterial deposits might display different conformations, but they are usually enriched in beta-sheet-rich assemblies resembling the amyloid fibrils characteristic of several human neurodegenerative diseases. This makes bacterial cells simple, but biologically relevant model systems to address the mechanisms behind amyloid formation and the cellular impact of protein aggregates. Interestingly, bacteria also exploit the structural principles behind amyloid formation for functional purposes such as adhesion or cytotoxicity. In the present research topic we collect papers addressing all the issues mentioned above from both the experimental and computational point of view.
Download or read book Protein Solubility and Aggregation in Bacteria written by and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins suffer many conformational changes and interactions through their life, from their synthesis at ribosomes to their controlled degradation. Only folded and soluble proteins are functional. Thus, protein folding and solubility are controlled genetically, transcriptionally, and at the protein sequence level. In addition, a well-conserved cellular machinery assists the folding of polypeptides to avoid misfolding and ensure the attainment of soluble and functional structures. When these redundant protective strategies are overcome, misfolded proteins are recruited into aggregates. Recombinant protein production is an essential tool for the biotechnology industry and also supports expanding areas of basic and biomedical research, including structural genomics and proteomics. Although bacteria still represent a convenient production system, many recombinant polypeptides produced in prokaryotic hosts undergo irregular or incomplete folding processes that usually result in their accumulation as insoluble aggregates, narrowing thus the spectrum of protein-based drugs that are available in the biotechnology market. In fact, the solubility of bacterially produced proteins is of major concern in production processes, and many orthogonal strategies have been exploited to try to increase soluble protein yields. Importantly, contrary to the usual assumption that the bacterial aggregates formed during protein production are totally inactive, the presence of a fraction of molecules in a native-like structure in these assemblies endorse them with a certain degree of biological activity, a property that is allowing the use of bacteria as factories to produce new functional materials and catalysts. The protein embedded in intracellular bacterial deposits might display different conformations, but they are usually enriched in beta-sheet-rich assemblies resembling the amyloid fibrils characteristic of several human neurodegenerative diseases. This makes bacterial cells simple, but biologically relevant model systems to address the mechanisms behind amyloid formation and the cellular impact of protein aggregates. Interestingly, bacteria also exploit the structural principles behind amyloid formation for functional purposes such as adhesion or cytotoxicity. In the present research topic we collect papers addressing all the issues mentioned above from both the experimental and computational point of view.
Download or read book Functions and Mechanisms of Bacterial Protein Homeostasis and Stress Responses written by Axel Mogk and published by Frontiers Media SA. This book was released on 2022-02-01 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Cover Image for This Research Topic is Used With Permission of the Authors and Publishers of the Following Article: Winkler J, Seybert A, König L, Pruggnaller S, Haselmann U, Sourjik V, Weiss M, Frangakis AS, Mogk A, Bukau B.EMBO J. 2010 Mar 3;29(5):910-23. doi: 10.1038/emboj.2009.412. Epub 2010 Jan 21
Download or read book Bacterial Persistence written by Jan Michiels and published by Humana. This book was released on 2015-10-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a comprehensive collection of methods that have been instrumental to the current understanding of bacterial persisters. Chapters in the book cover topics ranging from general methods for measuring persister levels in Escherichia coli cultures, protocols for the determination of the persister subpopulation in Candida albicans, quantitative measurements of Type I and Type II persisters using ScanLag, to in vitro and in vivo models for the study of the intracellular activity of antibiotics. 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, Bacterial Persistence: Methods and Protocols brings together the most respected researchers in bacterial persistence whose studies will remain vital to understanding this field for many years to come.
Download or read book Protein Aggregation written by Andrzej Stanisław Cieplak and published by Springer Nature. This book was released on 2022-10-30 with total page 673 pages. Available in PDF, EPUB and Kindle. Book excerpt: The volume details techniques, methods, and conceptual developments to further the study of protein aggregation with emphasis on the pleiomorphic proteins implicated in etiology of neurodegeneration. Chapters guide readers through in vitro and in vivo studies of fibrillization and liquid-liquid phase separation processes, and offer a comprehensive account of the state-of-art of structural studies of protein aggregation. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Aggregation: Methods and Protocols aims to be useful and practical guide to new researchers and experts looking to expand their knowledge.
Download or read book Contribution of the Ribosome and Molecular Chaperones to de Novo Protein Folding in Bacteria written by Rayna Addabbo and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is the critical process by which proteins achieve their native conformations, often necessary to perform life-sustaining functions for the cell. While all organisms rely on protein folding for survival, it is not well understood how proteins fold, especially within the complex environment of the cell. While evolution has optimized protein folding for success, it is not an infallible process. Aside from the many human diseases whose pathology is closely linked to protein misfolding and aggregation, aberrant folding has made it challenging for researchers to use recombinant DNA technologies to over-produce soluble functional proteins. This limitation has had significant consequences for research, biotechnology and medicine, particularly in the field of protein-based biopharmaceuticals. It follows that there is great motivation to understand how cells successfully produce structurally accurate proteins. In this thesis I will gain insights into the parameters that dictate whether a protein successfully folds or aggregates upon release from the ribosome. I will then examine how molecular chaperones promote protein folding and the prevention of protein aggregation. This thesis is divided into four chapters. Chapter 1 is an introductory chapter that reviews the current literature on protein folding in the cell and incorporates my current research findings. This chapter aims at highlighting why proteins need the cellular environment for successful folding and prevention of aggregation. In Chapter 2, I explore how co-and-posttranslational protein folding in the absence of molecular chaperones is related to successful native state formation and to detrimental aggregation. I describe investigations showing that the ribosome plays a critical role in promoting nascent-protein solubility during biosynthesis. Further, I describe the features of an important kinetic competition that takes place upon protein release from the ribosome immediately following translation. During this time, proteins are irreversibly channeled towards either their native state or aggregated conformations. I find that, to avoid aggregation, proteins must be able to fold faster than they aggregate, as they depart from the environment established by the ribosomal surface and its immediate vicinity. Before completion of translation, the ribosomal environment discourages aggregation due to the large size of the ribosome-nascent-protein complex (RNC). However, this translational-diffusion advantage vanishes after the newly synthesized protein departs from the ribosome. In summary, this chapter highlights the role of the ribosome in promoting the solubility of newly synthesized proteins. The sequence and structural diversity of proteins in the E. coli cytosol implies that not all proteins have the same ability to fold rapidly upon release from the ribosome. In Chapters 3 and 4, I focus on understanding how the highly conserved molecular chaperone Hsp70 mediates protein folding and helps preventing aggregation in bacteria. In Chapter 3, I experimentally demonstrate that the Hsp70 molecular chaperone (also known as DnaK in bacteria) promotes protein structural accuracy and native-state formation. When proteins are biosynthesized at sub-optimal Hsp70 concentration, a mixture of the native state and aggregated species is produced. Surprisingly, even proteins that are soluble after release from the ribosome in the absence of Hsp70 are not necessarily in their native conformation. These proteins often include a significant population of soluble aggregate as well as soluble native state. In summary, this chapter highlights the key role of the Hsp70 molecular chaperone for protein structural accuracy upon release from the ribosome. In Chapter 4, I employ a combination of experiments and computation to show that the Hsp70 chaperone concentration and the chaperone-to-protein ratio needed for protein solubility and structural accuracy are directly dependent on the features of the kinetic partitioning as nascent proteins are release from the ribosome (see Chapter 2). Proteins that aggregate rapidly relative to folding are more highly dependent upon interactions with DnaK upon release from the ribosome. It follows that Hsp70-mediated protein folding promotes the existence of a more diverse cellular proteome by allowing the cell to access slow-folding and aggregation-prone proteins that would otherwise not be accessible. The findings in this dissertation are consistent with a global view of cellular protein folding according to which folding begins on the ribosome. The role of the ribosome is to support conformational sampling and solubility while molecular chaperones ensure structural accuracy as well as high yields of native state. Depending upon the folding and aggregation properties of the protein under investigation, different proteins rely on the ribosome and molecular chaperones to a different extent, for successful protein folding. The dual dependence on the ribosome and molecular chaperones provides a robust machinery to produce a variety of proteins needed to support life and properly promote sequence, structural and functional diversity.
Download or read book Protein Aggregation in Bacteria written by Silvia Maria Doglia and published by Wiley. This book was released on 2014-04-14 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodies—and on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria Physiological importance and consequences of aggregation for the bacterial cell Factors inherent to the protein sequence responsible for aggregation and evolutionary mechanisms to keep proteins soluble Structural properties of proteins expressed as soluble aggregates and as inclusion bodies within bacterial cells both from a methodological point of view and with regard to their similarity with amyloids Control of the structural and functional properties of aggregated proteins and use thereof in biotechnology and medicine Protein Aggregation in Bacteria is ideal for researchers in protein science, biochemistry, bioengineering, biophysics, microbiology, medicine, and biotechnology, particularly if they are related with the production of recombinant proteins and pharmaceutical science.
Download or read book Recombinant protein expression in microbial systems written by Eduardo A. Ceccarelli and published by Frontiers E-books. This book was released on 2014-10-02 with total page 103 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the advent of recombinant DNA technology, expressing heterologous proteins in microorganisms rapidly became the method of choice for their production at laboratory and industrial scale. Bacteria, yeasts and other hosts can be grown to high biomass levels efficiently and inexpensively. Obtaining high yields of recombinant proteins from this material was only feasible thanks to constant research on microbial genetics and physiology that led to novel strains, plasmids and cultivation strategies. Despite the spectacular expansion of the field, there is still much room for progress. Improving the levels of expression and the solubility of a recombinant protein can be quite challenging. Accumulation of the product in the cell can lead to stress responses which affect cell growth. Buildup of insoluble and biologically inactive aggregates (inclusion bodies) lowers the yield of production. This is particularly true for obtaining membrane proteins or high-molecular weight and multi-domain proteins. Also, obtaining eukaryotic proteins in a prokaryotic background (for example, plant or animal proteins in bacteria) results in a product that lack post-translational modifications, often required for functionality. Changing to a eukaryotic host (yeasts or filamentous fungi) may not be a proper solution since the pattern of sugar modifications is different than in higher eukaryotes. Still, many advances in the last couple of decades have provided to researchers a wide variety of strategies to maximize the production of their recombinant protein of choice. Everything starts with the careful selection of the host. Be it bacteria or yeast, a broad list of strains is available for overcoming codon use bias, incorrect disulfide bond formation, protein toxicity and lack of post-translational modifications. Also, a huge catalog of plasmids allows choosing for different fusion partners for improving solubility, protein secretion, chaperone co-expression, antibiotic resistance and promoter strength. Next, controlling culture conditions like temperature, inducer and media composition can bolster recombinant protein production. With this Research Topic, we aim to provide an encyclopedic account of the existing approaches to the expression of recombinant proteins in microorganisms, highlight recent discoveries and analyze the future prospects of this exciting and ever-growing field.
Download or read book Microbial Aggregation written by Calleja and published by CRC Press. This book was released on 2018-05-04 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text covers in detail bacteria and yeasts, including an overall perspective of microbial aggregation as fundamental form and function, which is presented here to include systems still to be treated in detail.
Download or read book Protein Aggregation written by Douglas A. Stein and published by Nova Biomedical Books. This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein aggregation is the aggregation of mis-folded proteins, and is thought to be responsible for many degenerative diseases, such as Alzheimer's. This book presents current research from across the globe in the study of protein aggregation, including the processes of protein aggregation induced by freezing and lyophilization; functional amyloids; thermally induced aggregation of a model system protein - insulin; the aggregation of albumin; synucleins implicated in neurodegenerative diseases and some forms of cancer; yeast protein aggregates; and the folding and aggregation features of proteins.
Download or read book Protein Secretion in Bacteria written by Maria Sandkvist and published by John Wiley & Sons. This book was released on 2020-07-02 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein transport into and across membranes is a fundamental process in bacteria that touches upon and unites many areas of microbiology, including bacterial cell physiology, adhesion and motility, nutrient scavenging, intrabacterial signaling and social behavior, toxin deployment, interbacterial antagonism and collaboration, host invasion and disruption, and immune evasion. A broad repertoire of mechanisms and macromolecular machines are required to deliver protein substrates across bacterial cell membranes for intended effects. Some machines are common to most, if not all bacteria, whereas others are specific to Gram-negative or Gram-positive species or species with unique cell envelope properties such as members of Actinobacteria and Spirochetes. Protein Secretion in Bacteria, authored and edited by an international team of experts, draws together the many distinct functions and mechanisms involved in protein translocation in one concise tome. This comprehensive book presents updated information on all aspects of bacterial protein secretion encompassing: Individual secretory systems–Sec, Tat, and T1SS through the newly discovered T9SS Mechanisms, structures, and functions of bacterial secretion systems Lipoprotein sorting pathways, outer membrane vesicles, and the sortase system Structures and roles of surface organelles, including flagella, pili, and curli Emerging technologies and translational implications Protein Secretion in Bacteria serves as both an introductory guide for students and postdocs and a ready reference for seasoned researchers whose work touches on protein export and secretion. This volume synthesizes the diversity of mechanisms of bacterial secretion across the microbial world into a digestible resource to stimulate new research, inspire continued identification and characterization of novel systems, and bring about new ways to manipulate these systems for biotechnological, preventative, and therapeutic applications.
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 Protein Self Assembly written by Jennifer J. McManus and published by Humana. This book was released on 2020-08-08 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-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. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
Download or read book Protein Homeostasis in Survival and Persistence of Escherichia Coli Salmonella Typhimurium and Cronobacter Sakazakii at Alkaline PH and After Desiccation written by Tongbo Zhu and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria have evolved a protein homeostasis network to maintain the integrity of their proteome. Chaperones and proteases of the core genome can be complemented by accessory genes encoding additional elements of the protein homeostasis network. The transmissible locus of stress tolerance (tLST) confers exceptional tolerance to high temperature, chlorine, oxidative chemicals and high hydrostatic pressure by reducing protein aggregation. Highly expressed tLST proteins include intracellular small heat shock proteins sHsp20 and sHspGI, disaggregase ClpKGI, and periplasmic stress chaperones PscA and PscB. The tLST also encodes KefBGI, a Na+/H+ antiporter. This study aimed to determine the effects of improved protein homeostasis that is mediated by the tLST on bacterial tolerance to alkaline pH and desiccation. The expression of the Cpx, a two-component regulatory system in Escherichia coli which responds to envelope stress, was not altered by the presence of the tLST. The tolerance or resistance of E. coli to alkaline pH in the pH range of 6.9 to 9.2 and at pH 11, respectively, were also not changed by the presence of the tLST. The presence of the tLST improved, however, survival at pH 11 in presence of chlorine stress; this effect was attributed to KefBGI rather than protein homeostasis. The impact of protein homeostasis on desiccation tolerance was characterized in Salmonella enterica serovar Typhimurium, Cronobacter sakazakii and E. coli. The cloning and expression of the shsp20, shspGI and clpKGI decreased desiccation tolerance in S. Typhimurium and C. sakazakii but not in E. coli. Protein aggregates were visualized in vivo using an IbpA-Yfp fusion protein, demonstrating that cloning of shsp20, shspGI and clpKGI reduced intracellular protein aggregates in S. Typhimurium and C. sakazakii but not in E. coli. The presence of the elements intensively consuming cellular resources including high copy plasmids as well as cloning of highly expressed proteins had a detrimental effect on desiccation tolerance irrespective of the function of the expressed proteins. Abolishing the ATP-hydrolysis function of ClpKGI by substitution of two amino acids (E383A/E723A) increased cell counts of S. Typhimurium after desiccation more than 100-fold, demonstrating a direct contribution of protein aggregation to desiccation tolerance. Dry storage of S. Typhimurium and C. sakazakii for 112 days revealed that cloning of the tLST or of its protein homeostasis module decreased survival during desiccated storage in infant formula. In conclusion, additional protein quality control provided by tLST does not aid in alkaline resistance or tolerance in E. coli. The desiccation tolerance of S. Typhimurium and C. sakazakii positively correlates with the formation of protein aggregates but are negatively impacted by the presence of the elements intensively consuming cellular resources. Taken together, this study improves the understanding of how protein homeostasis affects bacterial stress tolerance by increasing tolerance to some stressors while reducing tolerance to others.
Download or read book Inclusions in Prokaryotes written by Jessup M. Shively and published by Springer Science & Business Media. This book was released on 2006-05-04 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: The new series "Microbiology Monographs" begins with two volumes on intracellular components in prokaryotes. In this first volume, "Inclusions in Prokaryotes", the components, labeled inclusions, are defined as discrete bodies resulting from synthesis of a metabolic product. Research on the biosynthesis and reutilization of the accumulated materials is still in progress, and interest in the inclusions is growing. This comprehensive volume provides historical background and comprehensive reviews of eight well-known prokaryotic inclusions.
Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.
