Download or read book Exploring Kinetic Controlled Protein Solubility Under Physiologically Relevant Conditions written by Hung Hoang Dang and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are responsible for driving a vast majority of biological processes in the cell. Therefore, it is important that proteins remain mostly folded to carry out their important functions, after transcription-translation. Prior proteome-wide studies showed that proteins in the Escherichia coli proteome are at risk of misfolding and extensive aggregation after translation, especially under cellular or environmental stresses. In addition, aggregates have been shown to be more thermodynamically stable than the native states, for many proteins. Therefore, if misfolding and aggregation in the cell were thermodynamically driven processes, many proteins in the E. coli proteome would spontaneously form aggregates in the cell. Despite a plethora of protein quality control and degradation systems employed by E. coli, it is clear that these systems are energetically expensive and can be overwhelmed, especially if many proteins in the proteome are at risk of thermodynamically driven aggregation. One popular proposed concept in the folding field is that the proteome is kinetically protected from aggregation, avoiding significant reliance on ATP-expensive protein quality control and degradation systems, under cellular conditions. However, there have not been experiments directly proving kinetic stability of proteins relative to aggregation on a proteome-wide scale. Moreover, aggregates are initially formed as soluble non-native oligomers, or soluble aggregates. These soluble aggregates may cause impairments of important biological processes in the cell and can eventually form larger insoluble assemblies. Yet, little is known about how soluble aggregates fit in the life cycle of E. coli proteins. To address the above fascinating biological questions, in this thesis, I will explore the kinetic stability and aggregation of a representative E. coli proteome (A19 cell strain). This Ph.D. thesis includes three Chapters. Chapter 1 includes background information on protein folding and aggregation in the cellular context. In addition, it discusses the importance of proteome-wide studies and the important findings on aggregation from current proteomic analyses and introduces the hypothesis of proteome kinetic stability relative to aggregation. This Chapter serves as the conceptual basis for the subsequent Chapters. Chapter 2 explores the proteome-wide kinetic stability of proteins in E. coli under physiologically relevant conditions. Here, I demonstrate that the free-energy landscape of the E. coli proteome includes extensive insoluble aggregates under physiologically relevant conditions. Further, the soluble and insoluble aggregates can exchange reversibly among each other and the apparent critical concentration for soluble-aggregate formation on a proteome-wide scale is very low (c.a., 0.04 [mu]g/mL). I demonstrate that over 80% of the proteome is kinetically protected from forming these soluble and insoluble aggregates on timescales longer than this organism's doubling time. Using bottom-up proteomics, I report that over 800 E. coli proteins are kinetically stable relative to aggregation regardless of structure, function, and cellular location. Finally, my results show that cytoplasmic/periplasmic molecular chaperones are amongst the most soluble proteins, both at higher temperature and under physiologically relevant conditions. This finding demonstrates that molecular chaperones are extremely robust members of the proteome. Chapter 3 focuses on the development of a novel isotopolog of tryptophan to enhance the sensitivity of NMR spectroscopy and enable monitoring protein behaviors in complex environments. Here, a novel selectively isotopic-labeled tryptophan was synthesized and successfully detected at very low concentrations in buffer and in a complex S30 cell extract (c.a., 20 nM and 1 [mu]M respectively) by low-concentration photochemically induced dynamic nuclear polarization (LC-photo-CIDNP) NMR. Our new selective labeling approach to LC-photo-CIDNP, in combination with existing biophysical analyses, can be utilized to study the effect of heterologous expression. For instance, this Trp isotopolog will enable the monitoring of folding and aggregation of model recombinant proteins within in complex cell-like environments. Overall, I propose that proteome-wide kinetic stability is an effective strategy to maintain a healthy and aggregation-free cellular environment in living systems, without reliance on energetically expensive degradation and disaggregation processes. These results also provide insights into the structural and functional determinants of bacterial kinetic stability and aggregation. In conclusion, it is hoped that the knowledge gained from this work will ultimately benefit the design and discovery of new strategies to prevent protein aggregation in the cell and to improve the shelf life of many protein-based biologics (e.g., monoclonal antibodies, etc).
Download or read book The Earliest Stages of a Protein s Life Influence Its Long term Solubility and Structural Accuracy written by Matthew Dalphin and published by . This book was released on 2020 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: Despite its fundamental importance for life, many details regarding how the cell promotes the solubility and structural accuracy of proteins remains poorly understood. This lack of knowledge poses serious challenges in basic science, biotechnology and medicine as the inability to prevent inclusion body formation limits the efficient overproduction of recombinant proteins and protein-based therapeutics. In this thesis, experimental and computational approaches were combined to explore factors that help discriminate folding and aggregation pathways at various stages of a protein's life in the cell. If folded properly, the native states of many proteins, including apomyoglobin and the soluble E. coli proteome, were shown to be kinetically-trapped from stable aggregate states under physiologically-relevant conditions. However, kinetic simulations suggest that this kinetic trapping can be circumvented at high protein concentrations and, importantly, in the presence of small pre-nucleated aggregate seeds capable of further elongation. In order to further explore how the intracellular environment further influences protein folding and aggregation, we developed a novel bacterial Hsp70 inhibitor which targets and inhibits DnaK. This inhibitor is functional in dilute buffer and cell-free systems. Importantly, it does not also inhibit nascent protein biosynthesis. Our novel inhibitor was then used to probe how the ribosome and DnaK coordinate co- and post-translational events which ultimately support proper protein folding. The ribosome was observed to act as a powerful facilitator of protein solubility during the earliest stages of translation and upon ribosome release. However, it requires additional help from molecular chaperones (e.g. DnaK) to ensure the soluble proteins produced are structurally accurate. Kinetic simulations further highlight that this chaperone requirement for proper folding increases for proteins which are slow to fold at the end of translation. This highlights the synergistic, yet distinct, roles of the ribosome and DnaK required to produce soluble, properly folded proteins which would otherwise be aggregation-prone on their own. Taken together, the work highlighted in this thesis sheds light on the unique mechanism by which the cell shapes, and ultimately traps, proteins into their native state during the earliest stages of protein life.
Download or read book Plant Breeding for Biotic Stress Resistance written by Roberto Fritsche-Neto and published by Springer Science & Business Media. This book was released on 2012-10-01 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experience shows that biotic stresses occur with different levels of intensity in nearly all agricultural areas around the world. The occurrence of insects, weeds and diseases caused by fungi, bacteria or viruses may not be relevant in a specific year but they usually harm yield in most years. Global warming has shifted the paradigm of biotic stresses in most growing areas, especially in the tropical countries, sparking intense discussions in scientific forums. This book was written with the idea of collecting in a single publication the most recent advances and discoveries concerning breeding for biotic stresses, covering all major classes of biotic challenges to agriculture and food production. Accordingly, it presents the state-of-the-art in plant stresses caused by all microorganisms, weeds and insects and how to breed for them. Complementing Plant Breeding for Abiotic Stress Tolerance, this book was written for scientists and students interested in learning how to breed for biotic stress scenarios, allowing them to develop a greater understanding of the basic mechanisms of resistance to biotic stresses and develop resistant cultivars.
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 Comprehensive Biophysics written by and published by Academic Press. This book was released on 2012-04-12 with total page 3533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a rapidly-evolving interdisciplinary science that applies theories and methods of the physical sciences to questions of biology. Biophysics encompasses many disciplines, including physics, chemistry, mathematics, biology, biochemistry, medicine, pharmacology, physiology, and neuroscience, and it is essential that scientists working in these varied fields are able to understand each other's research. Comprehensive Biophysics, Nine Volume Set will help bridge that communication gap. Written by a team of researchers at the forefront of their respective fields, under the guidance of Chief Editor Edward Egelman, Comprehensive Biophysics, Nine Volume Set provides definitive introductions to a broad array of topics, uniting different areas of biophysics research - from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource - a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge. Biophysical research today encompasses many areas of biology. These studies do not necessarily share a unique identifying factor. This work unites the different areas of research and allows users, regardless of their background, to navigate through the most essential concepts with ease, saving them time and vastly improving their understanding The field of biophysics counts several journals that are directly and indirectly concerned with the field. There is no reference work that encompasses the entire field and unites the different areas of research through deep foundational reviews. Comprehensive Biophysics fills this vacuum, being a definitive work on biophysics. It will help users apply context to the diverse journal literature offering, and aid them in identifying areas for further research Chief Editor Edward Egelman (E-I-C, Biophysical Journal) has assembled an impressive, world-class team of Volume Editors and Contributing Authors. Each chapter has been painstakingly reviewed and checked for consistent high quality. The result is an authoritative overview which ties the literature together and provides the user with a reliable background information and citation resource
Download or read book Drug Delivery Systems Advanced Technologies Potentially Applicable in Personalised Treatment written by Jorge Coelho and published by Springer Science & Business Media. This book was released on 2013-03-15 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is part of a series dedicated to recent advances on preventive, predictive and personalised medicine (PPPM). It focuses on the theme of “Drug delivery systems: advanced technologies potentially applicable in personalised treatments”. The critical topics involving the development and preparation of effective drug delivery systems, such as: polymers available, self-assembly, nanotechnology, pharmaceutical formulations, three dimensional structures, molecular modeling, tailor-made solutions and technological tendencies, are carefully discussed. The understanding of these areas constitutes a paramount route to establish personalised and effective solutions for specific diseases and individuals.
Download or read book Synthesis X ray Structures Spectroscopy DFT Electronic Configuration and Biological Relevance of Photolabile Ruthenium and Iron Nitrosyls Derived from Ligands Containing Carboxamido N Donors written by Michael J. Rose and published by . This book was released on 2009 with total page 866 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Dietary Strategies for Healthy Aging Caloric Restriction and Beyond written by Sebastian J. Hofer and published by Frontiers Media SA. This book was released on 2022-03-21 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Lead Its Effects on Environment and Health written by Astrid Sigel and published by Walter de Gruyter GmbH & Co KG. This book was released on 2017-04-10 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 17, entitled Lead: Its Effects on Environment and Health of the series Metal Ions in Life Sciences centers on the interrelations between biosystems and lead. The book provides an up-to-date review of the bioinorganic chemistry of this metal and its ions; it covers the biogeochemistry of lead, its use (not only as gasoline additive) and anthropogenic release into the environment, its cycling and speciation in the atmosphere, in waters, soils, and sediments, and also in mammalian organs. The analytical tools to determine and to quantify this toxic element in blood, saliva, urine, hair, etc. are described. The properties of lead(II) complexes formed with amino acids, peptides, proteins (including metallothioneins), nucleobases, nucleotides, nucleic acids, and other ligands of biological relevance are summarized for the solid state and for aqueous solutions as well. All this is important for obtaining a coherent picture on the properties of lead, its effects on plants and toxic actions on mammalian organs. This and more is treated in an authoritative and timely manner in the 16 stimulating chapters of Volume 17, which are written by 36 internationally recognized experts from 13 nations. The impact of this recently again vibrant research area is manifested in nearly 2000 references, over 50 tables and more than 100 illustrations (half in color). Lead: Its Effects on Environment and Health is an essential resource for scientists working in the wide range from material sciences, inorganic biochemistry all the way through to medicine including the clinic ... not forgetting that it also provides excellent information for teaching.
Download or read book Translational Advances in Alzheimer s Parkinson s and other Dementia Molecular Mechanisms Biomarkers Diagnosis and Therapies Volume II written by Jiehui Jiang and published by Frontiers Media SA. This book was released on 2022-11-15 with total page 713 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Research and Development in Progress written by U.S. Atomic Energy Commission. Division of Biology and Medicine and published by . This book was released on 1968 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Concise Encyclopedia of Biomedical Polymers and Polymeric Biomaterials written by Munmaya Mishra and published by CRC Press. This book was released on 2017-08-16 with total page 2663 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Concise Encyclopedia of Biomedical Polymers and Polymeric Biomaterials presents new and selected content from the 11-volume Biomedical Polymers and Polymeric Biomaterials Encyclopedia. The carefully culled content includes groundbreaking work from the earlier published work as well as exclusive online material added since its publication in print. A diverse and global team of renowned scientists provide cutting edge information concerning polymers and polymeric biomaterials. Acknowledging the evolving nature of the field, the encyclopedia also features newly added content in areas such as tissue engineering, tissue repair and reconstruction, and biomimetic materials.
Download or read book Regulation of Soluble Immune Mediators by Non Coding RNAs written by Flavia Bazzoni and published by Frontiers Media SA. This book was released on 2020-12-11 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Download or read book ESR Spectroscopy in Membrane Biophysics written by Marcus A. Hemminga and published by Springer Science & Business Media. This book was released on 2007-02-13 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Starting from a comprehensive quantum mechanical description, this book introduces the optical (IR, Raman, UV/Vis, CD, fluorescence and laser spectroscopy) and magnetic resonance (1D and 2D-NMR, ESR) techniques. The book offers a timely review of the increasing interest in using spin-label ESR as an alternative structural technique for NMR or X-ray diffraction. Future aspects are treated as well, but only as an illustration of the progress of ESR in this field.
Download or read book Recent Advances on Nitrogen Use Efficiency in Crop Plants and Climatic Challenges written by Hamada AbdElgawad and published by Frontiers Media SA. This book was released on 2023-08-25 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nitrogen (N) is a mineral nutrient that is essential for the normal growth and development of plants that is required in the highest quantity. It is an element of nucleic acids, proteins, and photosynthetic metabolites, therefore crucial for crop growth and metabolic processes. Recently, it was estimated that N fertilizers could meet the 48% demand of the world’s population. However, overuse and misuse of N fertilizers raised environmental concerns associated with N losses by nitrous oxide (N2O) emissions, ammonia (NH3) volatilization, and nitrate (NO3−) leaching. For instance, NH3 is a pollutant in the atmosphere, N2O is a greenhouse gas that has a warming potential 298 times higher than CO2 and contributes to ozone depletion, and NO3− causes eutrophication of water bodies. Agricultural practices account for about 90% of NH3 and 70% of N2O anthropogenic emissions worldwide. The efficient use of N chemical fertilizers can be attained through cultural and agronomic practices. Nitrogen use efficiency (NUE) is an important trait that has been studied for decades in different crops. The grain production or economic return from the per unit supply of N fertilizer simply explained the NUE. Several definitions were suggested by different researchers. NUE can be defined as the product of N uptake efficiency (NUpE) and N utilization efficiency (NUtE). An increase in NUE increases the yield, biomass, quality, and quantity of crops. N is generally applied as chemical fertilizer to the soil, whereas a small amount is added to some crops like grain legumes through the fixation process. On the other hand, crop plants take N through the root system in the form of nitrate or ammonium which is thereby used in different metabolic processes. A number of studies have been conducted to increase the NUE in different crops and it has been indicated that NUE can be improved by agronomic, physiological, biochemical, breeding as well as molecular approaches. Nitrogen is the main limiting nutrient after carbon, hydrogen, and oxygen for the photosynthetic process, phyto-hormonal and proteomic changes, and the growth-development of plants to complete their lifecycle. Excessive and inefficient use of N fertilizer results in enhanced crop production costs and atmospheric pollution. Atmospheric nitrogen (71%) in the molecular form is not available for the plants. For the world's sustainable food production and atmospheric benefits, there is an urgent need to upgrade nitrogen use efficiency in the agricultural farming system. Nitrogen losses are too high, due to excess amount, low plant population, poor application methods, etc., which can go up to 70% of total available nitrogen. These losses can be minimized up to 15–30% by adopting improved agronomic approaches such as optimal dosage of nitrogen, application of N by using canopy sensors, maintaining plant population, drip fertigation, and legume-based intercropping. Therefore, the major concern of modern days is to save economic resources without sacrificing farm yield as well as the safety of the global environment, i.e. greenhouse gas emissions, ammonium volatilization, and nitrate leaching.
