Download or read book Dynamics of EF Tu ternary Complex in Live E Coli Using Superresolution Imaging written by Mainak Mustafi and published by . This book was released on 2019 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt: Translation elongation is a complicated process where amino acids are added to the peptide chain within the ribosomes for protein production. In each elongation cycle the ribosome samples different aminoacyl tRNA (aa-tRNA) species to find a match for the mRNA codon. There are around 40-45 different tRNA species in E. coli and on an average all of them have to be sampled to find a match. Then the aa-tRNA transfers the amino acid to the growing peptide chain and the deacylated tRNA leaves. For cells growing in good growth medium, the entire cycle takes around 50 ms. Different proteins (elongation factors) are involved in different steps of the elongations cycle, the two major ones being EF-Tu and EF-G. EF-Tu forms a ternary complex with aa-tRNA and GTP and thus brings the aa-tRNA to the ribosome. The elongation cycle has been studied in great detail using both bulk and single molecule experiments, but the initial interaction of ternary complex with ribosome (specifically with L7/L12 stalk) is not properly understood, mainly due to the lack of structural data. Using superresolution imaging (PALM), we have studied dynamics of ternary complex and L7/L12 stalk interaction. Our results have shown that the interaction is highly transient and multiple ternary complexes can bind to translating ribosomes at the same time. This high binding stoichiometry can lead to high concentration of tRNA around ribosomes for efficient translation. We have further incorporated the effects of nutrient limitation, osmotic effects and various translation halting drug treatment on the dynamics of EF-Tu/ternary complex

Download or read book Biophysical Studies on the Elongation Factor EF Tu from Escherichia Coli written by Maria Johanna Schilstra and published by . This book was released on 1986 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Functional Mapping of the Components of the E Coli Translational Machinery written by Sonisilpa Mohapatra and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial cells generally lack membrane-bound organelles. Therefore, traditionally they were viewed as bags of freely diffusing macromolecules devoid of any internal organization. The development in imaging techniques in the last two decades has enabled better visualization of bacterial cells and led to careful investigation of their internal organization. Consequently, they are now shown to have an intricate internal organization of various proteins in their cytoplasmic space despite the absence of membrane boundaries. The spatiotemporal control of various cellular processes in bacteria is possibly regulated by this internal organization. Most cellular processes are regulated by complex networks of intermolecular interactions. A systematic study quantifying the correlation in spatial organization of various biomolecules might help to unravel their underlying interactions. A positive correlation might suggest binding to a common site or common sites of production, degradation or action. A negative correlation might suggest a mechanism that sequesters the molecules from each other. A commonly used method to quantify linear correlation between images of two different species is the Pearson Correlation Coefficient (PCC). PCC however fails both qualitatively and quantitatively in spherocylindrical cells such as E. coli. A modified PCC (MPCC) is proposed that corrects this issue by using a proper reference matrix for spherocylindrical cells (Chapter 2). The application of MPCC to experimental spatial distributions of RNA Polymerase and HU is demonstrated. A significantly positive correlation coefficient was obtained for the spatial distribution of the two DNA binding proteins. The MPCC concept could be generalizable to other cell shapes and can be used for both widefield and superresolution images. Translation is one of the most important cellular process. Ribosomes are the central component of translation engaged in protein synthesis from mRNA. Optimal usage of ribosomes is dependent on their spatial organization. In this dissertation, the spatial and temporal organization of translation and a translation elongation protein, Elongation Factor P (EF-P) was investigated in live E. coli cells using superresolution fluorescence microscopy. In rapidly growing E. coli and B. subtilis, strong nucleoid - ribosome segregation is observed. The picture of spatial organization in slowly growing C. crescentus is however completely different. The effect of growth rate on the segregation of ribosomes and nucleoids in E. coli is therefore investigated using two color superresolution fluorescence imaging in Chapter 3. MPCC was used to quantify the degree of segregation between spatial distribution of ribosomes and DNA in E. coli in the two different growth conditions. Slowly growing E. coli showed significant segregation of ribosomes from DNA, unlike slowly growing C. crescentus. Imaged ribosomes were classified as translating and non-translating based on their diffusive trajectories. The fraction of ribosomes engaged in translation in the two growth conditions was quantified. A small but significant reduction of translating ribosomes was observed in slowly growing cells. Simulated spatial distributions in spherocylinders of dimensions same as E. coli that best fit experimental spatial distributions of translating and non-translating ribosomes were used to obtain a cellular map of ribosomes based on their biological functions. Based on the functional map of translating and non-translating ribosomes, it was concluded that a "circulation model" of ribosomes evidently applies to E. coli in all growth conditions. In cells, the translation elongation is discontinuous, often suffering from periods of pauses. The cells have mechanisms to alleviate these pauses, irrespective of the reason for pausing. EF-P is a translation factor that alleviates pausing during translation of polyproline motifs. The spatial distribution and ribosome binding dynamics of EF-P were investigated in Chapter 4 to understand details of mechanism of interaction of EF-P with ribosomes during the translation elongation process. By localizing individual EF-P molecules, the spatial distribution of EF-P was shown to mimic the "three peaked" ribosome distribution in the cells. Photoactivated Localization Microscopy combined with single particle tracking (sptPALM) was employed to distinguish and quantify the different diffusive states of EF-P. The "slow" diffusing EF-P molecules are associated with translating ribosomes whereas the "fast" diffusing ones are EF-P copies searching for a potential binding site on ribosomes. Nearly 30% of EF-Ps are associated with translating ribosomes, implying 1500-6000 EF-P/ribosome complexes in a cell at any given time. This is significantly larger than the estimated 280 pausing events due to polyproline motifs being translated in the cell, suggesting interrogation of ribosomes by EF-P more frequently than the number of pausing events. In addition, faster imaging rates enabled measurement of binding/unbinding timescales of EF-P interactions with ribosomes (Chapter 4). Overall, the reported works explore the synergism of interactions between different components of translation and their spatiotemporal organization. The famous biologist Jacques Monod noted "What was true for the E. coli would be true for the elephant". A better understanding of the intracellular spatial organization of bacterial cells could elucidate the mechanisms that underlie spatial order in higher organisms

Download or read book Spatial Biology of Transcription and Translation in Live E Coli Using Super resolution Fluorescence Microscopy written by and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the lack of membrane bound organelles in bacteria, both transcription and translation take place inside the same compartment. The objective of this thesis is to understand the fundamental, as yet unanswered question of where transcription and translation take place inside bacteria. I have focused on the bacterium E. coli, as it is the best characterized organism, both molecularly and physiologically. I have used superresolution microscopy techniques in live E. coli cells to study the spatio-temporal organization of transcription and translation machinery. By localizing individual molecules with 30 nm scale accuracy, I was able to resolve the spatial distribution and dynamics of RNA polymerase (RNAP) and of the ribosomes. The spatial distribution of RNAP mimicked the spatial distribution of the chromosomal DNA, imaged by DNA-stains and superresolution imaging of DNA-binding protein HU. Ribosomes on the other hand were found to be segregated from the chromosomal DNA. By relating the position, dynamics and copy numbers of ribosomes and RNAPs, I was able to conclude that most translation in E. coli is taking place away from the nucleoid in the ribosome-rich regions without transcriptional coupling. This finding is consistent with the timescale of transcription and life time of mRNA. Based on the comparison of spatio-temporal dynamics of chromosomal loci and RNA polymerase, I was able to infer that transcription of protein genes is scattered more or less uniformly throughout the nucleoid. Here the mRNA is translated co-transcriptionally. Once the transcription is terminated, the mRNA diffuses out into the ribosomes-rich regions of the end cap of cytoplasm and is translated until it is degraded by the degradosome machinery. In sharp contrast, transcription of the ribosomal RNA seems to be localized to the periphery of the chromosomal DNA. Such placement of rRNA transcription at the interface between the dense nucleoids and the ribosome-rich regions may be functionally important for efficient ribosome assembly. I also found significant numbers of transcribing RNAPs and translating ribosomes near the cytoplasmic membrane. This provides circumstantial evidence for "transertion hypothesis", which posits the co-transcriptional translation of membrane proteins, which are evidently inserted into the membrane by the Sec-machinery.

Download or read book Antimicrobial Peptides written by Katsumi Matsuzaki and published by Springer. This book was released on 2019-04-12 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of antimicrobial peptides (AMPs), their mechanisms of antimicrobial action, other activities, and various problems that must still be overcome regarding their clinical application. Divided into four major parts, the book begins with a general overview of AMPs (Part I), and subsequently discusses the various mechanisms of antimicrobial action and methods for researching them (Part 2). It then addresses a range of activities other than antimicrobial action, such as cell penetration, antisepsis, anticancer, and immunomodulatory activities (Part 3), and explores the prospects of clinical application from various standpoints such as the selective toxicity, design, and discovery of AMPs (Part 4). A huge number of AMPs have been discovered in plants, insects, and vertebrates including humans, and constitute host defense systems against invading pathogenic microorganisms. Consequently, many attempts have been made to utilize AMPs as antibiotics. AMPs could help to solve the urgent problem of drug-resistant bacteria, and are also promising with regard to sepsis and cancer therapy. Gathering a wealth of information, this book will be a bible for all those seeking to develop antibiotics, anti-sepsis, or anticancer agents based on AMPs.

Download or read book Structural Aspects Of Protein Synthesis 2nd Edition written by Anders Liljas and published by World Scientific. This book was released on 2013-06-06 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: This highly illustrated book provides an up-to-date description of the structure and function of the translation system including ribosomes, tRNAs, translation factors, antibiotics and aminoacyl-tRNA synthetases.Research on translation is undergoing rapid changes and is receiving significant attention as evidenced by the Nobel Prize in Chemistry 2009. The structural research by crystallography and cryo-EM forms part of an interactive framework that involves biochemistry and molecular computation. The book provides a comprehensive overview of translation in light of the structural results. It is a valuable resource for scientists in this and related fields, as well as for students taking courses with a focus on translation.There is no other book in this field currently except the previous edition of this book. The authors have for a long time worked in the field of structure and function of the translation system.

Download or read book Oxidative Stress and Chronic Degenerative Diseases written by Jose Antonio Morales-Gonzalez and published by BoD – Books on Demand. This book was released on 2013-05-22 with total page 516 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work responds to the need to find, in a sole document, the affect of oxidative stress at different levels, as well as treatment with antioxidants to revert and diminish the damage. Oxidative Stress and Chronic Degenerative Diseases - a Role for Antioxidants is written for health professionals by researchers at diverse educative institutions (Mexico, Brazil, USA, Spain, Australia, and Slovenia). I would like to underscore that of the 19 chapters, 14 are by Mexican researchers, which demonstrates the commitment of Mexican institutions to academic life and to the prevention and treatment of chronic degenerative diseases.

Download or read book Make Life Visible written by Yoshiaki Toyama and published by Springer Nature. This book was released on 2019-10-02 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book describes marked advances in imaging technology that have enabled the visualization of phenomena in ways formerly believed to be completelyimpossible. These technologies have made major contributions to the elucidation of the pathology of diseases as well as to their diagnosis and therapy. The volume presents various studies from molecular imaging to clinical imaging. It also focuses on innovative, creative, advanced research that gives full play to imaging technology inthe broad sense, while exploring cross-disciplinary areas in which individual research fields interact and pursuing the development of new techniques where they fuse together. The book is separated into three parts, the first of which addresses the topic of visualizing and controlling molecules for life. Th e second part is devoted to imaging of disease mechanisms, while the final part comprises studies on the application of imaging technologies to diagnosis and therapy. Th e book contains the proceedings of the 12th Uehara International Symposium 2017, “Make Life Visible” sponsored by the Uehara Memorial Foundation and held from June 12 to 14, 2017. It is written by leading scientists in the field and is an open access publication under a CC BY 4.0 license.

Download or read book The Biophysics of Cell Membranes written by Richard M. Epand and published by Springer. This book was released on 2017-09-25 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the modulation of biological membranes by specific biophysical properties. The readers are introduced to emerging biophysical approaches that mimick specific states (like membrane lipid asymmetry, membrane curvature, lipid flip-flop, lipid phase separation) that are relevant to the functioning of biological membranes. The first chapter describes innovative methods to mimic the prevailing asymmetry in biological membranes by forming asymmetrical membranes made of monolayers with different compositions. One of the chapters illustrates how physical parameters, like curvature and elasticity, can affect and modulate the interactions between lipids and proteins. This volume also describes the sensitivity of certain ion channels to mechanical forces and it presents an analysis of how cell shape is determined by both the cytoskeleton and the lipid domains in the membrane. The last chapter provides evidence that liposomes can be used as a minimal cellular model to reconstitute processes related to the origin of life. Each topic covered in this volume is presented by leading experts in the field who are able to present clear, authoritative and up-to-date reviews. The novelty of the methods proposed and their potential for a deeper molecular description of membrane functioning are particularly relevant experts in the areas of biochemistry, biophysics and cell biology, while also presenting clear and thorough introductions, making the material suitable for students in these fields as well.

Download or read book Signals Switches Regulons and Cascades written by Society for General Microbiology. Symposium and published by Cambridge University Press. This book was released on 2002-04-18 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publisher Description

Download or read book The Yeast Two hybrid System written by Paul L. Bartel and published by Oxford University Press, USA. This book was released on 1997 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, part of the Advances in Molecular Biology series, presents work by pioneers in the field and is the first publication devoted solely to the yeast two-hybrid system. It includes detailed protocols, practical advice on troubleshooting, and suggestions for future development. In addition, it illustrates how to construct an activation domain hybrid library, how to identify mutations that disrupt an interaction, and how to use the system in mammalian cells. Many of the contributors have developed new applications and variations of the technique.

Download or read book The Ribosome written by Aleksandr S. Spirin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph is neither a historical outline of the development of the concepts of protein biosynthesis and the structure and functions of the ribosomes, nor an exhaustive survey of the literature on these questions. The monograph is based upon an analysis of the modern trends in this field. The purpose of the monograph was to formulate more or less generalized representations of the structure and" function of the ribosome, as we envision it at the present day. It may be that this attempt is premature for a number of reasons, and the concepts outlined here will very soon be revised. Nonetheless, despite this risk, we believe it to be advisable to undertake this attempt for the following reasons: firstly, the undertaken analysis could aid in the comprehension of the substantial mass of extremely scattered experimental data on the ribosomes presently available; secondly, in any event, even if most of the concepts outlined rapidly become obselete, they can still serve as a stimulus for a whole series of experiments; and thirdly, we hope that some of the concepts outlined will still remain essentially correct and relatively stable. In view of the aforementioned, we should make the following reservations. First of all, we made no attempt to cite all the literature on the problems discussed, but considered it sufficient to illustrate the various premises with one or several sample references.

Download or read book G Protein Coupled Receptor Dimers written by Katharine Herrick-Davis and published by Humana Press. This book was released on 2017-09-12 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: G-protein-coupled receptors (GPCRs) are believed to be the largest family of membrane proteins involved in signal transduction and cellular responses. They dimerize (form a pair of macromolecules) with a wide variety of other receptors. The proposed book will provide a comprehensive overview of GPCR dimers, starting with a historical perspective and including, basic information about the different dimers, how they synthesize, their signaling properties, and the many diverse physiological processes in which they are involved. In addition to presenting information about healthy GPCR dimer activity, the book will also include a section on their pathology and therapeutic potentials.

Download or read book Dynamics of Soft Matter written by VICTORIA GARCIA SAKAI and published by Springer Science & Business Media. This book was released on 2011-12-19 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dynamics of Soft Matter: Neutron Applications provides an overview of neutron scattering techniques that measure temporal and spatial correlations simultaneously, at the microscopic and/or mesoscopic scale. These techniques offer answers to new questions arising at the interface of physics, chemistry, and biology. Knowledge of the dynamics at these levels is crucial to understanding the soft matter field, which includes colloids, polymers, membranes, biological macromolecules, foams, emulsions towards biological & biomimetic systems, and phenomena involving wetting, friction, adhesion, or microfluidics. Emphasizing the complementarities of scattering techniques with other spectroscopic ones, this volume also highlights the potential gain in combining techniques such as rheology, NMR, light scattering, dielectric spectroscopy, as well as synchrotron radiation experiments. Key areas covered include polymer science, biological materials, complex fluids and surface science.

Download or read book RNA Metabolism in Neurodegenerative Diseases written by Rita Sattler and published by Springer. This book was released on 2018-06-18 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has become evident over the last years that abnormalities in RNA processing play a fundamental part in the pathogenesis of neurodegenerative diseases. Cellular viability depends on proper regulation of RNA metabolism and subsequent protein synthesis, which requires the interplay of many processes including transcription, pre--‐mRNA splicing, mRNA editing as well as mRNA stability, transport and translation. Dysfunction in any of these processes, often caused by mutations in the coding and non--‐ coding RNAs, can be very destructive to the cellular environment and consequently impair neural viability. The result of this RNA toxicity can lead to a toxic gain of function or a loss of function, depending on the nature of the mutation. For example, in repeat expansion disorders, such as the newly discovered hexanucleotide repeat expansion in theC9orf72 gene found in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a toxic gain of function leads to the formation of RNA foci and the sequestration of RNA binding proteins (RBPs). This in return leads to a loss of function of those RBPs, which is hypothesized to play a significant part in the disease progression of ALS and FTD. Other toxicities arising from repeat expansions are the formation of RNA foci, bi--‐directional transcription and production of repeat associated non--‐ATG (RAN) translation products. This book will touch upon most of these disease mechanisms triggered by aberrant RNA metabolism and will therefore provide a broad perspective of the role of RNA processing and its dysfunction in a variety of neurodegenerative disorders, including ALS, FTD, Alzheimer’s disease, Huntington’s disease, spinal muscular atrophy, myotonic dystrophy and ataxias. The proposed authors are leading scientists in the field and are expected to not only discuss their own work, but to be inclusive of historic as well as late breaking discoveries. The compiled chapters will therefore provide a unique collection of novel studies and hypotheses aimed to describe the consequences of altered RNA processing events and its newest molecular players and pathways.

Download or read book Endocytosis in Plants written by Jozef Šamaj and published by Springer Science & Business Media. This book was released on 2012-10-02 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Endocytosis is a fundamental cellular process by means of which cells internalize extracellular and plasma membrane cargos for recycling or degradation. It is important for the establishment and maintenance of cell polarity, subcellular signaling and uptake of nutrients into specialized cells, but also for plant cell interactions with pathogenic and symbiotic microbes. Endocytosis starts by vesicle formation at the plasma membrane and progresses through early and late endosomal compartments. In these endosomes cargo is sorted and it is either recycled back to the plasma membrane, or degraded in the lytic vacuole. This book presents an overview of our current knowledge of endocytosis in plants with a main focus on the key molecules undergoing and regulating endocytosis. It also provides up to date methodological approaches as well as principles of protein, structural lipid, sugar and microbe internalization in plant cells. The individual chapters describe clathrin-mediated and fluid-phase endocytosis, as well as flotillin-mediated endocytosis and internalization of microbes. The book was written for a broad spectrum of readers including students, teachers and researchers.

Download or read book Ras Superfamily Small G Proteins Biology and Mechanisms 1 written by Alfred Wittinghofer and published by Springer. This book was released on 2014-09-22 with total page 447 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first of two volumes provides a general overview of the genetics, structure, mechanism and regulation of the Ras superfamily proteins and describes in detail the signaling pathways and processes regulated by specific members of this family. The focus of this first volume is on the Rho and Ras subfamily of small G proteins. Renowned scientists provide insights into the biochemistry of the classical and non-classical small G-protein family members, their spatio-temporal regulation, their effectors and their roles in health and disease. Together with Volume 2, this book provides a comprehensive and state-of-the-art work on small G-proteins (GTPases). It is intended for graduates and professors in biochemistry and cell biology already working on small G-proteins (small GTPases), but also offers an extremely valuable resource for those readers who are new to the field.