Download or read book Magnetic Tweezers for the Study of Protein Structure and Function written by and published by Elsevier. This book was released on 2024-03-20 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Magnetic Tweezers for the Study of Protein Structure and Function, Volume 694 in the Methods in Enzymology serial highlights new advances in the field, with this new volume presenting interesting chapters on a variety of topics, including Single membrane protein tethering for magnetic tweezer experiments, Membrane protein folding studies using a robust magnetic tweezer method, Magnetic tweezers in cell mechanics, and more.
Download or read book Magnetic Tweezers for the Study of Protein Structure and Function written by and published by Elsevier. This book was released on 2024-03-14 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: Magnetic Tweezers for the Study of Protein Structure and Function, Volume 694 in the Methods in Enzymology serial highlights new advances in the field, with this new volume presenting interesting chapters on a variety of topics, including Single membrane protein tethering for magnetic tweezer experiments, Membrane protein folding studies using a robust magnetic tweezer method, Magnetic tweezers in cell mechanics, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology serials Updated release includes the latest information on Magnetic Tweezers for the Study of Protein Structure and Function
Download or read book Single Molecule Optical Magnetic Tweezers Microscopy Studies of Protein Dynamics written by Qing Guo and published by . This book was released on 2015 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation presents our research work aiming at conformational manipulation of single enzyme protein molecules, performed by single molecule magnetic tweezers correlated with optical fluorescence spectroscopy. To experimentally investigate the enzyme-substrate interactions and the related conformational fluctuations, we have developed a new approach to manipulate the enzymatic conformation and enzyme-substrate interaction at the single-molecule level by using a combined magnetic tweezers and simultaneous fluorescence resonance energy transfer (FRET) spectroscopic microscopy. By a repetitive pulling-releasing manipulation of a Cy3-Cy5 dye labeled 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) molecule under the conditions with and without enzymatic substrates, we have probed and analyzed the enzymatic conformational dynamics. Our results indicate that the enzymatic conformational flexibility can be regulated by enzyme-substrate interactions: (1) the enzyme at its conformation-perturbed state has less flexibility when binding substrates, and (2) substrate binding to the enzyme significantly changes the enzyme conformational flexibility, experimental evidence of so called entropy trapping in and enzyme-substrate reactive transition state. Furthermore, our results provide significant experimental analysis of folding-binding interactions of the enzyme-substrate interactions, and reveal the dynamic nature of the enzyme-substrate interactions. We also find supportive results from Steered Molecular Dynamics (SMD) Simulation, showing that in our studies, conformational manipulation by magnetic tweezers is able to distort the active domain of the enzyme molecules to an extent that significantly beyond thermal conformational fluctuations. Furthermore, we have also revealed the impact of partially unfolding the enzyme molecules on their activity by using single-molecule TIRF-magnetic tweezers spectroscopy to manipulate conformation of the enzyme molecules to a partially unfolded, yet not fully denatured condition. By conformationally distorting horseradish peroxidase (HRP) molecules via magnetic tweezers at the single molecule level, we successfully manipulated and examined the activity changes of the HRP catalyzed H2O2-Amplex Red reaction. We have observed significant tolerance of the enzyme activity to the enzyme conformation in its deformed or partially-unfolded states. We have identified that (1) enzymatic activity can be manipulated by our TIRF-magnetic tweezers at single molecule level; and (2) enzyme molecules in partially unfolded conformation are still capable of showing significant activity, although at a lower but measurable level, due to the enzymatic active site conformational fluctuation and substrate binding induced folding-binding conformational changes. We further provide our understanding of the enzyme behavior based on enzymatic conformational fluctuation, enzyme-substrate interactions, enzyme-substrate active complex formation, and protein folding-binding interactions.
Download or read book Mechanical Unfolding Response of Proteins written by Ionel Popa and published by American Chemical Society. This book was released on 2023-06-16 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mechanical Unfolding Response of Proteins is a thermodynamically motivated overview of when, why, and how proteins respond to mechanical perturbations and the experimental techniques used to probe single protein biophysics. Relative newcomers to the field (new graduate students), and those starting from a biological background hoping for an introduction to the physics behind protein behavior, will benefit from reading this primer.
Download or read book Frontiers in Protein Structure Function and Dynamics written by Dev Bukhsh Singh and published by Springer Nature. This book was released on 2020-07-02 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.
Download or read book Membrane Biomechanics written by and published by Academic Press. This book was released on 2020-10-23 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Membrane Biomechanics, Volume 86, the latest release in the Current Topics in Membranes series, highlights new advances in the field, with this new volume presenting interesting chapters on Lipid bilayers: phase behavior and mechanics, Molecular mechanisms of cell membrane structure modification by omega-3 fatty acids, Mechanical properties of magnetoliposomes, Mechanosensitive ion channels and membrane tension, From cell membrane to the nuclear membrane through modulation of cytoskeleton, Endothelial stiffness in dyslipidemia and aging, Vascular smooth muscle stiffness in aging and vascular disease, Mechanobiology of macrovesicle release and activation, Interplay of membrane cholesterol and substrate on vascular smooth muscle mechanics, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Current Topics in Membranes series Includes the latest information on Membrane Biomechanics
Download or read book Controlled Nanoscale Motion written by Heiner Linke and published by Springer Science & Business Media. This book was released on 2007-02-09 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt: When the size of a machine approaches the nanometer scale, thermal fluctuations become large compared to the energies that drive the motor. The control of motion at the nanoscale therefore requires physical understanding and technical approaches that are fundamentally different from those that are successful at the macroscale. This volume provides an introduction to the state-of-the-art of controlled nanoscale motion in biological and artificial systems. Topics include the control and function of protein motors, the physics of non-equilibrium Brownian motion, and the physics and fabrication of synthetic molecular motors. The chapters in this book are based on selected contributions on the 2005 Nobel Symposium to Controlled Nanoscale Motion and are written by leading experts in their fields.
Download or read book Chromatin and Chromatin Remodeling Enzymes Part B written by Carl Wu and published by Elsevier. This book was released on 2004-03-07 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA in the nucleus of plant and animal cells is stored in the form of chromatin. Chromatin and the Chromatin remodelling enzymes play an important role in gene transcription.
Download or read book Single Molecule Analysis written by Iddo Heller and published by Springer Nature. This book was released on 2023-11-13 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: This third edition volume expands on the previous editions with new discussions on the latest techniques and developments in the field. The chapters in this book are organized into four parts, and cover topics such as optical tweezers; single-molecule fluorescence tools; atomic force microscopy; magnetic tweezers; applications to virus protein shells, unfolding of proteins, nucleic acids, motor proteins, in vivo and in vitro; and protocols to establish specific surface interactions and perform force calibration. 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. Cutting-edge and thorough, Single Molecule Analysis: Methods and Protocols, Third Edition is a valuable resource for all researchers who want to learn more about this exciting and still expanding field. Chapters 2, 7, 8, 9, 12, 18, and 19 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Download or read book Biophysics of Molecular Chaperones written by Sebastian Hiller and published by Royal Society of Chemistry. This book was released on 2023-11-01 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular chaperones are critical to control protein quality in all living cells. Understanding chaperone function at the atomic level, and in particular its mode of interaction with client proteins, is crucial to understanding the fundamental roles chaperones play in biology. This book fills a gap in the literature by comprehensively summarizing and discussing new advanced experimental techniques for their analysis. Providing a comprehensive overview of advanced biophysical methods for the characterization of molecular mechanisms of molecular chaperones, the majority of the contributions are NMR methodology. This is the method of choice for atomic resolution studies of such systems. Additional notable biophysical approaches are considered to present all relevant current developments in exploring chaperone function and the transient and dynamic interactions with their client proteins. The book is targeted at both current practitioners of structural biology and biophysical chemistry and scientists who are interested in entering the field. It could be useful for graduate students as supplementary reading.
Download or read book Dissecting Structure function Relationships in Molecular Motors Using Protein Engineering and Single molecule Methods written by Athena Ierokomos and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological cells can harness the free energy of ATP hydrolysis to perform mechanical tasks using molecular motor proteins. These nanoscale machines are able to generate directional motion through mechanochemical cycles which rely on allosteric communication and large rearrangements of protein domains. In studies of molecular motors, protein engineering allows us to test our understanding of relationships between structure and function, while single-molecule methods allow us to directly observe motor dynamics. Here we consider two systems which undergo large conformational changes: cytoplasmic dynein and DNA gyrase. We use protein engineering to investigate structural features that contribute to dynein velocity and processivity. Building on our initial findings, we are able to design dynein motors that change speed in response to light. The speed and controllability of future designs may be improved with further engineering, in order to generate light-activatable, dynein-based tools which can be used to study transport functions in vivo. In the second half of this dissertation, we consider a single-molecule technique for multimodal measurements of mechanics and fluorescence in DNA and DNA:protein complexes. Mechanical measurements based on magnetic tweezers are combined with simultaneous fluorescence imaging that can report on macromolecular binding and local conformational changes. We outline how this method can be applied to study the mechanism of DNA gyrase, a motor which introduces negative supercoils by coordinating protein domain motions and ATP hydrolysis with DNA cleavage and religation. We observe binding coincident with mechanics and report on challenges in using FRET-labeled enzymes to correlate domain motions with mechanical substeps. We anticipate that correlative multimodal measurements will be valuable tools for characterizing the dynamics of DNA gyrase and other large nucleoprotein machines.
Download or read book Optical Tweezers written by Arne Gennerich and published by Springer Nature. This book was released on 2022-09-05 with total page 753 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume explores a wide variety of techniques involving optical tweezers, a technology that has become increasingly more accessible to a broad range of researchers. Beginning with recent technical advances, the book continues by covering the application of optical tweezers to study DNA-protein interactions and DNA motors, protocols to perform protein (un)folding experiments, the application of optical tweezers to study actin- and microtubule-associated motor proteins, and well as protocols for investigating the function and mechanical properties of microtubules and intermediate filaments, and more. 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, Optical Tweezers: Methods and Protocols, Second Edition serves as an ideal resource for expanding the accessibility and use of optical traps by scientists of diverse disciplines.
Download or read book Fermentation Microbiology and Biotechnology Fourth Edition written by E. M. T. El-Mansi and published by CRC Press. This book was released on 2018-12-17 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fermentation Microbiology and Biotechnology, 4th Edition explores and illustrates the broad array of metabolic pathways employed for the production of primary and secondary metabolites, as well as biopharmaceuticals. This updated and expanded edition addresses the whole spectrum of fermentation biotechnology, from fermentation kinetics and dynamics to protein and co-factor engineering. It also sheds light on the new strategies employed by industrialist for increasing tolerance and endurance of microorganisms to the accumulation of toxic wastes in microbial-cell factories. The new edition builds upon the fine pedigree of its earlier predecessors and extends the spectrum of the book to reflect the multidisciplinary and buoyant nature of this subject area. Key Features Covers the whole spectrum of the field from fermentation kinetics to control of fermentation and protein engineering. Includes case studies specifically designed to illustrate industrial applications and current state-of-the-art technologies. Presents the contributions of eminent international academics and industrial experts. Offers new chapters addressing: The prospects and the role of bio-fuels refineries, Control of metabolic efflux to product formation in microbial-cell factories and Improving tolerance of microorganisms to toxic byproduct accumulation in the fermentation vessel.
Download or read book RNA Structure and Function written by Jan Barciszewski and published by Springer Nature. This book was released on 2023-12-05 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved. RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine. In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases. This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.
Download or read book Protein Interactions written by Jianfeng Cai and published by BoD – Books on Demand. This book was released on 2012-03-16 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein interactions, which include interactions between proteins and other biomolecules, are essential to all aspects of biological processes, such as cell growth, differentiation, and apoptosis. Therefore, investigation and modulation of protein interactions are of significance as it not only reveals the mechanism governing cellular activity, but also leads to potential agents for the treatment of various diseases. The objective of this book is to highlight some of the latest approaches in the study of protein interactions, including modulation of protein interactions, development of analytical techniques, etc. Collectively they demonstrate the importance and the possibility for the further investigation and modulation of protein interactions as technology is evolving.
Download or read book Metabolic Engineering for Bioactive Compounds written by Vipin Chandra Kalia and published by Springer. This book was released on 2017-10-07 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprehensively discusses the latest research in the area of metabolic engineering. Metabolic engineering solutions for bioactive compounds are now being derived by means of heterologous gene expression, in a wide range of organisms. The book provides an overview of the model systems being employed for metabolic manipulation to yield bioactive molecules, such as single-cell proteins, antibody generation, metabolites, proteases, chaperones, therapeutic proteins, nanomaterials, polymeric conjugates, dendrimers and nanoassemblies, Escherichia coli, Agrobacterium, Saccharomyces cerevisiae and cell lines, etc. In addition, it shares insights into the scope of these methods in the areas of prevention, diagnosis and treatment of diseases, e.g. immunotherapy for curing various diseases like cancer, allergies, autoimmune diseases, etc.
Download or read book Non Protein Coding RNAs written by Nils Walter and published by Springer Science & Business Media. This book was released on 2008-11-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.
