Download or read book Engineering Protein Scaffolds for Ultrafast Broad Range Single molecule Analog PH Biosensors written by Ameed H. Hashmi and published by . This book was released on 2021 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: The research described in this thesis aims at exploiting recent important theoretical and experimental developments in protein folding towards developing advanced biosensors with improved/novel properties. Transforming this basic protein folding knowledge into engineering strategies for designing novel biosensors is an enormous challenge. Here we demonstrate the very first steps in that direction. Biosensors based on proteins that naturally toggle between two states (unfolded/folded) upon specific binding to a target molecule have been successfully used for real-time sensing. These devices behave as conformational switch sensors. Principles on how to engineer this type of conformational transducer onto any protein of interest have also been laid out. Our work takes this state of the art forward to design high-performance conformational rheostat sensors. The rationale is to develop sensors with expanded dynamic range and faster response time by using as conformational transducer the coupling of binding to the analyte and the gradual folding process of fast folding protein modules, and fluorescence as optical readout. As proof of concept, we investigate the pH sensing capabilities of engineered proteins based on two scaffolds: i) an anti-parallel coiled-coil, and ii) a tandem array of the small downhill folding domain BBL. Our results reveal that such pH sensors exhibit a linear response over at least 4 orders of magnitude in proton concentration. We also demonstrate that a pH sensor based on a conformational rheostat transducer can produce analog pH readouts at the single-molecule level together with ultrafast response (

Download or read book Protein Folding Upon Binding and Conformational Rheostats written by Thinh Luong and published by . This book was released on 2021 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the work horses of the cell that perform the vast majority of functions essential for life. The mechanism by which proteins fold to their functional native state has been a subject of extensive research for more than 50 years now. Downhill folders are the class of proteins whose folding reaction is heterogeneous, non-cooperative, and happens without encountering a significant free energy barrier, resulting in ultrafast kinetics. The single ensemble of conformations of a global downhill folding protein moves gradually from highly disordered to the unique native structure when thermodynamic parameters that affect the protein's stability are changed (one-state folding). The gradual morphing of a one-state downhill folding protein structure in response to thermodynamic bias is referred to as a conformational rheostat. When such a conformational rheostat is coupled to binding an analyte, it can result in an ultrafast, broad band, and single-molecule analog biosensors. This thesis explores conformational rheostats as the mechanism behind the folding upon binding behavior of intrinsically disordered proteins and as broadband transducers towards engineering high-performance biosensors.The second chapter of this thesis describes a new methodology that we have developed to study the conformational landscape of intrinsically partially disordered proteins (IPDP). This methodology is inspired by the LEGO game, where the sequence of an IPDP is deconstructed into its local structural elements and their possible combinations based on the 3D structure the IPDP acquires upon binding its partners. The local structural elements are hence analogous to LEGO building blocks, and their combinations report on the interactions among them, like the complementary indentations of LEGO pieces. In particular, we chose the IPDP NCBD as model IPDP to develop the proof of concept for the method. Our results showed that even though the NCBD is highly flexible and apparently disordered, there are strong local signals and different sets of long-range transient interactions. These sets of interactions stabilize the overall fold and compete with one another hence resulting in a dynamic ensemble. The methodology developed in Chapter 2 is expected to be extremely useful in characterizing the incipient cooperativity of virtually any IPDP in their unbound form, a capability that is currently unavailable. Chapters 3 and 4 of this thesis deal with the design of a pH biosensor using the downhill folding protein gpW as a scaffold and unfolding coupled to ionization as a transducer. In chapter 3, a methodology for engineering conformational pH transducing into pH insensitive proteins using a histidine grafting approach was developed. The methodology was applied to the protein gpW to demonstrate an engineered, tunable broadband pH transducer based on the conformational rheostat mechanism. Chapter 4 explores general strategies for introducing fluorescence readouts capable of converting the gradual conformational changes of the rheostatic pH transducer into broadband fluorescence-based pH biosensors. Strategies that exploit the Förster Resonance Energy Transfer (FRET) and Photo Induced Electron Transfer (PET) mechanisms were explored as potential means to convert changes in conformation into suitable fluorescence signals were explored and characterized. We discovered that FRET signals using fluorophores in the visible (required for high-sensitivity biosensing) are insensitive to the localized conformational changes associated with conformational rheostats in native-like conditions. In contrast, the very short-range distance dependence of PET (

Download or read book Fluorescent Analogs of Biomolecular Building Blocks written by Marcus Wilhelmsson and published by John Wiley & Sons. This book was released on 2016-04-04 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescent Analogs of Biomolecular Building Blocks focuses on the design of fluorescent probes for the four major families of macromolecular building blocks. Compiling the expertise of multiple authors, this book moves from introductory chapters to an exploration of the design, synthesis, and implementation of new fluorescent analogues of biomolecular building blocks, including examples of small-molecule fluorophores and sensors that are part of biomolecular assemblies.

Download or read book Single Molecule Spectroscopy written by R. Rigler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: The topics range from single molecule experiments in quantum optics and solid-state physics to analogous investigations in physical chemistry and biophysics.

Download or read book Ribosomes Structure Function and Dynamics written by Marina V. Rodnina and published by Springer Science & Business Media. This book was released on 2011-12-10 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.

Download or read book Protein Folding Misfolding and Aggregation written by Victor Muñoz and published by Royal Society of Chemistry. This book was released on 2008 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods h.

Download or read book Imaging Dopamine written by Paul Cumming and published by Cambridge University Press. This book was released on 2009-04-02 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: An illustrated biography of the dopamine molecule, with each chapter presenting a specific stage in the biochemical pathway for dopamine.

Download or read book Bionanotechnology written by David S. Goodsell and published by John Wiley & Sons. This book was released on 2004-04-16 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discussions of the basic structural, nanotechnology, and system engineering principles, as well as an introductory overview of essential concepts and methods in biotechnology, will be included. Text is presented side-by-side with extensive use of high-quality illustrations prepared using cutting edge computer graphics techniques. Includes numerous examples, such applications in genetic engineering. Represents the only available introduction and overview of this interdisciplinary field, merging the physical and biological sciences. Concludes with the authors' expert assessment of the future promise of nanotechnology, from molecular "tinkertoys" to nanomedicine. David Goodsell is author of two trade books, Machinery of Life and Our Molecular Nature, and Arthur Olson is the world's leader in molecular graphics and nano-scale representation.

Download or read book Functional Electrodes For Enzymatic And Microbial Electrochemical Systems written by Nicolas Brun and published by World Scientific. This book was released on 2017-10-27 with total page 658 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioelectrochemical Systems (BESs) are innovative and sustainable devices. They combine biological and electrochemical processes to engineer sensors, treat wastewater and/or produce electricity, fuel or high-value chemicals. In BESs, scientists have managed to incorporate biological catalysts, i.e. enzymes and/or microorganisms, and make them work in advanced electrochemical cells. BESs operate under mild conditions — at close to ambient temperature and pressure and at circumneutral pH — and represent a sustainable alternative to precious metal-based systems. Incorporating biological catalysts into devices while maintaining their activity and achieving electrical communication with electrode surfaces is a critical challenge when trying to advance the field of BESs.From implantable enzymatic biosensors to microbial electrosynthesis, and from laboratory-scale systems and fundamental studies to marketed devices, this book provides a comprehensive overview of recent advances related to functional electrodes for BESs. Suitable for researchers and graduate students of chemistry, biochemistry, materials science and environmental science and technology.

Download or read book Nanostructured Materials written by Vladimir M. Shalaev and published by . This book was released on 1997 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines the physics, chemistry, and structure-property relationships of nanomaterials, as well as nanoscale electronics and photonics devices. It also discusses metal and semiconductor clusters, composites, thin films, and molecular engineering.

Download or read book Activity Based Protein Profiling written by Stephan A. Sieber and published by Springer Science & Business Media. This book was released on 2012-02-21 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: ABPP Methodology: Introduction and Overview, by Matthew B. Nodwell und Stephan A. Sieber Activity-Based Protein Profiling for Natural Product Target Discovery, by Joanna Krysiak und Rolf Breinbauer Photoaffinity Labeling in Activity-Based Protein Profiling, by Paul P. Geurink, Laurette M. Prely, Gijs A. van der Marel, Rainer Bischoff und Herman S. Overkleeft Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis, by William P. Heal und Edward W. Tate Functional Analysis of Protein Targets by Metabolomic Approaches, by Yun-Gon Kim und Alan Saghatelian

Download or read book NanoBioEngineering written by Bhupinder Singh and published by CRC Press. This book was released on 2018-11-02 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: The objective of this book is to provide the fundamental comprehension of a broad range of topics in an integrated volume such that readership hailing from diverse disciplines can rapidly acquire the necessary background for applying it in pertinent research and development field.

Download or read book Combinatorial Methods for Chemical and Biological Sensors written by Radislav A. Potyrailo and published by Springer Science & Business Media. This book was released on 2009-03-21 with total page 495 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical sensors are in high demand for applications as varied as water pollution detection, medical diagnostics, and battlefield air analysis. Designing the next generation of sensors requires an interdisciplinary approach. The book provides a critical analysis of new opportunities in sensor materials research that have been opened up with the use of combinatorial and high-throughput technologies, with emphasis on experimental techniques. For a view of component selection with a more computational perspective, readers may refer to the complementary volume of Integrated Analytical Systems edited by M. Ryan et al., entitled “Computational Methods for Sensor Material Selection”.

Download or read book Transmembrane Transporters written by Michael W. Quick and published by Wiley-Liss. This book was released on 2002-09-09 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Families of transporters and their classification / Milton H. Saier, Jr. -- 2. Yeast as a model system for studying glucose transport / Eckhard Boles -- 3. Neurotransmitter transporters of drosophila / Martin G. Burg and William L. Pak -- 4. Transgenic mice in monoamine transporter research / Sara R. Jones -- 5. Searching for novel genetic variation in neurotransmitter transporters / Randy D. Blakely and Alexandra R. Belous -- 6. Non-viral gene transfer allows up- and down-expression of the brain serotonin transporter with functional consequences / Marie-Pascale Martres ... [et al.] -- 7. Methods in studying the regulation and trafficking of transmembrane transporters / Scott L. Deken, Dan Wang, and Michael W. Quick -- 8. Chemical modification strategies for structure-function studies / Gary Rudnick -- 9. Methanethiosulfonate reagent accessibility studies, cysteine scanning mutagenesis, protein overexpression and functional reconstitution / Ronald S. Kaplan -- 10. Peptide mapping of dopamine transporter ligand and substrate interaction sites / Margaret J. Lowe, Jon D. Gaffaney, and Roxanne A. Vaughan -- 11. Mass spectrometry of membrane transport proteins / Julian P. Whitelegge, H. Ronald Kaback and Johannes le Coutre -- 12. Amperometric recording of amphetamine-induced dopamine efflux / David Sulzer ... [et al.] -- 13. Voltage clamp and fluorometric techniques for studying glutamate transporter function / Anastassios Tzingounis, Hans Peter Larsson and Michael P. Kavanaugh -- 14. Studies of glial glutamate transporters in hippocampal microcultures / Steven Mennerick, Robert J. Cormier and Charles F. Zorumski -- 15. Imaging monoamine transporters in the brain / Hank F. Kung and Mei-Ping Kung -- 16. Measuring and modeling the spatiotemporal profile of GABA at the synapse / Linda S. Overstreet, Gary L. Westbrook and Mathew V. Jones

Download or read book Protein Engineering written by Huimin Zhao and published by John Wiley & Sons. This book was released on 2021-08-23 with total page 41 pages. Available in PDF, EPUB and Kindle. Book excerpt: A one-stop reference that reviews protein design strategies to applications in industrial and medical biotechnology Protein Engineering: Tools and Applications is a comprehensive resource that offers a systematic and comprehensive review of the most recent advances in the field, and contains detailed information on the methodologies and strategies behind these approaches. The authors—noted experts on the topic—explore the distinctive advantages and disadvantages of the presented methodologies and strategies in a targeted and focused manner that allows for the adaptation and implementation of the strategies for new applications. The book contains information on the directed evolution, rational design, and semi-rational design of proteins and offers a review of the most recent applications in industrial and medical biotechnology. This important book: Covers technologies and methodologies used in protein engineering Includes the strategies behind the approaches, designed to help with the adaptation and implementation of these strategies for new applications Offers a comprehensive and thorough treatment of protein engineering from primary strategies to applications in industrial and medical biotechnology Presents cutting edge advances in the continuously evolving field of protein engineering Written for students and professionals of bioengineering, biotechnology, biochemistry, Protein Engineering: Tools and Applications offers an essential resource to the design strategies in protein engineering and reviews recent applications.

Download or read book Protein Misassembly written by and published by Academic Press. This book was released on 1997-10-22 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: The role that primary amino acid sequences plays in influencing the partitioning of polypeptides between productive folding and irreversible aggregation pathways has introduced a whole new dimension to the folding problem. The volume deals with the structures of the products of protein misassembly and the role of amino acid sequences in favoring these structures.

Download or read book Activity Based Protein Profiling written by Benjamin F. Cravatt and published by Springer. This book was released on 2019-01-25 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of contemporary perspectives on using activity-based protein profiling (ABPP) for biological discoveries in protein science, microbiology, and immunology. A common theme throughout is the special utility of ABPP to interrogate protein function and small-molecule interactions on a global scale in native biological systems. Each chapter showcases distinct advantages of ABPP applied to diverse protein classes and biological systems. As such, the book offers readers valuable insights into the basic principles of ABPP technology and how to apply this approach to biological questions ranging from the study of post-translational modifications to targeting bacterial effectors in host-pathogen interactions.