Single-molecule Dynamics in Protein Interactions PDF Download
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Author: Hector Romero Gonzalez
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Author: Hector Romero Gonzalez
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Author: Dev Bukhsh Singh
Publisher: Springer Nature
ISBN: 9811555303
Category : Science
Languages : en
Pages : 458
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Book Description
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.
Author: Mark C. Williams
Publisher: Springer Science & Business Media
ISBN: 0387928081
Category : Science
Languages : en
Pages : 354
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Book Description
Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.
Author: Erwin J. G. Peterman
Publisher: Humana Press
ISBN: 9781617792816
Category : Science
Languages : en
Pages : 317
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Book Description
Life scientists believe that life is driven, directed, and shaped by biomolecules working on their own or in concert. It is only in the last few decades that technological breakthroughs in sensitive fluorescence microscopy and single-molecule manipulation techniques have made it possible to observe and manipulate single biomolecules and measure their individual properties. The methodologies presented in Single Molecule Techniques: Methods and Protocols are being applied more and more to the study of biologically relevant molecules, such as DNA, DNA-binding proteins, and motor proteins, and are becoming commonplace in molecular biophysics, biochemistry, and molecular and cell biology. The aim of Single Molecule Techniques: Methods and Protocols is to provide a broad overview of single-molecule approaches applied to biomolecules on the basis of clear and concise protocols, including a solid introduction to the most widely used single-molecule techniques, such as optical tweezers, single-molecule fluorescence tools, atomic force microscopy, magnetic tweezers, and tethered particle motion. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Single Molecule Techniques: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and provides a broad and thorough overview of the exciting and still-emerging field of single-molecule biology.
Author: Amy Davenport Migliori
Publisher:
ISBN: 9781303687983
Category :
Languages : en
Pages : 139
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Book Description
Often, proteins are studied using bulk techniques, in which the average properties of large ensembles of molecules are studied. Although this has led to substantial new knowledge, the use of single-molecule biophysics and computational techniques to understand individual molecular actions and dynamics and the role of each residue allows for a more complete picture of activity in some cases. We present two applications of such techniques, first to determine the relationship between structure and function of the DNA translocation motor gp17 in Bacteriophage T4, and second to study looping of DNA mediated by the tumor suppressor protein p53. Specifically, we studied the role of an interface between the N- and C-terminal subdomains in generation of the high packaging forces and translocation velocities using a dual-beam optical trap. Mutation of charged amino acids located within this interface region confirmed that electrostatic forces play a role in force and velocity generation, with mutants showing a reduction in forward velocity, average velocity, and percentage of time spent packaging at different applied forces. To explain these experimental results, we generated a two-state computational model to calculate the free energy of the translocation step in gp17. We found excellent correlation between experimental data and calculated free energy change of translocation. Decomposition of the free energy change allowed for the identification of key residues involved in gp17-mediated packaging, and the role of each was explained. These results reveal that the power stroke of the motor requires substantial contributions from charged residues, hydrophobic residues, and polar residues instead of charged residues alone. Finally, we propose that several of these key residues may be hot spot residues, contributing a significant portion of the free energy used to package DNA. p53-mediated loop formation in DNA was studied using direct measurement with a dual optical tweezer setup. Looping of DNA by p53 has previously been demonstrated qualitatively using cryo-electron microscopy as well as transcription assays. we demonstrated formation of loops in purified human Col18A promoter containing five p53 binding sites. This looping may be directly related to p53 activity at transcriptional start sites.
Author: Nan Jing
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
The objective of this work is to develop a micro/nanofluidic-based single molecule detection (SMD) scheme, which would allow us to inspect individual protein or protein complex study protein-protein interactions and their dynamics. This is a collaboration work with MD Anderson Cancer Center and we applied this scheme to study functions of various proteins related to cancer progression in hope to shed new light on cancer research. State-of-the-art micro/nano-fabrication technology is used to provide fused silica micro/nano-fluidic channel devices as our detection platform. Standard contact photolithography, projection photolithography and advanced electron-beam lithography are used to fabricate micro/nano-fluidic channel with width ranging from 100nm to 2[micron]. The dimensions of these miniaturized biochips are designed to ensure single molecule resolution during detection and shrinking the detection volume leads to increase in signal-to-noise ratio, which is very critical for SMD. To minimize surface adsorption of protein, a fused silica channel surface coating procedure is also developed and significantly improved the detection efficiency. A fluorescent-labeled protein sample solution is filled in the fluidic channel by capillary force, and proteins are electro-kinetically driven through the fluidic channel with external voltage source. Commercial functionalized Quantum Dots (Qdots) are used as fluorescent labels due to its various advantages over conventional organic dyes for single molecule multi-color detection application. A fluorescence correlation spectrometer system, equipped with a 375nm diode laser, 60x water immersion objective with N.A. of 1.2 and two avalanche photodiodes (APD) is implemented to excite single molecules as well as collect emitted fluorescence signals. A two-dimensional photon burst analysis technique (photon counts vs. burst width) is developed to analyze individual single molecule events. We are able to identify target protein or protein complex directly from cell lysate based on fluorescence photon counts, as well as study the dynamics of protein-protein interactions. More importantly, with this technique we are also able to assess interactions between three proteins, which cannot be done with current ensemble measurement techniques. In summary, the technique described in this work has the advantages of high sensitivity, short processing time (2-3 minutes), very small sample consumption and high resolution quantitative analysis. It could potentially revolutionize the area of protein interaction research and provides us with more clues for the future of cancer diagnostics and treatments.
Author: Mark C. Williams
Publisher: Springer
ISBN: 9780387928074
Category : Science
Languages : en
Pages : 350
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Book Description
Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.
Author: Gandhi Radis-Baptista
Publisher: BoD – Books on Demand
ISBN: 9535111515
Category : Medical
Languages : en
Pages : 548
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Book Description
Molecular Toxinology has been consolidated as a scientific area focused on the intertwined description of several aspects of animal toxins. In an inquiring biotechnological world, animal toxins appear as an invaluable source for the discovery of therapeutic polypeptides. Animal toxins rely on specific chemical interactions with their partner molecule to exert their biological actions. The comprehension of how molecules interact and recognize their target is essential for the rational exploration of bioactive polypeptides as therapeutics. Investigation on the mechanism of molecular interaction and recognition offers a window of opportunity for the pharmaceutical industry and clinical medicine. Thus, this book brings examples of two interconnected themes - molecular recognition and toxinology concerning to the integration between analytical procedures and biomedical applications.
Author: Mariam Iftikhar
Publisher:
ISBN: 9780355066067
Category :
Languages : en
Pages : 128
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Book Description
Molecular motions of proteins and their flexibility induce conformational states required for enzyme catalysis, signal transduction, and protein-protein interactions. However, the mechanisms for protein transitions between conformational states are often poorly understood, especially in the millisecond to microsecond range where conventional optical techniques and computational modeling are most limited. To investigate the microsecond dynamics of enzymes, single-walled carbon nanotube -- field-effect transistors (SWCNT-FETs) were used as single-molecule biosensors. The SWCNT-FETs have sufficient sensitivity and bandwidth to monitor the conformational motions and processivity of an individual cAMP-dependent protein kinase A (PKA) molecule. Protein attachment is accomplished by functionalizing a SWCNT-FET device with a single protein and measuring the conductance versus time through the device as it is submerged in an electrolyte solution. PKA-functionalized nanocircuits elucidated the time PKA spent traveling between three different conformational motions upon binding of its two substrates.To generalize this approach for the study of a wide variety of proteins at the single-molecule level, this dissertation investigates the bioconjugation process to determine and isolate the key parameters required for functionalizing a SWCNT with a single protein. Further analysis into the parameters implicated in the thiol-maleimide bioconjugation step of the SWCNT-FET device fabrication proved an exhausting effort. We developed improved linker molecules, anthracene maleimide, for attachment of three different proteins to the SWCNT and a new derivative of maleimide providing a solution to overcome side reactions associated with the reducing agent, tris(2-carboxyethyl)phosphine (TCEP). Protein purity and presence of detergent proved to play key roles in preventing nanocircuit surface fouling. An alternative bioconjugation method, utilizing an azide-functionalized hen egg-white lysozyme (HEWL) to tether the enzyme to the SWCNT through an alkyne linker molecule was developed. The work described here explores the current SWCNT attachment method as well as a new strategy to apply SWCNT-FET devices to study novel proteins. The results demonstrate SWCNT-FET as a sensitive technique for studying conformational dynamics of biological molecules in the microsecond range.
Author: M Michael Gromiha
Publisher: World Scientific
ISBN: 9811211884
Category : Science
Languages : en
Pages : 424
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Book Description
This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
