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Modeling Protein Dynamics In Solution Effects Of Ligand Binding And Crowding
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Book Synopsis Modeling Protein Dynamics in Solution: Effects of Ligand Binding and Crowding by : Cheng Lu
Download or read book Modeling Protein Dynamics in Solution: Effects of Ligand Binding and Crowding written by Cheng Lu and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Zusammenfassung: In this thesis, molecular dynamics simulations have been performed to understand the effect of ligand binding or crowding on the structure and dynamics of proteins or peptides.Our findings show a long-range conformational response of the PDZ2 domain of human tyrosine phosphatase 1E to ligand release in the form of a collective shift of several rigid secondary structure elements and the C terminal loop relative to the rest of the protein away from the N-terminus.Considering a multi-domain protein as a next step, the allosteric coupling in the ligand-controlled oligomeric bacterial protease DegS between the active site and (i) the binding pocket of the ligand, as well as (ii) the sites in contact with other protomers has been analyzed. Our results indicate that only trimeric and not monomeric DegS is functional. The pathways via which ligand release or the disassembly of DegS into monomers leads to response at functionally relevant allosteric sites are revealed.Finally, we have the relationship between biomolecular conformational changes and water mediation in crowded environments. We find that molecular crowding, though barely changing the structural distribution of the peptide, substantially affects the kinetics of conformational changes. In view of the weak interaction between the peptides observed (a prerequisite for good crowders), our results provide evidence for a non-trivial role of the solvent for the slowing down in the kinetics of conformational transitions of the peptides
Book Synopsis Protein Stability by : David S. Eisenberg
Download or read book Protein Stability written by David S. Eisenberg and published by . This book was released on 1995 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: The topics covered by this volume include: protein destabilization at low temperatures; engineering the stability and function of Gene V Protein; free energy balance in protein folding; modelling protein stability as a heteropolymer collapse; stability of alpha helices; protein stability with T4 Lysozyme.
Book Synopsis Protein Dynamics and Entropy by : Kyle William Harpole
Download or read book Protein Dynamics and Entropy written by Kyle William Harpole and published by . This book was released on 2015 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: The nature of macromolecular interactions has been an area of deep interest for understanding many facets of biology. While a great deal of insight has been gained from structural knowledge, the contribution of protein dynamics to macromolecular interactions is not fully appreciated. This plays out from a thermodynamic perspective as the conformational entropy. The role of conformational entropy in macromolecular interactions has been difficult to address experimentally. Recently, an empirical calibration has been developed to quantify the conformational entropy of proteins using solution NMR relaxation methods. This method has been demonstrated in two distinct protein systems. The goal of this work is to expand this calibration to assess whether conformational entropy can be effectively quantified from NMR-derived protein dynamics. First, we demonstrate that NMR dynamics do not correlate well between the solid and solution states, suggesting that the relationship between the conformational entropy of proteins is limited to solution state-derived NMR dynamics. We hypothesize that this may be partially due to the role of hydration of the protein in its dynamics. Next, we expand our empirical calibration to over 30 distinct protein systems and demonstrated that the relationship between NMR dynamics and conformational entropy is both robust and general. Furthermore, we demonstrate that conformational entropy plays a significant role in macromolecular interactions. Using our empirical calibration, we then look to address if conformational entropy could be an important contribution to drug design. The latter process is often a brute force approach, and subsequent optimization of initial drug candidates is often a guess and check process. In silico drug design was thought to offer a more efficient and rational approach, but often relies on static structures. This minimizes or completely neglects the role that conformational entropy may play in binding. Here we experimentally determine the role of conformational entropy in the drug target p38a MAPK in binding to two potent inhibitors. We demonstrate evidence that conformational entropy may represent a tunable parameter in affinity optimization of lead compounds. This has important implications for lead optimization and strongly suggests that the role of conformational entropy be considered in drug design efforts.
Book Synopsis Physical Biology of the Cell by : Rob Phillips
Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1088 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that
Book Synopsis Protein Dynamics in Enzyme Catalysis and Ligand Binding by : Yao Fan
Download or read book Protein Dynamics in Enzyme Catalysis and Ligand Binding written by Yao Fan and published by . This book was released on 2007 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Design of Ligand Binding Proteins by : Barry L. Stoddard
Download or read book Computational Design of Ligand Binding Proteins written by Barry L. Stoddard and published by Methods in Molecular Biology. This book was released on 2018-05-04 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of protocols and approaches for the creation of novel ligand binding proteins, compiled and described by many of today's leaders in the field of protein engineering. Chapters focus on modeling protein ligand binding sites, accurate modeling of protein-ligand conformational sampling, scoring of individual docked solutions, structure-based design program such as ROSETTA, protein engineering, and additional methodological approaches. Examples of applications include the design of metal-binding proteins and light-induced ligand binding proteins, the creation of binding proteins that also display catalytic activity, and the binding of larger peptide, protein, DNA and RNA ligands. 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.
Book Synopsis Effects of Small Molecule Crowding on Protein Structure and Equilibrium Thermodynamics of Protein-protein Interaction by : Artemiza Sorina Morar
Download or read book Effects of Small Molecule Crowding on Protein Structure and Equilibrium Thermodynamics of Protein-protein Interaction written by Artemiza Sorina Morar and published by . This book was released on 2001 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Lipid Domains written by and published by Academic Press. This book was released on 2015-06-08 with total page 393 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Topics in Membranes is targeted toward scientists and researchers in biochemistry and molecular and cellular biology, providing the necessary membrane research to assist them in discovering the current state of a particular field and in learning where that field is heading. This volume offers an up to date presentation of current knowledge in the field of Lipid Domains. Written by leading experts Contains original material, both textual and illustrative, that should become a very relevant reference material The material is presented in a very comprehensive manner Both researchers in the field and general readers should find relevant and up-to-date information
Author :VICTORIA GARCIA SAKAI Publisher :Springer Science & Business Media ISBN 13 :1461407265 Total Pages :455 pages Book Rating :4.4/5 (614 download)
Book Synopsis Dynamics of Soft Matter by : VICTORIA GARCIA SAKAI
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.
Book Synopsis Modeling of Protein Flexibility and Inter-molecular Interactions by : Rizi Ai
Download or read book Modeling of Protein Flexibility and Inter-molecular Interactions written by Rizi Ai and published by . This book was released on 2012 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Macromolecular Crowding Effects in the Mechanical Unfolding Forces of Proteins by : Marisa B. Roman
Download or read book Macromolecular Crowding Effects in the Mechanical Unfolding Forces of Proteins written by Marisa B. Roman and published by . This book was released on 2012 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Macromolecules can occupy a large fraction of the volume of a cell and this crowded environment influences the behavior and properties of the proteins, such as mechanical unfolding forces, thermal stability and rates of folding and diffusion. Although much is already known about molecular crowding, it is not well understood how it affects a protein's resistance to mechanical stress in a crowded environment and how the size of the crowders affect those changes. An atomic force microscope-based single molecule method was used to measure the effects of the crowding on the mechanical stability of a model protein, in this case I-27. As proteins tend to aggregate, single molecule methods provided a way to prevent aggregation because of the very low concentration of proteins in the solution under study. Dextran was used as the crowding agent with three different molecular weights 6kDa, 10 kDa and 40 kDa, with concentrations varying from zero to 300 grams per liter in a pH neutral buffer solution at room temperature. Results showed that the forces required to unfold biomolecules were increased when a high concentration of crowder molecules were added to the buffer solution and that the maximum force required to unfold a domain was when the crowder size was 10 kDa, which is comparable to the protein size. Unfolding rates obtained from Monte Carlo simulations showed that they were also affected in the presence of crowders. As a consequence, the energy barrier was also affected. These effects were most notable when the size of the crowder was 10 kDa, comparable to the size of the protein. On the other hand, distances to the transition state did not seem to change when crowders were added to the solution. The effect of Dextran on the energy barrier was modeled by using established theories such as Ogston's and scaled particle theory, neither of which was completely convincing at describing the results. It can be hypothesized that the composition of Dextran plays a role in the deviation of the predicted behavior with respect to the experimental data.
Book Synopsis Identification of Hydration Sites in Proteins and Their Impact on Ligand Binding by Molecular Dynamics Simulation by :
Download or read book Identification of Hydration Sites in Proteins and Their Impact on Ligand Binding by Molecular Dynamics Simulation written by and published by . This book was released on 2015 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by : Valentina Tozzini
Download or read book Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations written by Valentina Tozzini and published by Frontiers Media SA. This book was released on 2020-10-27 with total page 235 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.
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Book Synopsis Handbook of Surface Plasmon Resonance by : Richard B M Schasfoort
Download or read book Handbook of Surface Plasmon Resonance written by Richard B M Schasfoort and published by Royal Society of Chemistry. This book was released on 2008-03-10 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: Surface plasmon resonance (SPR) plays a dominant role in real-time interaction sensing of biomolecular binding events. This book focuses on a total system description including optics, fluidics and sensor surfaces. It covers all commercial SPR systems in the market. It is the first of its kind and fills a gap in the technical literature as no other handbook on SPR is currently available. The final chapter discussed new trends and a vision is given for future developments and needs of the SPR market. This excellent handbook provides comprehensive information with easy to use, stand-alone chapters and will be of great use to anyone one working with or affiliated to the technology.
Book Synopsis Life - As a Matter of Fat by : Ole G. Mouritsen
Download or read book Life - As a Matter of Fat written by Ole G. Mouritsen and published by Springer Science & Business Media. This book was released on 2005-10-24 with total page 273 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents a multi-disciplinary perspective on the physics of life and the particular role played by lipids and the lipid-bilayer component of cell membranes. Emphasizes the physical properties of lipid membranes seen as soft and molecularly structured interfaces. By combining and synthesizing insights obtained from a variety of recent studies, an attempt is made to clarify what membrane structure is and how it can be quantitatively described. Shows how biological function mediated by membranes is controlled by lipid membrane structure and organization on length scales ranging from the size of the individual molecule, across molecular assemblies of proteins and lipid domains in the range of nanometers, to the size of whole cells. Applications of lipids in nano-technology and biomedicine are also described.
Book Synopsis Understanding Protein Dynamics, Binding and Allostery for Drug Design by : Guang Hu
Download or read book Understanding Protein Dynamics, Binding and Allostery for Drug Design written by Guang Hu and published by Frontiers Media SA. This book was released on 2021-06-08 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
