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Protein Solvent Interactions
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Book Synopsis Protein-Solvent Interactions by : Roger Gregory
Download or read book Protein-Solvent Interactions written by Roger Gregory and published by CRC Press. This book was released on 1995-01-04 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.
Book Synopsis The Protein Folding Problem and Tertiary Structure Prediction by : Kenneth M.Jr. Merz
Download or read book The Protein Folding Problem and Tertiary Structure Prediction written by Kenneth M.Jr. Merz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.
Book Synopsis Protein-solvent Interactions and Classical Density Functional Theory by : Eric A. Mills
Download or read book Protein-solvent Interactions and Classical Density Functional Theory written by Eric A. Mills and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational and Experimental Characterization of Proteins With Respect to Protein-Solvent Interactions by : Sven Matthias Amrhein
Download or read book Computational and Experimental Characterization of Proteins With Respect to Protein-Solvent Interactions written by Sven Matthias Amrhein and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Effect of Solute-solvent Interactions on Protein Stability and Ligand Binding by : Ikbae Son
Download or read book Effect of Solute-solvent Interactions on Protein Stability and Ligand Binding written by Ikbae Son and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Interactions by : Peter Schuck
Download or read book Protein Interactions written by Peter Schuck and published by Springer Science & Business Media. This book was released on 2007-03-20 with total page 537 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume successfully and clearly examines how biophysical approaches can be used to study complex systems of reversibly interacting proteins. It deals with the methodology behind the research and shows how to synergistically incorporate several methodologies for use. Each chapter treats and introduces the reader to different biological systems, includes a brief summary of the physical principles, and mentions practical requirements.
Book Synopsis Study of Protein-protein, Protein-small Molecule and Protein-solvent Interactions by : Simone Cirri
Download or read book Study of Protein-protein, Protein-small Molecule and Protein-solvent Interactions written by Simone Cirri and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Interactions Between Proteins and Small Solutes at the Protein-solvent Interface by : Ran Friedman
Download or read book Interactions Between Proteins and Small Solutes at the Protein-solvent Interface written by Ran Friedman and published by . This book was released on 2006 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Structures and Protein-solvent Interactions by : Hannes Ponstingl
Download or read book Protein Structures and Protein-solvent Interactions written by Hannes Ponstingl and published by . This book was released on 1998 with total page 48 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Solute-Solvent Interactions in Folded and Unfolded Proteins by : Soyoung Lee
Download or read book Solute-Solvent Interactions in Folded and Unfolded Proteins written by Soyoung Lee and published by . This book was released on 2011 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis is devoted to understanding solute-solvent interactions in folded and unfolded proteins. To this end, we have studied partial molar volume, V°, and adiabatic compressibility, K°S, of 20 amino acid side chains using low weight molecular model compounds, N-acetyl amino acid amide and its derivatives, between 18°C and 55°C. We used our data to develop an additive scheme for calculating the partial specific volume and adiabatic compressibility of fully extended polypeptide chains as a function of pH and temperature. We compared our calculated volumetric characteristics of the fully extended conformations of apocytochrome c and apomyoglobin with the experimental values measured in neutral pH (for apocytochrome c) or acidic pH (for apomyoglobin). The comparison between the calculated and experimental volumetric characteristics suggested that neither apocytochrome c nor apomyoglobin are fully unfolded and retain solvent-inaccessible amino acid residues. To study cosolvent-solute interactions, we determined V° and K° S of amino acid side chains and glycyl units as a function of urea concentration. We analyzed these data within the framework of a statistical thermodynamic formalism to determine the association constants, k, for the reaction in which urea binds to each of the amino acid side chains and the glycyl unit replacing two water molecules in solvation shell. Our determined k range from 0.04 to 0.39 M with the average of 0.16 +/- 0.09 M. There was no apparent correlation between the values of k and the ratio of polar to nonpolar solvent accessible surface areas. This study supports a direct interaction model in which urea denatures a protein by concerted action via favorable interactions with a wide range of protein groups. In addition, we have presented buffer ionization effect on the volume of protein denaturation could be significant with the potential to affect not only its magnitude but also its sign using a pressure perturbation calorimetric technique. Our results identified buffer ionization as an important determinant of protein transition volume that needs to be carefully taken into account. Results described in this work provide fundamental understanding of solute-solvent interaction in both folded and unfolded proteins.
Book Synopsis Solvent Interactions with Proteins as Rev ... by : E. Baker
Download or read book Solvent Interactions with Proteins as Rev ... written by E. Baker and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Modelling of Protein-protein/protein-solvent Interactions by : Tyler Luchko
Download or read book Molecular Modelling of Protein-protein/protein-solvent Interactions written by Tyler Luchko and published by . This book was released on 2008 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Role of Local Electrostatic Fields in Protein-protein and Protein-solvent Interactions Determined by Vibrational Stark Effect Spectroscopy by : Christina Marie Ragain
Download or read book Role of Local Electrostatic Fields in Protein-protein and Protein-solvent Interactions Determined by Vibrational Stark Effect Spectroscopy written by Christina Marie Ragain and published by . This book was released on 2014 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: This examines the interplay of structure and local electrostatic fields in protein-protein and protein-solvent interactions. The partial charges of the protein amino acids and the polarization of the surrounding solvent create a complex system of electrostatic fields at protein-protein and protein-solvent interfaces. An approach incorporating vibrational Stark effect (VSE) spectroscopy, dissociation constant measurements, and molecular dynamics (MD) simulations was used to investigate the electrostatic interactions in these interfaces. Proteins p21Ras (Ras) and Rap1A (Rap) have nearly identical amino acid sequences and structures along the effector-binding region but bind with different affinities to Ral guanine nucleotide dissociation stimulator (RalGDS). A charge reversion mutation at position 31 alters the binding affinity of Ras and Rap with RalGDS from 0.1 [mu]M and 1 [mu]M, to 1 [mu]M and 0.5 [mu]M, respectively. A spectral probe was placed at various locations along the binding interface on the surface of RalGDS as it was docked with Ras and Rap single (position 30 or 31) and double mutants (both positions). By comparing the probes' absorption energies with the respective wild-type (WT) analogs, VSE spectroscopy was able to measure molecular-level electrostatic events across the protein-protein interface. MD simulations provided a basis for deconvoluting the structural and electrostatic changes observed by the probes. The mutation at position 31 was found to be responsible for both structural and electrostatic changes compared to the WT analogs. Furthermore, previous identification of positions N27 and N29 on RalGDS as "hot spots" that help discriminate between structurally similar GTPases was supported. The RalGDS probe-containing variants and three model compounds were placed in aqueous solvents with varying dielectric constants to measure changes in absorption energy. We investigated the ability of the Onsager solvent model to describe the solvent induced changes in absorption energy, while MD simulations were employed to determine the location and solvation of the probes at the protein-solvent interface. The solvent accessible-surface area, a measure of hydration, was determined to correlate well with the change in magnitude of the probe's absorption energy and the displaced solvent by the probe.
Book Synopsis Protein Structure, Stability, and Interactions by : John W. Shriver
Download or read book Protein Structure, Stability, and Interactions written by John W. Shriver and published by Humana. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the areas of biochemistry and cell biology, characterizations of stability and molecular interactions call for a quantitative approach with a level of precision that matches the fine tuning of these interactions in a living cell. Supporting and up-dating previous Methods in Molecular BiologyTM volumes, Protein Structure, Stability, and Interactions approaches its subject with a focus on theory and practical applications for both established methods as well as exciting new procedures. The volume presents an overview of many techniques currently used to study protein stability and interactions, including scanning and titration calorimetry, spectroscopic methods, high field NMR, and analytical ultracentrifugation. As a volume of the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and easy to reference, Protein Structure, Stability, and Interactions is an ideal guide for all scientists interested in biomolecular interactions.
Book Synopsis Protein-Ligand Interactions by : Holger Gohlke
Download or read book Protein-Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-05-21 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Book Synopsis Computational Modelling Approaches for Studying Protein-protein and Protein-solvent Interactions in Biopharmaceuticals by : Max Hebditch
Download or read book Computational Modelling Approaches for Studying Protein-protein and Protein-solvent Interactions in Biopharmaceuticals written by Max Hebditch and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Solvent-Induced Interactions and Forces in Protein Folding by : Arieh Ben-Naim
Download or read book Solvent-Induced Interactions and Forces in Protein Folding written by Arieh Ben-Naim and published by Springer Nature. This book was released on 2023-06-12 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph presents the molecular theory and necessary tools for the study of solvent-induced interactions and forces. After introducing the reader to the basic definitions of solvent-induced interactions, the author provides a brief analysis of the statistical thermodynamics. The book thoroughly overviews the connection of those interactions with thermodynamics and consequently focuses on specifically discussing the hydrophobic-hydrophilic interactions and forces. The importance of the implementation of hydrophilic interactions and forces in various biochemical processes is thoroughly analyzed, while evidence based on theory, experiments, and simulated calculations supporting that hydrophilic interactions and forces are far more important than the corresponding hydrophobic effects in many biochemical processes such as protein folding, self-assembly of proteins, molecular recognitions, are described in detail. This title is of great interest to students and researchers working in the fields of chemistry, physics, biochemistry, and molecular biology.
