Download or read book Probing the Mechanics of Protein Materials with Molecular Dynamics Simulations written by Senbo Xiao and published by . This book was released on 2011 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Probing the Protein Dynamics by a Combination Approach of Molecular Dynamics Simulation with Time resolved Fluorescence Spectroscopy and X ray Scattering written by 楊承翰 and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Probing Structure and Dynamics of Membrane Proteins by Molecular Dynamics Simulation written by Zoe Li (Ph. D. in pharmaceutics) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics (MD) simulation provides atomistic details of biomolecules’ behaviors and has become a pivotal tool in the study of protein structure, dynamics and drug discovery. In this thesis, MD simulations are used in combination with experimental results to address a variety of biological questions in three protein systems: the 5HT3A serotonin receptor, the acetylcholine binding receptor (AChBP), and the Insig (insulin-induced gene)-Scap (SREBP (sterol regulatory element-binding protein)-cleavage activating protein) complex. The objective of our first system is to investigate the key to generating a stable open structure of the 5HT3A serotonin receptor based on low resolution cryo-electron microscopy structures, which may also apply to other pentameric ligand-gated ion channels (pLGICs). We developed a refined equilibration protocol that involves the rearrangement of transmembrane helices to achieve stable open state structures of the 5-HT3 receptor that allow both water and ion permeation through the channel. Our study underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like state structures of the 5-HT3 receptor. Our second system aims to shed light on the nature of ligand recognition in the pLGICs that are activated upon ligand binding to their extracellular domains. The MD simulation-based absolute binding free energy calculation was carried out to study the electrostatic contribution in the binding of nicotine in a model system (AChBP). Finally, we performed extensive MD simulations on Scap to identify potential binding sites for a previously unknown SREBP activating molecule ammonia and to provide detailed structural mechanisms for how this molecule activates Scap.
Download or read book Protein Folding written by Victor Muñoz and published by Humana. This book was released on 2021-11-30 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides comprehensive protocols on experimental and computational methods that are used to study probe protein folding reactions and mechanisms. Chapters divided into five parts detail protein engineering, protein chemistry, experimental approaches to investigate the thermodynamics and kinetics of protein folding transitions, probe protein folding at the single molecule, analysis and interpretation of computer simulations, procedures and tools for the prediction of protein folding properties. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Folding: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.
Download or read book Computational Approaches for Understanding Dynamical Systems Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-05 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Download or read book Inspired by Biology written by National Research Council and published by National Academies Press. This book was released on 2008-06-17 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientists have long desired to create synthetic systems that function with the precision and efficiency of biological systems. Using new techniques, researchers are now uncovering principles that could allow the creation of synthetic materials that can perform tasks as precise as biological systems. To assess the current work and future promise of the biology-materials science intersection, the Department of Energy and the National Science Foundation asked the NRC to identify the most compelling questions and opportunities at this interface, suggest strategies to address them, and consider connections with national priorities such as healthcare and economic growth. This book presents a discussion of principles governing biomaterial design, a description of advanced materials for selected functions such as energy and national security, an assessment of biomolecular materials research tools, and an examination of infrastructure and resources for bridging biological and materials science.
Download or read book Size dependent Mechanical Properties of Beta structures in Protein Materials written by Sinan Keten and published by . This book was released on 2010 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein materials such as spider silk can be exceptionally strong, and they can stretch tremendously before failure. Notably, silks are made entirely of proteins, which owe their structure and stability to weak molecular interactions, in particular, hydrogen bonds (H-bonds). Beta-structures, a class of protein folds that employ dense arrays of H-bonds, are universal in strong protein materials such as silks, amyloids, muscle fibers and virulence factors. The biological recipe for creating strong, tough materials from weak bonds, however, has so far remained a secret. In this dissertation, size, geometry and deformation rate dependent properties of beta-structures are investigated, in order to provide a link between the nanostructure and mechanics of protein materials at multiple length scales. Large-scale molecular dynamics (MD) simulations show that beta-structures reinforce protein materials such as silk by forming H-bonded crystalline regions that cross-link polypeptide chains. A key finding is that superior strength and toughness can only be achieved if the size of the beta-sheet crystals is reduced to a few nanometers. Upon confinement into orderly nanocrystals, H-bond arrays achieve a strong character through cooperation under uniform shear deformation. Moreover, the size-dependent emergence of a molecular stick-slip failure mechanism enhances toughness of the material. Based on replica-exchange MD simulations, the first representative atomistic model for spider silk is proposed. The computational, bottom-up approach predicts a multi-phase material with beta-sheet nanocrystals dispersed within semi-amorphous domains, where the large-deformation and failure of silk is governed by the beta-structures. These findings explain a wide range of observations from single molecule experiments on proteins, as well as characterization studies on silks. Results illustrate how nano-scale confinement of weak bond clusters may lead to strong, tough polymer materials that self-assemble from common, simple building blocks.
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.
Download or read book Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
Download or read book Molecular Liquids written by A.J. Barnes and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 594 pages. Available in PDF, EPUB and Kindle. Book excerpt: This ASI was planned to make a major contribution to the teaching of the principles and methods used in liquid phase ~esearch and to encourage the setting up of collaborative projects, as advocated by the European Molecular Liquids Group (secretary: Dr J. Yarwood, University of Durham, U. K. ). During the past five years considerable progress has been made in studying molecular liquids. The undoubted advantages of international collaboration led to the formation of the European Molecular Liquids Group (EMLG) in July 1981. The activities of the EMLG were widely disseminated in a special session of the European Congress on Molecular Spectroscopy (EUCMOS) held in September 1981 (for details, see J. Mol. Structure, 80 (1982) 375 - 421). Following the success of this meeting, it was thought that the aims and objectives of the E~G would be best served by the organisation of a broader-based gathering designed to attract those interested in the study of the structure, dynamics and interactions in the liquid state. Thanks to the generous support by the Scientific Affairs Division of NATO, it was possible to hold a NATO ASI on Molecular Liquids at the Italian Centre of Stanford University, Florence, Italy during June-July 1983. This book is based on the lectures presented at that meeting. The contents of this volume cover the three broad areas of current liquid phase research: (a) Analytical theory.
Download or read book Advances in Cell Mechanics written by Shaofan Li and published by Springer Science & Business Media. This book was released on 2011-11-17 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Advances in Cell Mechanics" presents the latest developments in cell mechanics and biophysics, mainly focusing on interdisciplinary research in cell biology and the biophysics of cells. Moreover, a unique feature of the book is its emphasis on the molecular and complex continuum modeling and simulations of the cells. It may be the first work that brings rigorous and quantitative scientific analysis and state-of-the-art simulation technology into cell biology research. The book is intended for researchers and graduate students working in the fields of molecular cell biology, bio-engineering and bio-mechanics, soft matter physics, computational mechanics, bio-chemistry and bio-medicine. All contributors are leading scholars in their respective fields. Dr. Shaofan Li is a professor and an expert for computational mechanics at the University of California-Berkeley, USA; Dr. Bohua Sun is a professor at Cape Peninsula University of Technology, South Africa.
Download or read book Nuclear Magnetic Resonance Probes of Molecular Dynamics written by R. Tycko and published by Springer Science & Business Media. This book was released on 2003-07-31 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Magnetic Resonance Probes of Molecular Dynamics describes the theoretical basis and experimental techniques that make modern NMR spectroscopy a powerful and flexible tool for probing molecular dynamics in chemical, physical, and biochemical systems. Individual chapters, written by leaders in the development and application of NMR from around the world, treat systems that range from synthetic polymers, liquid crystals, and catalysts to proteins and oligonucleotides and techniques that include deuterium NMR, magic angle spinning, multidimensional spectroscopy, and magnetic resonance imaging. A combination of elementary and advanced material makes the book a useful introduction to the field for students at the graduate level as well as an important reference for practising NMR spectroscopists.
Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer. This book was released on 1995-08-18 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Download or read book Mechanochemistry in Materials written by Yoan C. Simon and published by Royal Society of Chemistry. This book was released on 2017-10-24 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mechanochemistry in materials science has experienced tremendous growth in the last 5 years and has developed to become one of the most important topics in polymer science today.
Download or read book Molecular Dynamics Simulations of Enforced Functional Protein Motions written by Frauke Gräter and published by . This book was released on 2005 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Basics of Liquids and Liquid Based Materials written by Katsura Nishiyama and published by Springer Nature. This book was released on 2022-01-03 with total page 469 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book sheds light on the molecular aspects of liquids and liquid-based materials such as organic or inorganic liquids, ionic liquids, proteins, biomaterials, and soft materials including gels. The reader discovers how the molecular basics of such systems are connected with their properties, dynamics, and functions. Once the use and application of liquids and liquid-based materials are understood, the book becomes a source of the latest, detailed knowledge of their structures, dynamics, and functions emerging from molecularity. The systems discussed in the book have structural dimensions varying from nanometers to millimeters, thus the precise estimation of structures and dynamics from experimental, theoretical, and simulation methods is of crucial importance. Outlines of the practical knowledge needed in research and development are helpfully included in the book.
Download or read book Normal Mode Analysis written by Qiang Cui and published by CRC Press. This book was released on 2005-12-12 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rapid developments in experimental techniques continue to push back the limits in the resolution, size, and complexity of the chemical and biological systems that can be investigated. This challenges the theoretical community to develop innovative methods for better interpreting experimental results. Normal Mode Analysis (NMA) is one such technique
