Investigating Native State Protein Dynamics Through Simulations Of Hydrogen Exchange Mass Spectrometry And Bayesian Analysis Of Experimental Data
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| Author | : Yawen Bai |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 332 |
| Release | : 2008-02-04 |
| Genre | : Science |
| ISBN | : 1597451894 |
Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences.
| Author | : David D. Weis |
| Publisher | : John Wiley & Sons |
| Total Pages | : 422 |
| Release | : 2016-03-21 |
| Genre | : Science |
| ISBN | : 1118616499 |
Hydrogen exchange mass spectrometry is widely recognized for its ability to probe the structure and dynamics of proteins. The application of this technique is becoming widespread due to its versatility for providing structural information about challenging biological macromolecules such as antibodies, flexible proteins and glycoproteins. Although the technique has been around for 25 years, this is the first definitive book devoted entirely to the topic. Hydrogen Exchange Mass Spectrometry of Proteins: Fundamentals, Methods and Applications brings into one comprehensive volume the theory, instrumentation and applications of Hydrogen Exchange Mass Spectrometry (HX-MS) - a technique relevant to bioanalytical chemistry, protein science and pharmaceuticals. The book provides a solid foundation in the basics of the technique and data interpretation to inform readers of current research in the method, and provides illustrative examples of its use in bio- and pharmaceutical chemistry and biophysics In-depth chapters on the fundamental theory of hydrogen exchange, and tutorial chapters on measurement and data analysis provide the essential background for those ready to adopt HX-MS. Expert users may advance their current understanding through chapters on methods including membrane protein analysis, alternative proteases, millisecond hydrogen exchange, top-down mass spectrometry, histidine exchange and method validation. All readers can explore the diversity of HX-MS applications in areas such as ligand binding, membrane proteins, drug discovery, therapeutic protein formulation, biocomparability, and intrinsically disordered proteins.
| Author | : Haruki Nakamura |
| Publisher | : Springer |
| Total Pages | : 270 |
| Release | : 2019-01-08 |
| Genre | : Science |
| ISBN | : 9811322007 |
This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.
| Author | : The Nuclear Magnetic Resonance Society of Japan |
| Publisher | : Springer |
| Total Pages | : 634 |
| Release | : 2017-11-23 |
| Genre | : Science |
| ISBN | : 9811059667 |
This book describes the advanced developments in methodology and applications of NMR spectroscopy to life science and materials science. Experts who are leaders in the development of new methods and applications of life and material sciences have contributed an exciting range of topics that cover recent advances in structural determination of biological and material molecules, dynamic aspects of biological and material molecules, and development of novel NMR techniques, including resolution and sensitivity enhancement. First, this book particularly emphasizes the experimental details for new researchers to use NMR spectroscopy and pick up the potentials of NMR spectroscopy. Second, the book is designed for those who are involved in either developing the technique or expanding the NMR application fields by applying them to specific samples. Third, the Nuclear Magnetic Resonance Society of Japan has organized this book not only for NMR members of Japan but also for readers worldwide who are interested in using NMR spectroscopy extensively.
| Author | : Darius M. Dziuda |
| Publisher | : John Wiley & Sons |
| Total Pages | : 348 |
| Release | : 2010-07-16 |
| Genre | : Computers |
| ISBN | : 0470593407 |
Data Mining for Genomics and Proteomics uses pragmatic examples and a complete case study to demonstrate step-by-step how biomedical studies can be used to maximize the chance of extracting new and useful biomedical knowledge from data. It is an excellent resource for students and professionals involved with gene or protein expression data in a variety of settings.
| Author | : Gregory R. Bowman |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 148 |
| Release | : 2013-12-02 |
| Genre | : Science |
| ISBN | : 9400776063 |
The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
| Author | : |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 1979 |
| Genre | : |
| ISBN | : |
| Author | : Bruce J Berne |
| Publisher | : World Scientific |
| Total Pages | : 881 |
| Release | : 1998-06-17 |
| Genre | : Science |
| ISBN | : 9814496057 |
The school held at Villa Marigola, Lerici, Italy, in July 1997 was very much an educational experiment aimed not just at teaching a new generation of students the latest developments in computer simulation methods and theory, but also at bringing together researchers from the condensed matter computer simulation community, the biophysical chemistry community and the quantum dynamics community to confront the shared problem: the development of methods to treat the dynamics of quantum condensed phase systems.This volume collects the lectures delivered there. Due to the focus of the school, the contributions divide along natural lines into two broad groups: (1) the most sophisticated forms of the art of computer simulation, including biased phase space sampling schemes, methods which address the multiplicity of time scales in condensed phase problems, and static equilibrium methods for treating quantum systems; (2) the contributions on quantum dynamics, including methods for mixing quantum and classical dynamics in condensed phase simulations and methods capable of treating all degrees of freedom quantum-mechanically.
| Author | : Ulrich Reineke |
| Publisher | : Humana Press |
| Total Pages | : 450 |
| Release | : 2009-05-20 |
| Genre | : Science |
| ISBN | : 9781934115176 |
Given the versatile utility of the determinination of epitopes, beneficial to a wide variety of scientists from immunologists to structural biologists to biotechnologists, the need for a thorough, state-of-the-art collection of experimental protocols is clear. In Epitope Mapping Protocols, Second Edition, expert contributors from a broad spectrum of scientific backgrounds update and expand the successful first edition with cutting-edge techniques and applications, including approaches to both antibody or B-cell epitope mapping and T-cell epitope mapping as well as a new section on the profiling of antibody signatures in biological fluids. Written in the popular Methods in Molecular BiologyTM series format, chapters include brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and Notes sections, which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Epitope Mapping Protocols, Second Edition is a reliable and valuable reference for all those who wish to understand and further investigate the diversifying field of epitope mapping.
| Author | : Andrew J. Clifford |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 413 |
| Release | : 2013-11-21 |
| Genre | : Science |
| ISBN | : 1489919597 |
Nutrients have been recognized as essential for maximum growth, successful reproduction, and infection prevention since the 1940s; since that time, the lion's share of nutrient research has focused on defining their role in these processes. Around 1990, however, a major shift began in the way that researchers viewed some nutrients particularly the vitamins. This shift was motivated by the discovery that modest declines in vitamin nutritional status are associated with an increased risk of ill-health and disease (such as neural tube defects, heart disease, and cancer), especially in those populations or individuals who are genetically predisposed. In an effort to expand upon this new understanding of nutrient action, nutritionists are increasingly turning their focus to the mathematical modeling of nutrient kinetic data. The availability of suitably-tagged (isotope) nutrients (such as B-carotene, vitamin A, folate, among others), sensitive analytical methods to trace them in humans (mass spectrometry and accelerator mass spectrometry), and powerful software (capable of solving and manipulating differential equations efficiently and accurately), has allowed researchers to construct mathematical models aimed at characterizing the dynamic and kinetic behavior of key nutrients in vivo in humans at an unparalleled level of detail.
