Statistical Models Of Protein Conformational Dynamics
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Statistical Models Of Protein Conformational Dynamics
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Author : Robert T. McGibbon
language : en
Publisher:
Release Date : 2016
Statistical Models Of Protein Conformational Dynamics written by Robert T. McGibbon and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Understanding the conformational dynamics of biological macromolecules at atomic resolution remains a grand challenge at the intersection of biology, chemistry, and physics. Molecular dynamics (MD) -- which refers to computational simulations of the atomic-level interactions and equations of motions that give rise to these dynamics -- is a powerful approach that now produces immense quantities of time series data on the dynamics of these systems. Here, I describe a variety of new methodologies for analyzing the rare events in these MD data sets in an automatic, statically-sound manner, and constructing the appropriate simplified models of these processes. These techniques are rooted in the theory of reversible Markov chains. They include new classes of Markov state models, hidden Markov models, and reaction coordinate finding algorithms, with applications to protein folding and conformational change. A particular focus herein is on methods for model selection and model comparison, and computationally efficient algorithms.
Protein Conformational Dynamics
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Author : Ke-li Han
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-20
Protein Conformational Dynamics written by Ke-li Han and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-01-20 with Medical categories.
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.
Understanding Protein Dynamics Binding And Allostery For Drug Design
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Author : Guang Hu
language : en
Publisher: Frontiers Media SA
Release Date : 2021-06-08
Understanding Protein Dynamics Binding And Allostery For Drug Design written by Guang Hu and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-08 with Science categories.
Protein Homeostasis Diseases
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Author : Angel L. Pey
language : en
Publisher: Academic Press
Release Date : 2020-02-13
Protein Homeostasis Diseases written by Angel L. Pey and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-02-13 with Science categories.
Protein Homeostasis Diseases: Mechanisms and Novel Therapies offers an interdisciplinary examination of the fundamental aspects, biochemistry and molecular biology of protein homeostasis disease, including the use of natural and pharmacological small molecules to treat common and rare protein homeostasis disorders. Contributions from international experts discuss the biochemical and genetic components of protein homeostasis disorders, the mechanisms by which genetic variants may cause loss-of-function and gain-of-toxic-function, and how natural ligands can restore protein function and homeostasis in genetic diseases. Applied chapters provide guidance on employing high throughput sequencing and screening methodologies to develop pharmacological chaperones and repurpose approved drugs to treat protein homeostasis disorders. - Provides an interdisciplinary examination of protein homeostasis disorders, with an emphasis on treatment strategies employing small natural and pharmacological ligands - Offers applied approaches in employing high throughput sequencing and screening to develop pharmacological chaperones to treat protein homeostasis disease - Gathers expertise from a range of international chapter authors who work across various biological methods and disease specific disciplines of relevance
Aggregation Of Therapeutic Proteins
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Author : Wei Wang
language : en
Publisher: John Wiley & Sons
Release Date : 2010-12-28
Aggregation Of Therapeutic Proteins written by Wei Wang and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-28 with Medical categories.
This book gives pharmaceutical scientists an up-to-date resource on protein aggregation and its consequences, and available methods to control or slow down the aggregation process. While significant progress has been made in the past decade, the current understanding of protein aggregation and its consequences is still immature. Prevention or even moderate inhibition of protein aggregation has been mostly experimental. The knowledge in this book can greatly help pharmaceutical scientists in the development of therapeutic proteins, and also instigate further scientific investigations in this area. This book fills such a need by providing an overview on the causes, consequences, characterization, and control of the aggregation of therapeutic proteins.
Encyclopedia Of Bioinformatics And Computational Biology
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Author :
language : en
Publisher: Elsevier
Release Date : 2018-08-21
Encyclopedia Of Bioinformatics And Computational Biology written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-21 with Medical categories.
Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Dancing Protein Clouds Intrinsically Disordered Proteins In The Norm And Pathology Part C
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Author :
language : en
Publisher: Academic Press
Release Date : 2021-10-14
Dancing Protein Clouds Intrinsically Disordered Proteins In The Norm And Pathology Part C written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-14 with Science categories.
Dancing Protein Clouds: Intrinsically Disordered Proteins in the Norm and Pathology, Part C, Volume 183 represents a set of selected studies on a variety of research topics related to intrinsically disordered proteins. Topics in this volume include discussions on the evolution of disorder, consideration of the peculiarities of phase separation of the prion protein, a general discussion of the relationships between intrinsic disorder and protein functions, coverage of the structural and functional characterization of several important intrinsically disordered proteins, such as transcription factors, outer membrane porins, trans-membrane and membrane associated proteins with ID regions, discussion of molecular simulations of IDPs, and much more. - Provides recent studies on the intrinsically disordered proteins and their functions, along with the involvement of intrinsically disordered proteins in the pathogenesis of various diseases - Contains numerous illustrative materials (color figures, diagrams and tables) to help readers delve into the information provided - Includes contributions from recognized experts in the field
Osmolytes And Intrinsically Disordered Proteins From Functional Regulation To Disease Pathogenesis
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Author :
language : en
Publisher: Elsevier
Release Date : 2025-02-18
Osmolytes And Intrinsically Disordered Proteins From Functional Regulation To Disease Pathogenesis written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-02-18 with Science categories.
Osmolytes and Intrinsically Disordered Proteins: From Functional Regulation to Disease Pathogenesis, Volume 112 delves into the fascinating interplay between osmolytes and intrinsically disordered proteins (IDPs), exploring their pivotal roles in cellular function and disease mechanisms. This volume brings together experts to present cutting-edge research on how osmolytes regulate functional behavior of IDPs and ensure cellular stability and adaptability under stress conditions. Specific chapters cover Functional diversity of IDPs and their structural heterogeneity: Protein structure-function continuum, Osmolytes as structure-function regulators of intrinsically disordered casein, Synergism of the effects of osmolytes and crowders on structure and function of IDPs/IDRs: The natural habitat, and more.Additional chapters delve into Osmolyte-IDP Interactions during Desiccation, Modulation of aggregation/fibrillation propensity of IDPs by osmolytes, Osmolytes in modulating the structural and functional integrity of α-synuclein: a study based on Parkinson's disease, Regulation of the structural dynamics, aggregation, and pathogenicity of polyQ-expanded Huntingtin by osmolytes, Aggregation and inhibitory strategies of amyloid fibrillation, and much more. - Offers an in-depth exploration of the relationship between osmolytes and intrinsically disordered proteins (IDPs), spanning from basic functional regulation to roles in the pathogenesis of various disease - Features chapters written by leading researchers and experts in the field - Provides the latest findings on osmolyte-IDP interactions in molecular levels and implications in important biological processes - Elucidates on the fundamental science behind IDPs and osmolytes - It highlights potential therapeutic approaches, making it a valuable resource for both researchers and clinicians aiming to develop new treatments for related diseases
Bayesian Statistics And Single Molecule Trajectories
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Author : Daniel L. Ensign
language : en
Publisher: Stanford University
Release Date : 2010
Bayesian Statistics And Single Molecule Trajectories written by Daniel L. Ensign and has been published by Stanford University this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Bayesian statistics is a powerful method for inference--possibly the uniquely correct method for inference. As described herein, when applied to a few degrees of freedom from single molecule trajectories, Bayesian statistics yield useful insights into rates, states, and motions.
Theory Of Phase Transitions In Polypeptides And Proteins
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Author : Alexander V. Yakubovich
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-09-01
Theory Of Phase Transitions In Polypeptides And Proteins written by Alexander V. Yakubovich and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-01 with Science categories.
There are nearly 100 000 different protein sequences encoded in the human genome, each with its own specific fold. Understanding how a newly formed polypeptide sequence finds its way to the correct fold is one of the greatest challenges in the modern structural biology. The aim of this thesis is to provide novel insights into protein folding by considering the problem from the point of view of statistical mechanics. The thesis starts by investigating the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. This knowledge is then applied in the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized to the case of proteins in an aqueous environment. The major novelty of this work lies in combining (a) a formalism based on fundamental physical properties of the system and (b) the resulting possibility of describing the folding↔unfolding transitions quantitatively. The clear physical nature of the formalism opens the way to further applications in a large variety of systems and processes.