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Author: Amandeep Kaur Sangha Publisher: ISBN: Category : Languages : en Pages : 224
Book Description
Abstract: Conformational dynamics is of fundamental importance for the folding and the function of proteins. Structural changes occur over a wide range of time scales, and folding itself is the slowest, long-time process, Rates vary with the extent of folding, as measured by an order parameter, Q. The dynamics of the order parameter is studied in detail using a coarse-grained model of the protein and classical molecular dynamics simulations. A description of folding is attempted in terms of the Smoluchowski equation (SE), based on a picture of diffusion of the order parameter under the influence of a thermodynamic force. A new method is developed to obtain the order parameter dependent diffusion coefficient, D ( Q ), from short-time simulations. D ( Q ) is shown to change significantly as the protein folds. It is found that folding obeys neither the one-dimensional SE nor a normal-diffusion continuous time random walk (CTRW), because the order parameter follows sub-diffusion. The anomalous nature of the order parameter dynamics is incorporated into the ordinary SE based on the idea that the folding pathways have fractal character. Obtaining the free energy from the statistical temperature molecular dynamics (STMD) enhanced sampling algorithm and D ( Q ) from short-time simulations, mean first passage times of folding (MFPT) calculated from our fractal SE theory are in quantitative agreement with simulated long-time folding dynamics. Protein folding occurs in a crowded and heterogeneous environment inside the cell. Interactions of the protein with other cellular biomolecules may hamper the folding process. Chaperones are known to help a large fraction of newly synthesized proteins in their proper folding. To understand the mechanism of chaperonin-mediated protein folding, the thermodynamics and kinetics of a frustrated model protein are studied inside a chaperonin cavity modeled as a sphere of tunable hydrophobicity. Using the inherent structure (IS) approach, we found that folding is preferred over misfolding inside a slightly hydrophobic chaperonin cavity. The occupation probabilities of the misfolded states are entropically suppressed due to smaller associated configurational volumes.
Author: Amandeep Kaur Sangha Publisher: ISBN: Category : Languages : en Pages : 224
Book Description
Abstract: Conformational dynamics is of fundamental importance for the folding and the function of proteins. Structural changes occur over a wide range of time scales, and folding itself is the slowest, long-time process, Rates vary with the extent of folding, as measured by an order parameter, Q. The dynamics of the order parameter is studied in detail using a coarse-grained model of the protein and classical molecular dynamics simulations. A description of folding is attempted in terms of the Smoluchowski equation (SE), based on a picture of diffusion of the order parameter under the influence of a thermodynamic force. A new method is developed to obtain the order parameter dependent diffusion coefficient, D ( Q ), from short-time simulations. D ( Q ) is shown to change significantly as the protein folds. It is found that folding obeys neither the one-dimensional SE nor a normal-diffusion continuous time random walk (CTRW), because the order parameter follows sub-diffusion. The anomalous nature of the order parameter dynamics is incorporated into the ordinary SE based on the idea that the folding pathways have fractal character. Obtaining the free energy from the statistical temperature molecular dynamics (STMD) enhanced sampling algorithm and D ( Q ) from short-time simulations, mean first passage times of folding (MFPT) calculated from our fractal SE theory are in quantitative agreement with simulated long-time folding dynamics. Protein folding occurs in a crowded and heterogeneous environment inside the cell. Interactions of the protein with other cellular biomolecules may hamper the folding process. Chaperones are known to help a large fraction of newly synthesized proteins in their proper folding. To understand the mechanism of chaperonin-mediated protein folding, the thermodynamics and kinetics of a frustrated model protein are studied inside a chaperonin cavity modeled as a sphere of tunable hydrophobicity. Using the inherent structure (IS) approach, we found that folding is preferred over misfolding inside a slightly hydrophobic chaperonin cavity. The occupation probabilities of the misfolded states are entropically suppressed due to smaller associated configurational volumes.
Author: Kerson Huang Publisher: World Scientific ISBN: 9812561439 Category : Science Languages : en Pages : 159
Book Description
This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestion on possible research directions, as developed by the author in collaboration with C. C. Lin. The first half of this invaluable book contains a concise but relatively complete review of relevant topics in statistical mechanics and kinetic theory. It includes standard topics such as thermodynamics, the Maxwell-Boltzmann distribution, and ensemble theory. Special discussions include the dynamics of phase transitions, and Brownian motion as an illustration of stochastic processes. The second half develops topics in molecular biology and protein structure, with a view to discovering mechanisms underlying protein folding. Attention is focused on the energy flow through the protein in its folded state. A mathematical model, based on the Brownian motion of coupled harmonic oscillators, is worked out in the appendix.
Author: Prakash Saudagar Publisher: Springer Nature ISBN: 9819920795 Category : Science Languages : en Pages : 287
Book Description
This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.
Author: Miriam R. Friedel Publisher: ProQuest ISBN: 9780542855962 Category : Languages : en Pages : 354
Book Description
Although the information necessary for a protein to fold is encoded in its amino acid sequence, the environment in which it folds can have a significant impact on the folding process. To date, the majority of protein folding studies (theoretical, computational and experimental) have been carried out in an idealized, dilute environment. In this work, we use molecular dynamics simulations of minimalist model proteins and peptides to examine the impact of two types of confinement on protein folding and peptide assembly. First, we utilize a spherical potential to emulate the cellular confinement and crowding that proteins experience when folding in vivo. Using this potential, we examine the impact on the thermodynamics and kinetics of both protein folding and peptide assembly. Then, we examine how tethering a protein to a surface impacts its stability and folding mechanism. Both types of confinement can have a significant impact on the thermodynamic stability, unfolded state, and mechanisms of folding and assembly, but they do so in unique ways. In addition to examining in detail the specific ways confinement impacts protein folding, we will also discuss the implications of our results for various biological problems and technological applications.
Author: R. A. Broglia Publisher: IOS Press ISBN: 9781586031664 Category : Science Languages : en Pages : 378
Book Description
This text presents the results of broad interdisciplinary effort to study proteins in physical and evolutionary prospectives. Among the authors are physicists, chemists, crystallographers, and evolutionary biologists. Experimental and theoretical developments from molecules to cells are presented providing a broad picture of modern biophysical chemistry.
Author: Grace E. Orellana Publisher: American Chemical Society ISBN: 0841296383 Category : Science Languages : en Pages : 170
Book Description
Life as we know it would not exist if proteins did not fold into functional three-dimensional structures, where α-helices, loops, and β-sheets act together to form active sites that drive a myriad of biochemical reactions in the cell. The failure of this process is linked to the pathology of various diseases, such as neurodegenerative disorders like Alzheimer’s, genetic conditions (like cystic fibrosis), and cancer. It is no wonder that close to $2 billion in worldwide research funding has been devoted over the last five years (2019–2025) to helping scientists understand the molecular details of protein folding, how it can fail in ways that promote disease in humans, and clinical paths to treat or prevent diseases linked to protein misfolding. This primer is prerequisite reading to the literature on this important topic for readers new to the field. Chapter one provides exposure to the three-dimensional structure of proteins; readers will learn how to identify secondary structures, protein motifs, and domains involved in biological function. Chapter two introduces methodologies to determine the three-dimensional structure of proteins; readers will learn modern techniques to determine the secondary structure composition and the orientation of atoms in three-dimensional space. By providing exposure to how the physical environment (i.e., chemical denaturants, pH, pressure, and temperature) controls protein denaturation, readers will learn how such information can be used to study the biophysical characteristics of proteins through various probes and methodologies.
Author: Richard A. Friesner Publisher: John Wiley & Sons ISBN: 0471465232 Category : Science Languages : en Pages : 544
Book Description
Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.
Author: Kenneth M.Jr. Merz Publisher: Springer Science & Business Media ISBN: 1468468316 Category : Science Languages : en Pages : 585
Book Description
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.
Author: Cláudio M. Gomes Publisher: Springer ISBN: 331900882X Category : Science Languages : en Pages : 63
Book Description
This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.
Author: Amandeep Kaur Sangha
Author: Amandeep Kaur Sangha
Author: Kerson Huang
Author: Guanghui Ping
Author: Prakash Saudagar
Author: Miriam R. Friedel
Author: R. A. Broglia
Author: Grace E. Orellana
Author: Richard A. Friesner
Author: Kenneth M.Jr. Merz
Author: Cláudio M. Gomes