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Author: Ron Elber
Publisher: World Scientific
ISBN: 9789810221966
Category : Science
Languages : en
Pages : 422
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Book Description
Experts provide a unique and broad perspective of the theoretical tools available today to analyze protein structure and function. Topics at the frontier of computational biophysics, such as dynamics and thermodynamics of proteins, reaction path studies, optimization techniques, analytical theories of protein folding, sequence alignment algorithms and electrostatics of proteins are discussed in a pedagogical and complete way. Those entering the field will find the book to be a useful introduction. It will also serve as a complementary text to existing ones that focus on just one of the above subjects.
Author: Ron Elber
Publisher: World Scientific
ISBN: 9789810221966
Category : Science
Languages : en
Pages : 422
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Book Description
Experts provide a unique and broad perspective of the theoretical tools available today to analyze protein structure and function. Topics at the frontier of computational biophysics, such as dynamics and thermodynamics of proteins, reaction path studies, optimization techniques, analytical theories of protein folding, sequence alignment algorithms and electrostatics of proteins are discussed in a pedagogical and complete way. Those entering the field will find the book to be a useful introduction. It will also serve as a complementary text to existing ones that focus on just one of the above subjects.
Author: Gregory Thomas Kapp
Publisher:
ISBN:
Category : Protein folding
Languages : en
Pages : 310
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Book Description
Author: 蔡旻燁
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: Charis Ghélis
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 592
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Book Description
Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nome ...
Author: John Karanicolas
Publisher:
ISBN: 9780599195479
Category : Cytochrome c
Languages : en
Pages : 332
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Book Description
Hemes assume many different roles in nature as protein environments modulate their specific functions. Protein engineering can be used to provide a glimpse into enzyme mechanism by elucidating factors involved in dictating heme specificity and activity. Design of novel function in an enzyme may result in a protein with a specific function or simply explain what interactions are necessary and sufficient for particular activities. Three unique protein engineering investigations in cytochrome c peroxidase (CCP) are described: complementation of the heme iron ligand, introduction of manganese binding and oxidation, and modulation of small substrate activity. First, exogenous imidazole replacement of the axial His ligand results in a complicated series of gated active site modes. Functional, spectroscopic, kinetic, and structural studies suggest that protonated imidazole occupies the cavity created by this mutation and forms a crucial hydrogen bond interaction in the proximal pocket, but does not bind the iron. Neutral imidazole binds the iron, but weakens the hydrogen bond. Since both of these interactions are crucial to formation of an Asp-His-Fe triad in the native protein, imidazole is unable to rescue this mutant. Second, a metal site has been created near the heme, that binds and catalyzes the oxidation of Mn 2+ . Electron transfer from Mn2+ to the ferryl iron is specifically enhanced. Structural studies confirm that Mn2+ interacts with the protein at the site designed. Finally, Ala 147 was replaced by Met and Tyr to investigate the hypothesis that small molecules are oxidized at the o-meso edge of the heme. Crystallographic analyses confirm that the side chains of A147M and A147Y rest over the o-meso position. Steady-state kinetics show that small molecule oxidation is altered to varying degrees depending on the substrate and mutant. These results show that protein engineering is a powerful tool that can be used to address diverse functional questions. These studies have revealed a delicate balance of interactions established by the precise geometry of the native active site, the ability to introduce novel activity, and the existence of multiple mechanisms for small substrate oxidation. Such revelations can lead to further improvements in the cycle of protein design.
Author: Charis Ghelis
Publisher: Academic Press
ISBN: 0323140920
Category : Science
Languages : en
Pages : 580
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Book Description
Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nomenclature are given, including the structural organization of globular proteins deduced from X-ray crystallographic data. Folding mechanisms are tentatively deduced from the observation of invariants in the architecture of folded proteins. The next chapters focus on the energetics of protein conformation and structure, indicating the principles of thermodynamic stability of the native structure, along with theoretical computation studies of protein folding, structure prediction, and folding simulation. The reader is also introduced to various experimental approaches; the reversibility of the unfolding-folding process; equilibrium and kinetic studies; and detection and characterization of intermediates in protein folding. This text concludes with a chapter dealing with problems specific to oligomeric proteins. This book is intended for research scientists, specialists, biochemists, and students of biochemistry and biology.
Author: Kenneth M.Jr. Merz
Publisher: Springer Science & Business Media
ISBN: 1468468316
Category : Science
Languages : en
Pages : 585
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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: Zhijing Dang
Publisher:
ISBN:
Category : Circular dichroism
Languages : en
Pages : 360
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Book Description
Author: Michael Patrick Morrissey
Publisher:
ISBN:
Category : Protein folding
Languages : en
Pages : 460
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Book Description
Author: Maksim Skorobogatiy
Publisher:
ISBN:
Category :
Languages : en
Pages : 292
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Book Description
"My thesis is organized as follows. First, I introduce a general overview on the nature of real proteins. Then I address the thermodynamics of proteins and how one can model it. After that I introduce a microscopic model for proteins and I discuss the reasons for its construction. After a thorough theoretical investigation of this model I make several predictions for its thermodynamic and dynamic behavior. I then introduce a dynamics for protein folding, including a master equation approach for the description of protein kinetics. Using the protein thermodynamics introduced earlier I implement some extensive Monte-Carlo computer calculation to elucidate the non Arrhenius modes in the protein folding. A mesoscopic model of the hierarchically constrained dynamics will be introduced after that to account for the observed behavior. Finally, I investigate an abstract but exactly solvable model which could serve as a cornerstone for the dream of protein designers---an ultimately fast folding protein. (Abstract shortened by UMI.)" --
