The Protein Folding Problem and Tertiary Structure Prediction

The Protein Folding Problem and Tertiary Structure Prediction PDF

Author: Kenneth M.Jr. Merz

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 585

ISBN-13: 1468468316

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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.

Protein Folds

Protein Folds PDF

Author: Henrik Bohr

Publisher: CRC Press

Published: 1995-10-20

Total Pages: 352

ISBN-13: 9780849340093

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Written by outstanding scientists in physics and molecular biology, this book addresses the most recent advances in the analysis of the protein folding processes and protein structure determination. Emphasis is also placed on modelling and presentation of experimental results of structural membrane bound proteins. Many color plates help to illustrate structural aspects covered including: Defining folds of protein domains Structure determination from sequence Distance geometry Lattice theories Membrane proteins Protein-Ligand interaction Topological considerations Docking onto receptors All analysis is presented with proven theory and experimentation. Protein Folds: A Distance-Based Approach is an excellent text/reference for biotechnologists and biochemists as well as graduate students studying in the research sciences.

Protein Folding

Protein Folding PDF

Author: Grace E. Orellana

Publisher: American Chemical Society

Published: 2024-05-08

Total Pages: 170

ISBN-13: 0841296383

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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.

Protein Folding and Metal Ions

Protein Folding and Metal Ions PDF

Author: Cláudio M. Gomes

Publisher: CRC Press

Published: 2016-04-19

Total Pages: 302

ISBN-13: 1439809658

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The role of metal ions in protein folding and structure is a critical topic to a range of scientists in numerous fields, particularly those working in structural biology and bioinorganic chemistry, those studying protein folding and disease, and those involved in the molecular and cellular aspects of metals in biological systems. Protein Folding an

Protein Folding

Protein Folding PDF

Author: C. M. Dobson

Publisher: Cambridge University Press

Published: 1995

Total Pages: 128

ISBN-13: 9780521576369

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Discusses the molecular mechanisms controlling protein folding in vivo and in vitro.

Protein Folding

Protein Folding PDF

Author: Charis Ghelis

Publisher: Academic Press

Published: 2012-12-02

Total Pages: 580

ISBN-13: 0323140920

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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.

Protein Folding

Protein Folding PDF

Author: Tony R. Obalinsky

Publisher: Nova Publishers

Published: 2006

Total Pages: 294

ISBN-13: 9781594548352

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Proteins are one of the most basic components of all living cells and therefore serve a vital purpose in the cells of animals, plants and bacteria. They are comprised of chains of amino acids, which are held together by ribosome. These chains have many different patterns, which are known as `folds.' These folds are complicated, and therefore susceptible to irregularities that are known to be the source of many diseases. Cystic fibrosis, mad cow disease, Alzheimer's disease, emphysema and others are all initiated by improper protein folds. It is clear that, improving our understanding of protein folding is a key to fighting these diseases. This book presents recently performed research from around the world on this important subject.

Protein Folding, Evolution and Design

Protein Folding, Evolution and Design PDF

Author: Eugene I. Shakhnovich

Publisher: IOS Press

Published: 2001

Total Pages: 364

ISBN-13: 9781586031695

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This text presents the results of broad, interdisciplinary effort to study proteins in physical and evolutionary perpective. Among authors are physicists, computational, chemists, crystallographers and evolutionary biologists. Experimental and theoretical developments from molecules to cells are presented, providing a broad picture of modern biophysical chemistry.

Protein Folding Protocols

Protein Folding Protocols PDF

Author: Yawen Bai

Publisher: Springer Science & Business Media

Published: 2008-02-04

Total Pages: 332

ISBN-13: 1597451894

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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.