The Protein Folding Problem and Tertiary Structure Prediction
The Protein Folding Problem and Tertiary Structure Prediction

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 Folding and Misfolding
Protein Folding and Misfolding

Author: Heinz Fabian

Publisher: Springer Science & Business Media

Published: 2011-09-18

Total Pages: 257

ISBN-13: 3642222307

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Infrared spectroscopy is a new and innovative technology to study protein folding/misfolding events in the broad arsenal of techniques conventionally used in this field. The progress in understanding protein folding and misfolding is primarily due to the development of biophysical methods which permit to probe conformational changes with high kinetic and structural resolution. The most commonly used approaches rely on rapid mixing methods to initiate the folding event via a sudden change in solvent conditions. Traditionally, techniques such as fluorescence, circular dichroism or visible absorption are applied to probe the process. In contrast to these techniques, infrared spectroscopy came into play only very recently, and the progress made in this field up to date which now permits to probe folding events over the time scale from picoseconds to minutes has not yet been discussed in a book. The aim of this book is to provide an overview of the developments as seen by some of the main contributors to the field. The chapters are not intended to give exhaustive reviews of the literature but, instead to illustrate examples demonstrating the sort of information, which infrared techniques can provide and how this information can be extracted from the experimental data. By discussing the strengths and limitations of the infrared approaches for the investigation of folding and misfolding mechanisms this book helps the reader to evaluate whether a particular system is appropriate for studies by infrared spectroscopy and which specific advantages the techniques offer to solve specific problems.

Protein Folding
Protein Folding

Author: Cláudio M. Gomes

Publisher: Springer

Published: 2019-02-25

Total Pages: 63

ISBN-13: 331900882X

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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.

Protein Structure, Stability, and Folding
Protein Structure, Stability, and Folding

Author: Kenneth P. Murphy

Publisher: Springer Science & Business Media

Published: 2008-02-04

Total Pages: 258

ISBN-13: 1592591930

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In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating many of protein stability and dynamics from knowledge of the structure, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of some of this complex area by detailing many of the major techniques in use today.

Protein Stability and Folding
Protein Stability and Folding

Author: Wolfgang Pfeil

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 662

ISBN-13: 3642587607

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Protein folding remains one of the most exclusive problems of modern biochemistry. Structure analysis has given access to the wealth of the molecular architecture of pro teins. As architecture needs static calculations, protein structure is always related to thermodynamic factors that govern folding and stability of a particular folded protein over the non-organized polypeptide chain. During the past decades a huge amount of thermodynamic data related to protein folding and stability has been accumulated. The data are certainly of importance in dechiffring the protein folding problem. At the same time, the data can guide the con struction of modified and newly synthesized proteins with properties optimized for particular application. The intention of this book is a generation of a data collection which makes the vast amount of present data accessible for multidisciplinary research where chemistry, phy sics, biology, and medicine are involved and also pharmaceutical and food research and technology. It took several years to compile all the data and the author wishes to thank everyone who provided data, ideas or even unpublished results. The author is, in particular, indebted to Prof. Wadso (Lund, Sweden) and IUPAC's Steering Committee on Bio physical Chemistry. Furthermore, support by the Deutsche Forschungsgemeinschafi (INK 16 AI-I) is acknowledged.

Lectures On Statistical Physics And Protein Folding
Lectures On Statistical Physics And Protein Folding

Author: Kerson Huang

Publisher: World Scientific

Published: 2005-05-30

Total Pages: 159

ISBN-13: 9814481068

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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 suggestions 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.

Protein Folding in Silico
Protein Folding in Silico

Author: Irena Roterman-Konieczna

Publisher: Elsevier

Published: 2012-10-04

Total Pages: 241

ISBN-13: 1908818255

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Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory

Protein Folding Kinetics
Protein Folding Kinetics

Author: Bengt Nölting

Publisher: Springer Science & Business Media

Published: 2005-12-05

Total Pages: 222

ISBN-13: 354027278X

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First methods book which includes many detailed descriptions Absolutely needed and thus timely for the scientific community Comprises 15% more content and includes the mentioned special features

Protein Folding
Protein Folding

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

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.