Protein Sequencing Protocols
Protein Sequencing Protocols

Author: Bryan John Smith

Publisher: Springer Science & Business Media

Published: 2008-02-02

Total Pages: 489

ISBN-13: 1592593429

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Determination of the protein sequence is as important today as it was a half century ago, even though the techniques and purposes have changed over time. Mass spectrometry has continued its recent rapid development to find notable application in the characterization of small amounts of protein, for example, in the field of proteomics. The “traditional” chemical N-terminal sequencing is still of great value in quality assurance of the increasing number of biopharmaceuticals that are to be found in the clinic, checking processing events of recombinant proteins, and so on. It is joined in the armory of me- ods of protein analysis by such techniques as C-terminal sequencing and amino acid analysis. These methods are continually developing. The first edition of Protein Sequencing Protocols was a “snapshot” of methods in use in protein biochemistry laboratories at the time, and this, the second edition, is likewise. Methods have evolved in the intervening period, and the content of this book has similarly changed, the content of some chapters having been superceded and replaced by other approaches. Thus, in this edition, there is inclusion of approaches to validation of methods for quality assurance work, reflecting the current importance of biopharmaceuticals, and also a guide to further analysis of protein sequence information, acknowledging the importance of bioinformatics.

Protein Structure Prediction
Protein Structure Prediction

Author: David Webster

Publisher: Springer Science & Business Media

Published: 2008-02-03

Total Pages: 425

ISBN-13: 1592593682

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The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.

2-D Proteome Analysis Protocols
2-D Proteome Analysis Protocols

Author: Andrew J. Link

Publisher: Springer Science & Business Media

Published: 2008-02-02

Total Pages: 585

ISBN-13: 1592595847

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With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics—the study of the expressed part of the genome—has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry—especially in the fields of molecular biology, biochemistry, microbiology, and cell biology—should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.

Therapeutic Proteins
Therapeutic Proteins

Author: C. Mark Smales

Publisher: Springer Science & Business Media

Published: 2008-02-04

Total Pages: 481

ISBN-13: 1592599222

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With the recent completion of the sequencing of the human genome, it is widely anticipated that the number of potential new protein drugs and targets will escalate at an even greater rate than that observed in recent years. However, identification of a potential target is only part of the process in developing these new next generation protein-based “drugs” that are increasingly being used to treat human disease. Once a potential protein drug has been identified, the next rate-limiting step on the road to development is the production of sufficient authentic material for testing, charact- ization, clinical trials, and so on. If a protein drug does actually make it through this lengthy and costly process, methodology that allows the production of the protein on a scale large enough to meet demand must be implemented. Furthermore, large-scale production must not compromise the authenticity of the final product. It is also nec- sary to have robust methods for the purification, characterization, viral inactivation and continued testing of the authenticity of the final protein product and to be able to formulate it in a manner that retains both its biological activity and lends itself to easy administration. Therapeutic Proteins: Methods and Protocols covers all aspects of protein drug production downstream of the discovery stage. This volume contains contributions from leaders in the field of therapeutic protein expression, purification, characterization, f- mulation, and viral inactivation.

Protein Crystallography
Protein Crystallography

Author: Alexander Wlodawer

Publisher: Humana Press

Published: 2017-06-02

Total Pages: 672

ISBN-13: 9781493969982

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This volume provides methods for modern macromolecular crystallography, including all steps leading to crystal structure determination and analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Crystallography aims to ensure successful results in the further study of this vital field.

Computational Methods in Protein Evolution
Computational Methods in Protein Evolution

Author: Tobias Sikosek

Publisher: Humana

Published: 2018-10-09

Total Pages: 0

ISBN-13: 9781493987351

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This volume presents a diverse collection of methodologies used to study various problems at the protein sequence and structure level. The chapters in this book look at issues ranging from broad concepts like protein space to specifics like antibody modeling. Topics include point mutations, gene duplication, de novo emergence of new genes, pairwise correlated mutations, ancestral protein reconstruction, homology modelling, protein stability and dynamics, and protein-protein interactions. The book also covers a wide range of computational approaches, including sequence and structure alignments, phylogenies, physics-based and mathematical approaches, machine learning, and more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and prerequisites, step-by-step, readily reproducible computational protocols (using command line or graphical user interfaces, sometimes including computer code), and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Computational Methods in Protein Evolution is a valuable resource that offers useful workflows and techniques that will help both novice and expert researchers working with proteins computationally.

RNA
RNA

Author: Henrik Nielsen

Publisher: Humana Press

Published: 2010-12-10

Total Pages: 329

ISBN-13: 9781588299130

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Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the procedures and methods used to describe the structure of messenger RNAs and non-coding RNAs that are transcribed by RNA polymerase II as the immediate gene products in mammalian cells. Focused on the structure of the RNA products of “gene X” and the mapping of proteins associated with these RNAs, the volume presents appropriate information for non-specialists in RNA biology. Written in the highly successful Methods in Molecular BiologyTM series format, many chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, RNA: Methods and Protocols views the transcriptional landscape with an appreciation for the role that proteins play in the processing and interpretation of genetic information in an attempt to further our crucial knowledge of the many products and sophisticated regulatory networks that result from it.

High Throughput Protein Expression and Purification
High Throughput Protein Expression and Purification

Author: Sharon A. Doyle

Publisher: Humana Press

Published: 2010-11-19

Total Pages: 0

ISBN-13: 9781617378218

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Despite exciting advances in genome sequencing, isolating a protein from its expression system in its native form still presents a complex challenge. In High Throughput Protein Expression and Purification: Methods and Protocols, leading scientists detail the most successful protocols currently in use, including various high throughput cloning schemes, protein expression analysis, and production protocols. This volume describes the use of E. coli, insect, and mammalian cells, as well as cell-free systems for the production of a wide variety of proteins, including glycoproteins and membrane proteins, in order to best represent strategies that create and exploit common features to enable simplified cloning, stable expression, and purification of proteins. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters present brief introductions to the subject, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section for tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, High Throughput Protein Expression and Purification: Methods and Protocols is an ideal reference for protein biochemists and all those who wish to apply these easy-to-use protocols to the many applicable fields.

Plant Virology Protocols
Plant Virology Protocols

Author: Gary Foster

Publisher: Humana Press

Published: 2010-10-28

Total Pages: 677

ISBN-13: 9781617377945

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Following the considerable success of the first edition of Plant Virology Protocols, this exciting new edition covers the many new techniques that are now applied to the examination and understanding of plant viruses. Each section presents the most novel methods and step-by-step reproducible laboratory protocols to allow researchers more effective approaches to study plant viruses. This updated book will prove indispensable to laboratory investigators studying plant viruses.