Описание: Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions.In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.
Автор: Ren-Jang Lin Название: RNA-Protein Interaction Protocols ISBN: 1617375551 ISBN-13(EAN): 9781617375552 Издательство: Springer Рейтинг: Цена: 23058.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: This updated and expanded second edition examines cutting-edge techniques developed recently, along with tried-and-tested methods. Expert contributors explore the isolation and characterization of RNA-protein complexes and related novel techniques.
Автор: Adrienne E. Clarke; Ian A. Wilson Название: Carbohydrate-Protein Interaction ISBN: 3642466435 ISBN-13(EAN): 9783642466434 Издательство: Springer Рейтинг: Цена: 13974.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: Until relatively recently, interest in complex carbohydrates focussed on their structural role in the extracellular matrix/ cell wall of animal, plant, and microbial cells and on their role as energy sources (e.g., starch and glycogen) and struc- tural components (e.g., cellulose) in natural products.
Автор: Andrew Emili; Jack Greenblatt; Shoshana Wodak Название: Systems Analysis of Chromatin-Related Protein Complexes in Cancer ISBN: 1493900897 ISBN-13(EAN): 9781493900893 Издательство: Springer Рейтинг: Цена: 19589.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: This book identifies RNA molecules associated with various chromatin-modifying machines. It explores the biological significance of chromatin machines in cancer (and the development and differentiation of stem cells).
Автор: Ren-Jang Lin Название: RNA-Protein Complexes and Interactions ISBN: 1493935895 ISBN-13(EAN): 9781493935895 Издательство: Springer Рейтинг: Цена: 19564.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание:
1. Characterization of RNA-Protein Interactions: Lessons from Two RNA-Binding Proteins, SRSF1 and SRSF2
Lindsey Skrdlant and Ren-Jang Lin
2. Identification of mRNA-Interacting Factors by MS2-TRAP (MS2-Tagged RNA Affinity Purification)
Je-Hyun Yoon and Myriam Gorospe
3. Biotin-Streptavidin Affinity Purification of RNA-Protein Complexes Assembled In Vitro
Shuai Hou, Lei Shi, and Haixin Lei
4. Detecting RNA-Protein Interaction Using End-Labeled Biotinylated RNA Oligonucleotides and Immunoblotting
Xuexiu Zheng, Sunghee Cho, Heegyum Moon, Tiing Jen Loh, Hana Jang, and Haihong Shen
5. Purification of RNA-Protein Splicing Complexes Using a Tagged Protein from In Vitro Splicing Reaction Mixture
Naoyuki Kataoka
6. Loading of Argonaute Protein with Small Duplex RNA in Cellular Extracts
Keith T. Gagnon
7. In Vitro Analysis of Ribonucleoprotein Complex Remodeling and Disassembly
Hua-Lin Zhou and Hua Lou
8. Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases
Ya-Ming Hou
9. Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles
Chao Huang, Guowei Wu, and Yi-Tao Yu
10. Northwestern Blot Analysis: Detecting RNA-Protein Interaction After Gel Separation of Protein Mixture
Shangbing Zang and Ren-Jang Lin
11. Measuring mRNA Translation by Polysome Profiling
Marek Kudla and Fedor V. Karginov
12. Genome-Wide Profiling of RNA-Protein Interactions Using CLIP-Seq
Cheryl Stork and Sika Zheng
13. Identification of Endogenous mRNA-Binding Proteins in Yeast Using Crosslinking and PolyA Enrichment
Sarah F. Mitchell and Roy Parker
14. Ribo-Proteomics Approach to Profile RNA-Protein and Protein-Protein Interaction Networks
Hsin-Sung Yeh, Jae-Woong Chang, and Jeongsik Yong
15. Detection of Protein-Protein Interaction Within an RNA-Protein Complex Via Unnatural-Amino-Acid-Mediated Photochemical Crosslinking
Fu-Lung Yeh, Luh Tung, and Tien-Hsien Chang
16. Evolution of Cell-Type-Specific RNA Aptamers Via Live Cell-Based SELEX
Jiehua Zhou and John J. Rossi
17. mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA Binding Proteins
Описание: This book examines the evolvability and robustness of an evolutionary GRN paradigm, in simple differentiated multicellularity and in evolving artificial `organisms` which grow and express an ontogeny from a single cell to a changing neighborhood of cells.
Описание: They are key components of a protein quality machinery in the cell which insures that the folding process of any newly-synthesized polypeptide chain results in the formation of a properly folded protein and that the folded protein is maintained in an active conformation throughout its functional lifetime.
Описание: Framed by a statistical physics perspective, this volume describes both the process of self-assembly and the impact of spatial organization on the function of membrane proteins. Using methods from equilibrium and non-equilibrium statistical mechanics, the text demonstrates the importance of the protein-protein interactions.
Автор: Anna Panchenko; Teresa M. Przytycka Название: Protein-protein Interactions and Networks ISBN: 1849967318 ISBN-13(EAN): 9781849967310 Издательство: Springer Рейтинг: Цена: 19589.00 р. Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse.
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