Download or read book Protein Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.

Download or read book Protein Protein Interactions written by Haian Fu and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the mysteries stored in our DNA have been more completely revealed, scientists have begun to face the extraordinary challenge of unraveling the int- cate network of protein–protein interactions established by that DNA fra- work. It is increasingly clear that proteins continuously interact with one another in a highly regulated fashion to determine cell fate, such as proliferation, diff- entiation, or death. These protein–protein interactions enable and exert str- gent control over DNA replication, RNA transcription, protein translation, macromolecular assembly and degradation, and signal transduction; essentially all cellular functions involve protein–protein interactions. Thus, protein–p- tein interactions are fundamental for normal physiology in all organisms. Alt- ation of critical protein–protein interactions is thought to be involved in the development of many diseases, such as neurodegenerative disorders, cancers, and infectious diseases. Therefore, examination of when and how protein–p- tein interactions occur and how they are controlled is essential for understa- ing diverse biological processes as well as for elucidating the molecular basis of diseases and identifying potential targets for therapeutic interventions. Over the years, many innovative biochemical, biophysical, genetic, and computational approaches have been developed to detect and analyze p- tein–protein interactions. This multitude of techniques is mandated by the diversity of physical and chemical properties of proteins and the sensitivity of protein–protein interactions to cellular conditions.

Download or read book Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and published by World Scientific. This book was released on 2020-03-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.

Download or read book Protein Protein Interactions Techniques and Applications written by Brian O'Neill and published by Larsen and Keller Education. This book was released on 2018-05-16 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Any interactions between two protein molecules enabled by electrostatic forces like hydrophobic effect is known as protein-protein interaction. The examples of these interactions are cell metabolism, signal transduction, muscle contraction, transport across membranes, etc. The process is used in many subjects namely quantum chemistry, molecular dynamics, biochemistry, etc. This book is a compilation of chapters that discuss the most vital concepts in the field of protein-protein interactions. It discusses in detail the various applications and techniques of the subject. For someone with an interest and eye for detail, this textbook covers the most significant topics in this field. It will serve as a reference to a broad spectrum of readers.

Download or read book Peptides Targeting Protein Protein Interactions Methods and Applications written by Luca Domenico D’Andrea and published by Frontiers Media SA. This book was released on 2021-12-06 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Ligand Interactions written by Mark A. Williams and published by Humana. This book was released on 2016-11-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the cell’s workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions – whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.

Download or read book Protein Ligand Interactions written by G. Ulrich Nienhaus and published by Humana Press. This book was released on 2005-03-21 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: A readily reproducible collection of established and emerging techniques for studying the interaction between proteins and ligands, including biochemical/bulk techniques, structure analysis, spectroscopy, single-molecule studies, and theoretical/computational tools. Among the highlights are surface plasmon resonance (SPR) and reflectometric biosensor approaches, high-throughput screening with confocal optics microscopy, single molecule fluorescence and fluorescence correlation spectroscopy (FCS), atomic force microscopy (AFM), crystallography of reaction intermediates, and time-resolved x-ray crystallography. The protocols follow the successful Methods in Molecular BiologyTM series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

Download or read book Protein protein Interactions written by Erica A. Golemis and published by CSHL Press. This book was released on 2005 with total page 954 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reflecting the various advances in the field, this book provides comprehensive coverage of protein-protein interactions. It presents a collection of the technical and theoretical issues involved in the study of protein associations, including biophysical approaches. It also offers a collection of computational methods for analyzing interactions.

Download or read book Protein Purification and Analysis I written by IConcept Press Staff and published by CreateSpace. This book was released on 2013-12 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter 1 is a review of the bioinformatics literature on protein-protein interactions (PPIs). A protein-protein interaction network (PPIN) is a collection of PPIs, often deposited in online databases. PPINs may complement other datasets, such as protein structural information. Chapter 2 describes the usability and advantages of the micro-patterning technique to study protein-protein interactions in a live cell context. It summarizes results achieved so far, discusses latest technical developments and describes potential future applications. Chapter 3 describes a strategy for identification of protein peptides cross-linked to radiolabeled RNA derivatives in specific complexes of proteins or ribonucleoproteins with these derivatives. This strategy is alternative to the identification based on mass-spectrometry and can be used for determination of protein sites involved in interactions with specific RNAs when mass-spectrometry is not applicable. Chapter 4 describes biochemical methods for assessing interaction between distinct ligand-gated channels. This chapter proposes also methods to examine functional impact of these receptor-receptor interactions in the nervous system. Chapter 5 proposes a statistical approach based on Structural Equation Modeling, in combination with step-wise factor analysis, to infer protein-DNA interactions for gene transcriptional control in the absence of protein information. Such approach only uses gene expression profiles. Chapter 6 describes procedures for the biochemical analysis of amyloid proteins in transgenic Drosophila, specifically the prion protein. The authors show that protocols from the mammalian literature can be easily adapted and scaled to these small flies and by ensuring robust expression of the prion protein and proper handling of these delicate samples. Chapter 7 discusses DEAD-box proteins. DEAD-box protein family members participate in many aspects of RNA metabolism, particularly in the ATP-driven disruption of secondary structures of RNA. Genes coding for these types of proteins are recognised in all free living bacteria. Chapter 8 provides an experimental model of restriction-modification enzyme fusion and proposes a molecular mechanism for appearance of type IIC restriction-modification and M.SsoII-related enzymes, as well as other multifunctional proteins. Chapter 9 describes the role of branched chain amino acids, leucine, isoleucine and valine, in exercise with respect to performance, muscle kinetics, fatigue and immunity. It also discusses the existing evidence on any superior benefits of branched chain amino acid supplements to exercising individuals and athletes. Chapter 10 provides an overview of the protein-peptide based research in dermatology and the recent emergence of many new dermatologic therapeutic modalities. Chapter 11 summarizes the adverse health effects of prenatal or early postnatal exposure to environmental pollutants (lead, arsenic and dioxins are the best known), pharmaceuticals, some food additives, and other chemicals through the mechanism of cell deprogramming or imprinting. Chapter 12 put forward 2D-PAGE as an important tool, especially for clinical laboratories involved in the determination of protein expression levels and disease biomarker discovery. Chapter 13 shows how to investigate and characterize an open reading frame, from exploiting the similarity in amino acid sequence, until the cloning, expression, purification and activity of the protein and its biological partners. Chapter 14 focuses on the cloning, heterologous expression and physicochemical characterization of Als5, one of the GPI-anchored adhesins from Candida albicans.

Download or read book Protein Protein Interactions written by Krishna Mohan Poluri and published by Springer Nature. This book was released on 2021-05-19 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of the fundamental aspects of protein-protein interactions (PPI), including a detailed account of the energetics and thermodynamics involved in these interactions. It also discusses a number of computational and experimental approaches for the prediction of PPI interactions and reviews their principles, advantages, drawbacks, and the recent developments. Further, it offers structural and mechanistic insights into the formation of protein-protein complexes and maps different PPIs into networks to delineate various pathways that operate at the cellular level. Lastly, it describes computational protein-protein docking techniques and discusses their implications for further experimental research. Given its scope, this book is a valuable resource for students, researchers, scientists, entrepreneurs, and medical/healthcare professionals.

Download or read book Novel Methods in Computational Analysis and Design of Protein protein Interactions written by Brian Alan Joughin and published by . This book was released on 2007 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis presents a number of novel computational methods for the analysis and design of protein-protein complexes, and their application to the study of the interactions of phosphopeptides with phosphopeptide-binding domain interactions. A novel protein-protein interaction type, the action-at-a-distance interaction, is described in the complex of the TEM1 P-lactamase with the 3-lactamase inhibitor protein (BLIP). New action-at-a-distance interactions were designed on the surface of BLIP and computed to enhance the affinity of that complex. A new method is described for the characterization and prediction of protein ligand-binding sites. This method was used to analyze the phosphoresidue-contacting sites of known phosphopeptide-binding domains, and to predict the sites of phosphoresidue-contact on some protein domains for which the correct site was not known. The design of a library of variant WW domains that is predicted to be enriched in domains that might have specificity for "pS/pT-Q" peptide ligands is detailed. General methods for designing libraries of degenerate oligonucleotides for expressing protein libraries as accurately as possible are given, and applied to the described WW domain variant library.

Download or read book Protein Protein Interaction written by Meike Werther and published by Springer. This book was released on 2008-08-28 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers trends in modern biotechnology. It treats all aspects of this interdisciplinary technology, where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science.

Download or read book Protein Protein Interaction Networks written by Stefan Canzar and published by Humana. This book was released on 2019-10-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.

Download or read book Applications of Chimeric Genes and Hybrid Proteins Part C Protein Protein Interactions and Genomics written by and published by Elsevier. This book was released on 2000-10-28 with total page 701 pages. Available in PDF, EPUB and Kindle. Book excerpt: The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.

Download or read book Biological Data Mining in Protein Interaction Networks written by Li, Xiao-Li and published by IGI Global. This book was released on 2009-05-31 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The goal of this book is to disseminate research results and best practices from cross-disciplinary researchers and practitioners interested in, and working on bioinformatics, data mining, and proteomics"--Provided by publisher.

Download or read book Protein Protein Interaction Assays written by Mahmood-Ur-Rahman Ansari and published by BoD – Books on Demand. This book was released on 2018-07-18 with total page 91 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chapters in this book are written by a team of well-reputed international researchers. The objective is to provide advanced and updated information related to protein-protein interactions. I hope the methods, resources and approaches described here will enhance the available knowledge of the reader significantly.

Download or read book Protein Interaction Networks written by Aidong Zhang and published by Cambridge University Press. This book was released on 2009-04-06 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: The analysis of protein-protein interactions is fundamental to the understanding of cellular organization, processes, and functions. Proteins seldom act as single isolated species; rather, proteins involved in the same cellular processes often interact with each other. Functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. Recent large-scale investigations of protein-protein interactions using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated protein-protein interaction networks. The resulting large volume of protein-protein interaction data has posed a challenge to experimental investigation. This book provides a comprehensive understanding of the computational methods available for the analysis of protein-protein interaction networks. It offers an in-depth survey of a range of approaches, including statistical, topological, data-mining, and ontology-based methods. The author discusses the fundamental principles underlying each of these approaches and their respective benefits and drawbacks, and she offers suggestions for future research.