Protein Protein Interaction Assays
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| Author | : Weibo Cai |
| Publisher | : BoD – Books on Demand |
| Total Pages | : 488 |
| Release | : 2012-03-30 |
| Genre | : Science |
| ISBN | : 9535103970 |
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.
| Author | : Ali Tavassoli |
| Publisher | : Royal Society of Chemistry |
| Total Pages | : 357 |
| Release | : 2020-12-07 |
| Genre | : Science |
| ISBN | : 178801569X |
Protein-protein interactions (PPI) are at the heart of the majority of cellular processes, and are frequently dysregulated or usurped in disease. Given this central role, the inhibition of PPIs has been of significant interest as a means of treating a wide variety of diseases. However, there are inherent challenges in developing molecules capable of disrupting the relatively featureless and large interfacial areas involved. Despite this, there have been a number of successes in this field in recent years using both traditional drug discovery approaches and innovative, interdisciplinary strategies using novel chemical scaffolds. This book comprehensively covers the various aspects of PPI inhibition, encompassing small molecules, peptidomimetics, cyclic peptides, stapled peptides and macrocycles. Illustrated throughout with successful case studies, this book provides a holistic, cutting-edge view of the subject area and is ideal for chemical biologists and medicinal chemists interested in developing PPI inhibitors.
| Author | : Laure Journet |
| Publisher | : Humana Press |
| Total Pages | : 528 |
| Release | : 2017-07-01 |
| Genre | : Science |
| ISBN | : 9781493970315 |
This volume details protocols that cover the broad arsenal of techniques used to study a secretion system from A to Z. Chapters focus on identifying and localizing the different subunits, defining interactions within subunits, monitoring conformational changes, purifying and imaging of large complexes, defining the assembly pathway by fluorescence microscopy and the role of energy during assembly and/or secretion, identifying secreted effectors as well as reporters to follow effector transport. 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 cutting-edge, Bacterial Protein Secretion Systems: Methods and Protocol aims to provide techniques that are not restricted to the study of secretion systems but are also of specific interest for any researcher interested on multi-protein complexes of the bacterial cell envelope.
| Author | : Jean-Paul Renaud |
| Publisher | : John Wiley & Sons |
| Total Pages | : 1437 |
| Release | : 2020-01-09 |
| Genre | : Medical |
| ISBN | : 1118900502 |
With the most comprehensive and up-to-date overview of structure-based drug discovery covering both experimental and computational approaches, Structural Biology in Drug Discovery: Methods, Techniques, and Practices describes principles, methods, applications, and emerging paradigms of structural biology as a tool for more efficient drug development. Coverage includes successful examples, academic and industry insights, novel concepts, and advances in a rapidly evolving field. The combined chapters, by authors writing from the frontlines of structural biology and drug discovery, give readers a valuable reference and resource that: Presents the benefits, limitations, and potentiality of major techniques in the field such as X-ray crystallography, NMR, neutron crystallography, cryo-EM, mass spectrometry and other biophysical techniques, and computational structural biology Includes detailed chapters on druggability, allostery, complementary use of thermodynamic and kinetic information, and powerful approaches such as structural chemogenomics and fragment-based drug design Emphasizes the need for the in-depth biophysical characterization of protein targets as well as of therapeutic proteins, and for a thorough quality assessment of experimental structures Illustrates advances in the field of established therapeutic targets like kinases, serine proteinases, GPCRs, and epigenetic proteins, and of more challenging ones like protein-protein interactions and intrinsically disordered proteins
| Author | : Stefan Canzar |
| Publisher | : Humana |
| Total Pages | : 0 |
| Release | : 2019-10-04 |
| Genre | : Science |
| ISBN | : 9781493998722 |
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.
| Author | : Jurriaan Huskens |
| Publisher | : John Wiley & Sons |
| Total Pages | : 434 |
| Release | : 2018-02-05 |
| Genre | : Science |
| ISBN | : 1119143462 |
Connects fundamental knowledge of multivalent interactions with current practice and state-of-the-art applications Multivalency is a widespread phenomenon, with applications spanning supramolecular chemistry, materials chemistry, pharmaceutical chemistry and biochemistry. This advanced textbook provides students and junior scientists with an excellent introduction to the fundamentals of multivalent interactions, whilst expanding the knowledge of experienced researchers in the field. Multivalency: Concepts, Research & Applications is divided into three parts. Part one provides background knowledge on various aspects of multivalency and cooperativity and presents practical methods for their study. Fundamental aspects such as thermodynamics, kinetics and the principle of effective molarity are described, and characterisation methods, experimental methodologies and data treatment methods are also discussed. Parts two and three provide an overview of current systems in which multivalency plays an important role in chemistry and biology, with a focus on the design rules, underlying chemistry and the fundamental principles of multivalency. The systems covered range from chemical/materials-based ones such as dendrimers and sensors, to biological systems including cell recognition and protein binding. Examples and case studies from biochemistry/bioorganic chemistry as well as synthetic systems feature throughout the book. Introduces students and young scientists to the field of multivalent interactions and assists experienced researchers utilising the methodologies in their work Features examples and case studies from biochemistry/bioorganic chemistry, as well as synthetic systems throughout the book Edited by leading experts in the field with contributions from established scientists Multivalency: Concepts, Research & Applications is recommended for graduate students and junior scientists in supramolecular chemistry and related fields, looking for an introduction to multivalent interactions. It is also highly useful to experienced academics and scientists in industry working on research relating to multivalent and cooperative systems in supramolecular chemistry, organic chemistry, pharmaceutical chemistry, chemical biology, biochemistry, materials science and nanotechnology.
| Author | : M Michael Gromiha |
| Publisher | : World Scientific |
| Total Pages | : 424 |
| Release | : 2020-03-05 |
| Genre | : Science |
| ISBN | : 9811211884 |
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.
| Author | : Sajad Majeed Zargar |
| Publisher | : Springer |
| Total Pages | : 358 |
| Release | : 2018-02-20 |
| Genre | : Science |
| ISBN | : 9811074798 |
The natural environment for plants is composed of a complex set of abiotic and biotic stresses; plant responses to these stresses are equally complex. Systems biology allows us to identify regulatory hubs in complex networks. It also examines the molecular “parts” (transcripts, proteins and metabolites) of an organism and attempts to combine them into functional networks or models that effectively describe and predict the dynamic activities of that organism in different environments. This book focuses on research advances regarding plant responses to abiotic stresses, from the physiological level to the molecular level. It highlights new insights gained from the integration of omics datasets and identifies remaining gaps in our knowledge, outlining additional focus areas for future crop improvement research. Plants have evolved a wide range of mechanisms for coping with various abiotic stresses. In many crop plants, the molecular mechanisms involved in a single type of stress tolerance have since been identified; however, in order to arrive at a holistic understanding of major and common events concerning abiotic stresses, the signaling pathways involved must also be elucidated. To date several molecules, like transcription factors and kinases, have been identified as promising candidates that are involved in crosstalk between stress signalling pathways. However, there is a need to better understand the tolerance mechanisms for different abiotic stresses by thoroughly grasping the signalling and sensing mechanisms involved. Accordingly, this book covers a range of topics, including the impacts of different abiotic stresses on plants, the molecular mechanisms leading to tolerance for different abiotic stresses, signaling cascades revealing cross-talk among various abiotic stresses, and elucidation of major candidate molecules that may provide abiotic stress tolerance in plants.
| Author | : |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2002 |
| Genre | : Cells |
| ISBN | : 9780815332183 |
| Author | : Aidong Zhang |
| Publisher | : Cambridge University Press |
| Total Pages | : 283 |
| Release | : 2009-04-06 |
| Genre | : Computers |
| ISBN | : 1139479032 |
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.
