Modeling Peptide-Protein Interactions
Modeling Peptide-Protein Interactions

Author: Ora Schueler-Furman

Publisher: Humana

Published: 2017-02-27

Total Pages: 0

ISBN-13: 9781493967964

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This volume covers an array of techniques available for studying peptide-protein docking and design. The book is divided into four sections: peptide binding site prediction; peptide-protein docking; prediction and design of peptide binding specificity; and the design of inhibitory peptides. The chapters in Modeling Peptide-Protein Interactions: Methods and Protocols cover topics such as the usage of ACCLUSTER and PeptiMap for peptide binding site prediction; AnchorDock and ATTRACT for blind, flexible docking of peptides to proteins; flexible peptide docking using HADDOCK and FlexPepDock; identifying loop-mediated protein-protein interactions using LoopFinder; and protein-peptide interaction design using PinaColada. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary details for successful application of the different approaches and step-by-step, readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Modeling Peptide-Protein Interactions: Methods and Protocols provides a diverse and unified overview of this rapidly advancing field of major interest and applicability.

Multivalency
Multivalency

Author: Jurriaan Huskens

Publisher: John Wiley & Sons

Published: 2018-02-05

Total Pages: 434

ISBN-13: 1119143462

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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.

Protein-protein Complexes
Protein-protein Complexes

Author: Martin Zacharias

Publisher: World Scientific

Published: 2010

Total Pages: 401

ISBN-13: 1848163398

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Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Crystallography Made Crystal Clear
Crystallography Made Crystal Clear

Author: Gale Rhodes

Publisher: Academic Press

Published: 2012-12-02

Total Pages: 217

ISBN-13: 0323137784

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Crystallography Made Crystal Clear is designed to meet the need for an X-ray analysis that is between brief textbook sections and complete treatments. The book provides non-crystallographers with an intellectually satisfying explanation of the principles of how protein models are gleaned from X-ray analysis. The understanding of these concepts will foster wise use of the models, including the recognition of the strengths and weaknesses of pictures or computer graphics. Since proteins comprise the majority of the mass of macromolecules in cells and carry out biologically important tasks, the book will be of interest to biologists.Provides accessible descriptions of principles of x-ray crystallography, built on simple foundations for anyone with a basic science backgroundLeads the reader through clear, thorough, unintimidating explanations of the mathematics behind crystallographyExplains how to read crystallography papers in research journalsIf you use computer-generated models of proteins or nucleic acids for:Studying molecular interactionsDesigning ligands, inhibitors, or drugsEngineering new protein functionsInterpreting chemical, kinetic, thermodynamic, or spectroscopic dataStudying protein foldingTeaching macromolecule structure,and if you want to read new structure papers intelligently; become a wiser user of macromolecular models; and want to introduce undergraduates to the important subject of x-ray crystallography, then this book is for you.

Peptide-Lipid Interactions
Peptide-Lipid Interactions

Author: Sidney A. Simon

Publisher: Academic Press

Published: 2002-11-13

Total Pages: 606

ISBN-13: 0080925855

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This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction

Structural Biology in Drug Discovery
Structural Biology in Drug Discovery

Author: Jean-Paul Renaud

Publisher: John Wiley & Sons

Published: 2020-01-09

Total Pages: 1437

ISBN-13: 1118900502

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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

The Resonant Recognition Model of Macromolecular Bioactivity
The Resonant Recognition Model of Macromolecular Bioactivity

Author: Irena Cosic

Publisher: Birkhäuser

Published: 2012-12-06

Total Pages: 154

ISBN-13: 3034874758

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Biological processes in any living organism are based on selective interactions be tween particular biomolecules. In most cases, these interactions involve and are driven by proteins, which are the main conductors of any life process within the organism. The physical nature of these interactions is still not well known. This book presents an entirely new approach to analysis of biomolecular in teractions, in particular protein-protein and protein-DNA interactions, based on the assumption that these interactions are electromagnetic in nature. This new ap proach is the basis of the Resonant Recognition Model (RRM), which was devel oped over the last 15 years. Certain periodicities within the distribution of energies of delocalised electrons along a protein molecule are crucial to the protein's biological function, i.e. inter action with its target. If protein conductivity were introduced, then charges mov ing through the protein backbone might produce electromagnetic irradiation or ab sorption with spectral characteristics corresponding to energy distribution along the protein. The RRM is capable of calculating these spectral characteristics, which we hypothesized would be in the range of the infrared and visible light. These characteristics were confirmed with frequency characteristics obtained ex perimentally for certain light-induced biological processes.

Multiscale Approaches to Protein Modeling
Multiscale Approaches to Protein Modeling

Author: Andrzej Kolinski

Publisher: Springer Science & Business Media

Published: 2010-10-13

Total Pages: 360

ISBN-13: 144196889X

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The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.

Inhibitors of Protein–Protein Interactions
Inhibitors of Protein–Protein Interactions

Author: Ali Tavassoli

Publisher: Royal Society of Chemistry

Published: 2020-12-07

Total Pages: 357

ISBN-13: 178801569X

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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.