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Chapter Three Targeting the Architecture of Deregulated Protein Complexes in Cancer
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 111 Author(s): Eduard Stefan, Jakob Troppmair, Klaus Bister The architectures of central signaling hubs are precisely organized by static and dynamic protein–protein interactions (PPIs). Upon deregulation, these PPI platforms are capable to propagate or initiate pathophysiological signaling events. This causes the acquisition of molecular features contributing to the etiology or progression of many diseases, including cancer, where deregulated molecular interactions of signaling proteins have been best studied. The reason...
Source: Advances in Protein Chemistry and Structural Biology - February 16, 2018 Category: Biochemistry Source Type: research

Chapter Two Targeting Intramembrane Protein –Protein Interactions: Novel Therapeutic Strategy of Millions Years Old
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 111 Author(s): Alexander B. Sigalov Intramembrane protein–protein interactions (PPIs) are involved in transmembrane signal transduction mediated by cell surface receptors and play an important role in health and disease. Recently, receptor-specific modulatory peptides rationally designed using a general platform of transmembrane signaling, the signaling chain homooligomerization (SCHOOL) model, have been proposed to therapeutically target these interactions in a variety of serious diseases with unmet needs including cancer, s...
Source: Advances in Protein Chemistry and Structural Biology - February 16, 2018 Category: Biochemistry Source Type: research

Chapter One Homo- and Heterodimerization of Proteins in Cell Signaling: Inhibition and Drug Design
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 111 Author(s): Sitanshu S. Singh, Seetharama D. Jois Protein dimerization controls many physiological processes in the body. Proteins form homo-, hetero-, or oligomerization in the cellular environment to regulate the cellular processes. Any deregulation of these processes may result in a disease state. Protein–protein interactions (PPIs) can be inhibited by antibodies, small molecules, or peptides, and inhibition of PPI has therapeutic value. PPI drug discovery research has steadily increased in the last decade, and a few ...
Source: Advances in Protein Chemistry and Structural Biology - February 16, 2018 Category: Biochemistry Source Type: research

Transglutaminase and Sialyltransferase Enzymatic Approaches for Polymer Conjugation to Proteins
Publication date: Available online 12 February 2018 Source:Advances in Protein Chemistry and Structural Biology Author(s): Katia Maso, Antonella Grigoletto, Gianfranco Pasut Proteins hold a central role in medicine and biology, also confirmed by the several therapeutic applications based on biologic drugs. Such therapies are of great relevance thanks to high potency and safety of proteins. Nevertheless, many proteins as therapeutics might present issues like fast kidney clearance, rapid enzymatic degradation, or immunogenicity. Such defects implicate frequent administrations or administrations at high doses of th...
Source: Advances in Protein Chemistry and Structural Biology - February 12, 2018 Category: Biochemistry Source Type: research

Chapter Eight Computational Resources for Predicting Protein –Protein Interactions
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Himani Tanwar, C. George Priya Doss Proteins are the essential building blocks and functional components of a cell. They account for the vital functions of an organism. Proteins interact with each other and form protein interaction networks. These protein interactions play a major role in all the biological processes and pathways. The previous methods of predicting protein interactions were experimental which focused on a small set of proteins or a particular protein. However, these experimental approaches are ...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter Seven Structural Prediction of Protein –Protein Interactions by Docking: Application to Biomedical Problems
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Didier Barradas-Bautista, Mireia Rosell, Chiara Pallara, Juan Fernández-Recio A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains elusive. One of the reasons is that proteins are not acting alone, but are specifically interacting with other proteins and biomolecules, forming intricate interaction networks that are essential for the majorit...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter Six Probing the Protein –Protein Interaction Network of Proteins Causing Maturity Onset Diabetes of the Young
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): P. Sneha, D. Thirumal Kumar, Jose Lijo, M. Megha, R. Siva, C. George Priya Doss Protein–protein interactions (PPIs) play vital roles in various cellular pathways. Most of the proteins perform their responsibilities by interacting with an enormous number of proteins. Understanding these interactions of the proteins and their interacting partners has shed light toward the field of drug discovery. Also, PPIs enable us to understand the functions of a protein by understanding their interacting partners. C...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter Five Targeting Protein –Protein Interactions in the Ubiquitin–Proteasome Pathway
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Maria Gaczynska, Pawel A. Osmulski The ubiquitin–proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein–p...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter Four Intrinsic Disorder, Protein –Protein Interactions, and Disease
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Vladimir N. Uversky It is recognized now that biologically active proteins without stable tertiary structure (known as intrinsically disordered proteins, IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are important players found in any given proteome. These IDPs/IDPRs possess functions that complement functional repertoire of their ordered counterparts, being commonly related to recognition, as well as control and regulation of various signaling pathways....
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter Three Protein –Protein Interaction Modulators for Epigenetic Therapies
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Bárbara I. Díaz-Eufracio, J. Jesús Naveja, José L. Medina-Franco Targeting protein–protein interactions (PPIs) is becoming an attractive approach for drug discovery. This is particularly true for difficult or emerging targets, such as epitargets that may be elusive to drugs that fall into the traditional chemical space. The chemical nature of the PPIs makes attractive the use of peptides or peptidomimetics to selectively modulate such interactions. Despite the fact peptide-based drug discovery has been ...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter Two Using TR-FRET to Investigate Protein –Protein Interactions: A Case Study of PXR-Coregulator Interaction
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Wenwei Lin, Taosheng Chen Time-resolved fluorescence resonance energy transfer (TR-FRET) protein–protein interaction assays, especially in the format of receptor coregulator (coactivator and corepressor) recruitment/repression assays, have been widely used in nuclear receptor research to characterize the modes of action, efficacies, and binding affinities of ligands (including their properties as agonists, antagonists, and inverse agonists). However, there has been only limited progress in using this assay fo...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Chapter One Analysis of Protein Interactions by Surface Plasmon Resonance
Publication date: 2018 Source:Advances in Protein Chemistry and Structural Biology, Volume 110 Author(s): Dennis G. Drescher, Dakshnamurthy Selvakumar, Marian J. Drescher Surface plasmon resonance is an optical technique that is utilized for detecting molecular interactions, such as interactions that occur between proteins or other classes of molecules. Binding of a mobile molecule (analyte) to a molecule immobilized on a thin metal film (ligand) changes the refractive index of the film. The angle of extinction of light that is completely reflected after polarized light impinges upon the film, is altered and moni...
Source: Advances in Protein Chemistry and Structural Biology - February 2, 2018 Category: Biochemistry Source Type: research

Defining Pharmacological Targets by Analysis of Virus –Host Protein Interactions
Publication date: Available online 18 December 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Manuel Llano, Mario A. Peña-Hernandez Viruses are obligate parasites that depend on cellular factors for replication. Pharmacological inhibition of essential viral proteins, mostly enzymes, is an effective therapeutic alternative in the absence of effective vaccines. However, this strategy commonly encounters drug resistance mechanisms that allow these pathogens to evade control. Due to the dependency on host factors for viral replication, pharmacological disruption of the host-pathogen protei...
Source: Advances in Protein Chemistry and Structural Biology - December 20, 2017 Category: Biochemistry Source Type: research

Human Interactomics: Comparative Analysis of Different Protein Interaction Resources and Construction of a Cancer Protein –Drug Bipartite Network
Publication date: Available online 6 November 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Javier De Las Rivas, Diego Alonso-López, Mónica M. Arroyo Unraveling the protein interaction wiring that occurs in human cells as a scaffold of biological processes requires the identification of all elements that constitute such molecular interaction networks. Proteome-wide experimental studies and bioinformatic comprehensive efforts have provided reliable and updated compendiums of the human protein interactome. In this work, we present a current view of available databases of human protei...
Source: Advances in Protein Chemistry and Structural Biology - November 7, 2017 Category: Biochemistry Source Type: research

Targeting Protein –Protein Interactions in the Ubiquitin–Proteasome Pathway
Publication date: Available online 18 October 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Maria Gaczynska, Pawel A. Osmulski The ubiquitin–proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreogra...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2017 Category: Biochemistry Source Type: research