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Computational Resources for Predicting Protein –Protein Interactions
Publication date: Available online 12 October 2017 Source:Advances in Protein Chemistry and Structural Biology 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...
Source: Advances in Protein Chemistry and Structural Biology - October 14, 2017 Category: Biochemistry Source Type: research

Investigating the Influence of Hotspot Mutations in Protein –Protein Interaction of IDH1 Homodimer Protein: A Computational Approach
In this study, we have used extensive computational approaches to identify the impact of missense mutations (R132C, R132G, R132H, R132L, R132S, and V178I) occurring in the interacting region of the IDH1 homodimer. By in silico pathogenicity analysis, all the mutations occurring at the position 132 and 178 were found to be pathogenic and neutral. Furthermore, the mutants R132C and R132G were found to be responsible for increasing the stability, whereas the mutants R132H, R132L, and R132S were found to be responsible for the decrease in stability by stability analysis. R132H, R132L, and R132S mutants exhibited higher destabi...
Source: Advances in Protein Chemistry and Structural Biology - October 14, 2017 Category: Biochemistry Source Type: research

Probing the Protein –Protein Interaction Network of Proteins Causing Maturity Onset Diabetes of the Young
Publication date: Available online 10 October 2017 Source:Advances in Protein Chemistry and Structural Biology 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 interac...
Source: Advances in Protein Chemistry and Structural Biology - October 10, 2017 Category: Biochemistry Source Type: research

Homo- and Heterodimerization of Proteins in Cell Signaling: Inhibition and Drug Design
Publication date: Available online 6 October 2017 Source:Advances in Protein Chemistry and Structural Biology 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 dec...
Source: Advances in Protein Chemistry and Structural Biology - October 7, 2017 Category: Biochemistry Source Type: research

Multifaceted Nucleolin Protein and Its Molecular Partners in Oncogenesis
Publication date: Available online 6 October 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Iva Ugrinova, Maria Petrova, Mounira Chalabi-Dchar, Philippe Bouvet Discovered in 1973, nucleolin is one of the most abundant phosphoproteins of the nucleolus. The ability of nucleolin to be involved in many cellular processes is probably related to its structural organization and its capability to form many different interactions with other proteins. Many functions of nucleolin affect cellular processes involved in oncogenesis—for instance: in ribosome biogenesis; in DNA repair, remodeling...
Source: Advances in Protein Chemistry and Structural Biology - October 6, 2017 Category: Biochemistry Source Type: research

Analysis of Protein Interactions by Surface Plasmon Resonance
Publication date: Available online 12 September 2017 Source:Advances in Protein Chemistry and Structural Biology 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, i...
Source: Advances in Protein Chemistry and Structural Biology - September 13, 2017 Category: Biochemistry Source Type: research

Structural Prediction of Protein –Protein Interactions by Docking: Application to Biomedical Problems
Publication date: Available online 31 August 2017 Source:Advances in Protein Chemistry and Structural Biology 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 ...
Source: Advances in Protein Chemistry and Structural Biology - September 1, 2017 Category: Biochemistry Source Type: research

Using TR-FRET to Investigate Protein –Protein Interactions: A Case Study of PXR-Coregulator Interaction
Publication date: Available online 31 August 2017 Source:Advances in Protein Chemistry and Structural Biology 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 usin...
Source: Advances in Protein Chemistry and Structural Biology - September 1, 2017 Category: Biochemistry Source Type: research

Development of Protein –Protein Interaction Inhibitors for the Treatment of Infectious Diseases
Publication date: Available online 24 August 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Andrew F. Voter, James L. Keck Protein–protein interaction (PPI) inhibitors are a rapidly expanding class of therapeutics. Recent advances in our understanding of PPIs and success of early examples of PPI inhibitors demonstrate the feasibility of targeting PPIs. This review summarizes the techniques used for the discovery and optimization of a diverse set PPI inhibitors, focusing on the development of PPI inhibitors as new antibacterial and antiviral agents. We close with a summary of the advan...
Source: Advances in Protein Chemistry and Structural Biology - August 25, 2017 Category: Biochemistry Source Type: research

Subcellular Targeting of Nitric Oxide Synthases Mediated by Their N-Terminal Motifs
Publication date: Available online 24 August 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Carlos Costas-Insua, Javier Merino-Gracia, Clara Aicart-Ramos, Ignacio Rodríguez-Crespo From a catalytic point of view, the three mammalian nitric oxide synthases (NOSs) function in an almost identical way. The N-terminal oxygenase domain catalyzes the conversion of l-arginine to l-citrulline plus ·NO in two sequential oxidation steps. Once l-arginine binds to the active site positioned above the heme moiety, two consecutive monooxygenation reactions take place. In the first step, l-arginin...
Source: Advances in Protein Chemistry and Structural Biology - August 25, 2017 Category: Biochemistry Source Type: research

Targeting the Architecture of Deregulated Protein Complexes in Cancer
Publication date: Available online 18 August 2017 Source:Advances in Protein Chemistry and Structural Biology 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 stud...
Source: Advances in Protein Chemistry and Structural Biology - August 19, 2017 Category: Biochemistry Source Type: research

Targeting Intramembrane Protein –Protein Interactions: Novel Therapeutic Strategy of Millions Years Old
Publication date: Available online 24 July 2017 Source:Advances in Protein Chemistry and Structural Biology 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 includ...
Source: Advances in Protein Chemistry and Structural Biology - July 25, 2017 Category: Biochemistry Source Type: research

Protein –Protein Interaction Modulators for Epigenetic Therapies
Publication date: Available online 25 July 2017 Source:Advances in Protein Chemistry and Structural Biology 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 discov...
Source: Advances in Protein Chemistry and Structural Biology - July 25, 2017 Category: Biochemistry Source Type: research

Intrinsic Disorder, Protein –Protein Interactions, and Disease
Publication date: Available online 24 July 2017 Source:Advances in Protein Chemistry and Structural Biology 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 signal...
Source: Advances in Protein Chemistry and Structural Biology - July 24, 2017 Category: Biochemistry Source Type: research

Chapter Nine Mechanistic Insights Into Catalytic RNA –Protein Complexes Involved in Translation of the Genetic Code
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Satya B. Routh, Rajan Sankaranarayanan The contemporary world is an “RNA–protein world” rather than a “protein world” and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome—the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence—epitomizes such an associ...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research