Most of a cell’s functional processes involve interactions among proteins, and a key challenge in proteomics is to better understand these complex interaction graphs at a systems level. Because of their importance in development and disease, protein-protein interactions (PPIs) have been the subject of intense research in recent years. In addition, a greater understanding of PPIs can be achieved...

Elucidation of Protein-Protein Interactions (PPIs) in living cells/animals is very important for the study basic biology and development novel therapeutics. Recent advances techniques profiling PPIs, such as fluorescence microscopy various proximity labeling-based methods coupled with mass spectrometry (MS), have provided a great opportunity to PPIs their native states spatiotemporal resolution...

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a robust and powerful tool for studying biomacromolecules their interactions. However, quantitative detection of high-mass analytes (kDa to MDa range) remains challenging MALDI-MS. Herein, we successfully used commercially available purified proteins (?-galactosidase BSA) as internal standards MALDI-MS analysis achieved...

BACKGROUND Regulated protein-protein interactions (PPIs) are pivotal molecular switches that are important for the regulation of signaling processes within eukaryotic cells. Cellular signaling is altered in various disease conditions and offers interesting options for pharmacological interventions. Constitutive PPIs are usually mediated by large interaction domains. In contrast, stimulus-regula...

Whole genome duplication (WGD) has made a significant contribution to many eukaryotic genomes including yeast, plants, and vertebrates. Following WGD, some ohnologs (WGD paralogs) remain in the genome arranged in blocks of conserved gene order and content (paralogons). However, the most common outcome is loss of one of the ohnolog pair. It is unclear what factors, if any, govern gene loss from ...

Protein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist da...

Protein-protein interactions (PPIs) are essential to all biological processes and they represent increasingly important therapeutic targets. Here, we present a new method for accurately predicting protein-protein interfaces, understanding their properties, origins and binding to multiple partners. Contrary to machine learning approaches, our method combines in a rational and very straightforwar...

BACKGROUND One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein-protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been propose...

Characterization of protein–protein interactions (PPIs) is essential for understanding cellular signal transduction pathways. However, quantitative measurement the binding strength remains challenging. Building upon classical bacterial adenylate cyclase two-hybrid (BACTH) system, we previously demonstrated that relative reporter protein expression (RRPE), defined as level normalized to interact...

While the genomic revolution has dramatically accelerated the discovery of disease-associated genes, the functional characterization of the corresponding proteins lags behind. Most proteins fulfill their tasks in complexes with other proteins, and analysis of protein-protein interactions (PPIs) can therefore provide insights into protein function. Several methods can be used to generate large-s...