We consider a model of early events in signaling by the epidermal growth factor (EGF) receptor (EGFR). The model includes EGF, EGFR, the adapter proteins Grb2 and Shc, and the guanine nucleotide exchange factor Sos, which is activated through EGF-induced formation of EGFR-Grb2-Sos and EGFR-Shc-Grb2-Sos assemblies at the plasma membrane. The protein interactions involved in signaling can potenti...

one of the most important targets in alzheimer disease is beta site amyloid precursor protein cleaving enzyme-1 (bace-1). it is a membrane associated protein and is one of the main enzymes responsible for amyloid β (aβ) production. up to now, a considerable number of peptidic and non-peptidic inhibitors of bace-1 have been developed. recently, small molecule bace-1 inhibitors have attracted the...

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in t...

RNA-protein interactions play important roles within the cell. Using a variation of the widely-used chromatin immunoprecipitation (ChIP) assay, the potential association of cellular RNAs and candidate proteins can be evaluated in a process named “RNA-ChIP”. This technique has been successfully used in mammalian cells, for example to examine the relationship of noncoding RNAs with histone protei...

objective: druggability of a target protein depends on the interacting micro-environment between the target protein and drugs. therefore, a precise knowledge of the interacting micro-environment between the target protein and drugs is requisite for drug discovery process. to understand such micro-environment, we performed in silico interaction analysis between a human target protein, dipeptidyl...

Although the majority of noncovalent interactions associated with hydrogen and heavy atoms in proteins and other biomolecules are classical hydrogen bonds between polar N-H or O-H moieties and O atoms or aromatic π electrons, high-resolution X-ray crystallographic models deposited in the Protein Data Bank show evidence for weaker C-H···O hydrogen bonds, including ones involving sp(3)-hybridized...

Chemical denaturant titrations can be used to accurately determine protein stability. However, data acquisition is typically labour intensive, has low throughput and is difficult to automate. These factors, combined with high protein consumption, have limited the adoption of chemical denaturant titrations in commercial settings. Thermal denaturation assays can be automated, sometimes with very ...