Protein blotting was originally introduced as a solid-phase immunoassay (Gershoni & Palade, 1983; Towbin & Gordon, 1984). However, this technique can also be employed for the analysis of ligand-receptor interactions. In principle, a protein sample containing a receptor is resolved by gel electrophoresis and then blotted to an immobilizing matrix, such as a nitrocellulose membrane filter, as wou...

When we consider investigating function of macromole-cules, it is hardly possible to draw an experiment map without taking interactions of other molecules (ligands) into account, whether they could be metal ion, ATP, hormone, carbohydrate, lipid, nucleic acid, DNA, RNA, peptide and protein. In other words, no biological function can be elucidated without molecular interactions. Therefore, the s...

Solution-state NMR has become an accepted method for studying the structure of small proteins in solution. This has resulted in over 3000 NMR-based co-ordinate sets being deposited in the Protein Databank. It is becoming increasingly apparent, however, that NMR is also a very powerful tool for accessing interactions between macromolecules and various ligands. These interactions can be assessed ...

Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine-tuned for different cellular actions. The study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. During the last two decades MS, and its associated techniques, has become accepted as a method for the...

the antidiuretic effect of arginine vasopressin (avp) is mediated by the vasopressin v2 receptor. the docking study of avp as a ligand to v2 receptor helps in identifying important amino acid residues that might be involved in avp binding for predicting the lowest free energy state of the protein complex. whereas previous researchers were not able to detect the exact site of the ligand-receptor...

BACKGROUND Shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset ...

We describe a graphical system for automatically generating multiple 2D diagrams of ligand-protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond interaction patterns and hydrophobic contacts between the ligand(s) and the main-chain or side-chain elements of the protein. The system is able to plot, in the same orientation, related sets of ligand-protein interactions. T...

Identification of small molecule ligands that bind to proteins is a critical step in drug discovery. Computational methods have been developed to accelerate the prediction of protein-ligand binding, but often depend on 3D protein structures. As only a limited number of protein 3D structures have been resolved, the ability to predict protein-ligand interactions without relying on a 3D representa...

Interactions between a protein and a ligand are essential to all biological processes. Binding and dissociation are the two fundamental steps of ligand-protein interactions, and determine the binding affinity. Intrinsic conformational dynamics of proteins have been suggested to play crucial roles in ligand binding and dissociation. Here, we demonstrate how protein dynamics dictate the binding a...