Question

explain the distinction between binding site and binding region

Answer 1

A binding site is a region on a protein or piece of DNA or RNA to which ligands (specific molecules and/or ions) may form a chemical bond. An equilibrium exists between unbound ligands and bound ligands. Binding sites also exhibit chemical specificity, a measure of the types of ligands that will bond, and affinity, which is a measure of the strength of the chemical bond. Binding sites are often an important component of the functional characterization of biomolecules. For example, the characterization of the binding site of a substrate to anenzyme is essential to model the reaction mechanism responsible for the chemical change from substrate to product.

Many disordered proteins function via binding to a structured partner and undergo a disorder-to-order transition. The coupled folding and binding can confer several functional advantages such as the precise control of binding specificity without increased affinity. Additionally, the inherent flexibility allows the binding site to adopt various conformations and to bind to multiple partners. These features explain the prevalence of such binding elements in signaling and regulatory processes. In this work, we report ANCHOR, a method for the prediction of disordered binding regions. ANCHOR relies on the pairwise energy estimation approach that is the basis of IUPred, a previous general disorder prediction method. In order to predict disordered binding regions, we seek to identify segments that are in disordered regions, cannot form enough favorable intrachain interactions to fold on their own, and are likely to gain stabilizing energy by interacting with a globular protein partner.