Analysis of ligand binding to macromolecules using kinetic and polynomial approaches

Abstract

One of the most interesting property exhibited by most of the proteins is its ligand binding and cooperative interaction ability. The cooperative interactions occur when ligand binding on one site alters the interactions at a distant ligand binding site of same protein. This cooperative and allosteric interactions are an important and interesting phenomenon, and they can be seen throughout biology. The first and probably the most studied cooperative molecule is Haemoglobin which was studied by Bohr, who showed that the binding curve of Hb-O₂ interaction is sigmoidal instead of hyperbolic. The process of cooperative binding and allosteric binding of ligands to the macromolecules or proteins adds complexity to the ligand binding process studies. To understand these functions we have to look beyond the scope of sequence of nucleotides encoding proteins required for a process and look into the network of interactive and interdependent regulatory networks as system which allows certain regulatory expressions to happen. The expression of these networks in the form of computer models that extracts the topology of events occurring in the systems representing it in a systematic way, makes the system easy to explain and predict. There are a number of ways in which a process or network can be modelled for easy explanations and understanding. In the current study we will be analysing ligand binding interactions using two different approaches (1) BP (Binding polynomial) approach; (2) Kinetic modelling approach. The use of BP and kinetic modelling approach will be discussed in this study on two cooperative ligand binding proteins (1) TRAP (tryptophan RNA-binding Attenuation protein) and (2) CaM (Calmodulin). The BP approach has been used to analyse the cooperativity in the ligand binding sites in TRAP protein in B. Subtilis but it is new to be used on cooperative binding in CaM highlighting the possible use of this technique on the interaction analysis of cooperativity in Ca²⁺ – CaM system. The kinetic modelling approaches are more popular, and therefore have already been used on both TRAP and CaM analysis. In the current study we will explain and analyse these approaches in order to give an easier and detailed picture of the interaction to the readers, along with extracting useful insights from the models revealing better interaction properties and biological significances of different parameters and concentration values on the ligand binding process. The current study will not only help readers in getting detailed insight about the cooperative step-by-step binding on TRAP and CaM, but also help in getting an application based comparison of the two modelling approaches for analysing cooperativity.