A single-molecule stochastic theory of protein-ligand binding in the presence of multiple unfolding/folding and ligand binding pathways

Abstract

Protein folding is a biophysical process by which a protein chain is translated to its native (folded) structure through several intermediate states such that the folded conformation becomes biologically functional. This folded protein can again exist in multiple conformations in its native state and its intrinsic conformational fluctuations are responsible for the protein-ligand recognition and binding to form a specific complex. In this study, we introduce an exactly solvable kinetic model based on a discrete stochastic approach to study the protein-ligand binding by taking into account an arbitrary number of the transient intermediates between the unfolded and the native folded state of the protein. We also examine the conformational fluctuations in the folded state explicitly. The dynamic properties of the system are explicitly evaluated to understand the role of short-lived conformations in the process of protein folding and also conformational fluctuations existing in the folded state of the protein.