Molecular Recognition Mechanism of Calmodulin Examined by Perturbation-Response Scanning

Abstract

Calmodulin (CaM) has a pivotal role as an intracellular Ca2+ receptor that is involved in calcium signaling pathways in eukaryotic cells [1,2]. Binding of Ca2+ and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner [1,3,4]. To design drugs that inhibit Ca2+-CaM formation, the molecular binding mechanism must be thoroughly understood.In this study, we use a new tool called perturbation-response scanning that is based on systematically exerting directed forces on the residues of the protein [5] and recording the changes in fluctuation profiles as the response. Different conformations of CaM are investigated to locate domains or key residues controlling ligand binding and release. We perform 200 ns long MD simulations on the apo form of CaM. The simulation is divided into chunks which resemble different conformations of the apo form. Using the cross-correlation matrices obtained from these chunks as the kernel in linear response, we determine the residues whose perturbation yields the experimentally determined displacement profiles of the apo and holo forms. We find that it is possible to induce the different conformational changes relevant to the binding of five different ligands, by perturbing varying ligand binding residues, and/or residues on the distant helices in the single apo-form. The findings thus give information on how the flexible linker region acts as a transducer of binding information to distant parts of the protein. This new tool enables us to reveal the essence of ligand recognition mechanisms by which CaM controls a wide variety of Ca2+ signaling processes.1. Ikura M. et.al., PNAS 103:1159-1164.2. Fallon J.L., et.al Structure 11:1303-1307.3. Vandonselaar M.,et.al., Struct.Biol. 1:795-801.4. Shepherd C.M., Vogel H.J., Biophys.J. 87:780-791.5. Atilgan C., Atilgan A.R., PloS Comput.Biol. 5:e1000544.