Interaction energy between neuronal cell receptors and peptoid ligands

• Published in: Journal of biomechanics 2021-05, Vol.121, p.110381-110381, Article 110381
• Main Authors: Yasodharababu, Mohan, Servoss, Shannon L., Nair, Arun K.
• Format: Article
• Language: English
• Subjects: Affinity; Binding; Binding sites; Biocompatibility; Biopolymers; Cell adhesion; Cell adhesion molecules; Cell culture; Energy; Extracellular matrix; Free energy; Hydrophobicity; Integrin; Ligands; Mechanotransduction; Molecular dynamics; Neural cell adhesion molecule; Neural cellular adhesion molecule; Neurodegeneration; Nitrogen; Open source software; Peptoid; Proteins; Receptors; Residues; Self-assembly; Structural stability; Umbrella sampling
• ISSN: 0021-9290; 1873-2380
• DOI: 10.1016/j.jbiomech.2021.110381

Peptoids as an extracellular matrix (ECM) material is gaining importance in in vitro neuronal cell culture studies due to their biocompatibility, self-assembling structure, and stability. Mechanotransduction between a neuronal cell and an ECM is mediated by neuronal cell receptors such as integrin and neural cellular adhesion molecule. In this study, using molecular dynamics, we investigate the interaction energies between peptoid and neuronal cell receptors, and also study the effect of peptoid bundle size. We investigate the interaction surface between peptoid bundles and neuronal cell receptors, integrin and neural cellular adhesion molecule, using the solvent accessible surface area method to find the influence of hydrophobic and hydrophilic residues of the peptoid chain. We find the free energy landscape using the umbrella sampling method and then evaluate the potential mean force (PMF) and unbinding force during the dissociation between peptoid bundles and neuronal cell receptors. We find that the peptoid bundles have a higher affinity for the neuronal cell receptors, however increasing the size of peptoid bundles increases the affinity for integrin and neural cell adhesion molecule. PMF data for peptoid and neuronal cell receptor dissociation indicates that binding force increases as the size of the peptoid bundle increases. The higher binding strength during peptoid and neuronal cell receptors are due to the hydrophobic residue cluster area in the binding region. These findings will provide a better insight into using peptoid as an ECM.