A coarse-grained molecular simulation for biomacromolecule adsorption: conformation and dynamics

Sabater i Serra Roser, Torregrosa Cabanilles Constantino, Meseguer Dueñas José María, Gómez Ribelles José Luís, Molina Mateo José

2015

A coarse-grained molecular simulation for biomacromolecule adsorption: conformation and dynamics

Many biological macromolecules present a linear chain of monomers as primary structure. From this viewpoint, they do not differ from most synthetic polymers. However, in proteins the secondary and tertiary structures often play an essential role in their biological behaviour. Knowledge about protein adsorption to surfaces is crucial for many disciplines, especially for tissue engineering. Protein adsorption is a very complex process, which is driven by different protein-surface forces, including van der Waals, hydrophobic and electrostatic forces. Adsorption of the chain to the surface occurs if the interaction potential between chain and surface is strong enough. In this work, we have developed a model for the study of conformation and dynamics of a long macromolecule on an adsorbing surface at a mesoscopic level of detail. Monte Carlo simulations were used to study structural properties with the aim to provide a deeper understanding of the adsorption process. This model can be applied to biological macromolecules with elongated structure such as collagen, a fibrous protein present in the extracellular matrix, which has successfully been used to modify biomaterial surfaces in order to enhance their bioactivity. We focus on the simulation of a single biomacrolecule adsorption, considering the chain as the primary structure of a protein. A coarse-grained model (Bond fluctuation model) was used as a high-throughput approach. Coarse-grained simulations can address the time-scale issue via simplification of the representation of the constituent molecules of biomolecular systems. We have used three interaction potentials: intermolecular (Lennard–Jones potential), intramolecular (bond length and bond angle potential) and surface-macromolecule interactions, compiled in a simple Lennard-Jones potential. The influence of the surface-biomolecule interaction in the conformation of the chain was investigated. The presence of an adsorbing surface in the proximity of the macromolecule produces different structures depending on wall–chain interaction values and the thermal history applied.