ABSTRACT
ABSTRACT Various computational methods used for the simulation of protein-surface interaction are reviewed in this work. Among these methods, molecular simulations based on empirical force elds are used extensively in modeling protein-surface adsorption since they are able to provide detailed structural information of a molecular system in reasonable computational time. However, force elds that have been specically developed for modeling the behavior of proteins in aqueous solution or the bulk behavior of solid materials may not accurately represent protein adsorption behavior simply because the force eld parameters were never tuned to represent interfacial interactions. In order to accurately represent these types of interactions, interfacial force eld (IFF) parameters must be specically developed, tested, and validated. For this purpose, the adsorption of host-guest peptides on self-assembled monolayer surfaces has been used as a model system in both experimental and simulation studies. Experimentally, adsorption free energies have been determined from adsorption isotherms, while the biased-energy replicaexchange molecular dynamics method has been used to calculate the adsorption free energy for various combinations of these adsorption systems. By matching the calculated adsorption free energies with the corresponding experimental results, IFF parameters can be developed that accurately represent peptide adsorption afnity to these types of surfaces. Once IFF parameters are determined, simulations can then be condently extended to model protein adsorption behavior. Given the substantial increase in the size and complexity of the molecular systems involved, additional advanced sampling methods and coarse-graining techniques are required to increase the efciency of simulations of proteinsurface interactions, and these methods are also introduced.
