Computer simulation of polypeptide adsorption on model biomaterials

Abstract

When biomaterials are inserted in a biological environment, for instance in a body implant, proteins do quickly adsorb on the exposed surface. Such process is of fundamental importance, since it directs the subsequent cell adhesion. Here we review recent advances in this field obtained with molecular simulations. While coarse-grained models can provide important general results, as it has long been recognized in polymer science, the hierarchical structure of a very complex copolymer such as a protein, together with the nature of the biomaterial surface suggest that atomistic models are better suited to investigate these phenomena. Thus, after briefly mentioning some common features of coarse-grained and atomistic force fields, we first discuss early theoretical and coarse-grained simulation results about protein adsorption, and then we highlight the main results recently obtained by us with atomistic models. In particular, we discuss some conformational and energetic aspects of the adsorption of protein fragments with different secondary structure on surfaces of different wettability, including hydrophobic graphite and hydrophilic poly(vinylalcohol). We also consider other features, such as the simulation of the materials wettability, the hydration of the adsorbed fragments, their kinetics of spreading, and the sequential adsorption of two protein fragments on top of each other, highlighting the results of general interest.

Molecular modelling of protein adsorption on the surface of titanium dioxide polymorphs

“…The simulation strategies can be somewhat different, and here we report our simulation protocol [4][5][6]8,10], followed also here. However, other groups have independently chosen a somewhat similar strategy [12], or have explicitly adopted our procedure [16].…”

“…From a theoretical viewpoint, the surface peculiarities and the hierarchical structure of proteins cannot be handled analytically or through coarse-grained simulations, except for very broad and general features, but require a fully atomistic description [1,4]. Moreover, owing to the large system size typically involving tens of thousands of atoms, quantum methods cannot be used.…”

“…For instance, in our group, we considered the adsorption of unlike protein subdomains and of lysozyme on hydrophobic graphite and on the amorphous surface of a hydrophilic polymer, together with sequential adsorption on graphite [4][5][6][7][8][9][10]. With similar methods, other groups considered different ceramic surfaces, such as titanium dioxide (TiO 2 ) (rutile) [11], MgO [12], SiO 2 (assumed to mimic atomically flat mica) [13,14], hydroxyapatite, the mineral component of bones [15], or a silicate surface of chrysotile [16], but self-assembled monolayers were also modelled [17].…”

A review of protein adsorption on bioceramics

“…The conformational change of HSA in the process of adsorption on a carbon nanotube surface also is simulated by the MD method based on the Charmm force field [157]. The interactive behaviours between different subdomains of HSA and graphite surfaces with or without water [158,159], and adsorption behaviour of certain oligopeptides on quartz surfaces have been evaluated by MD based on the CVFF force field [160].…”

Adsorption of human serum albumin on the chrysotile surface: a molecular dynamics and spectroscopic investigation

“…The interaction of biological macromolecules, in particular proteins, with a foreign surface is a closely related field that play an important role in a wide range of biological processes (such as cell aggregation and interaction of ligands with membrane receptors) and is not easily amenable to theory owing to the structural details at the atomistic level and the denaturation process these molecules can undergo upon adsorption. In recent years, computer simulations have added significant new insights, complementing both theory and experiments (Noinville et al 1995;Euston 2004;Ganazzoli & Raffaini 2005). The atomistic computer simulations are the only techniques that can deal with this task, providing a realistic description of the adsorption process, although the size and the complexity of the problem are often discouraging.…”