Fibronectin Module FN^III9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics

Abstract

ABSTRACT:The mechanism of FN III 9 fibronectin domain adsorption at pH7 onto various and contrasting surface models has been studied using atomistic molecular dynamics (MD) simulations. We use an ionic model to mimic mica surface charge density, but without a long-range electric field above the surface; a silica model with a long-range electric field similar to that found experimentally; and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Since it is negatively charged (-1e), FN III 9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN III 9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these surfaces does not require wholesale FN III 9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved.3

Lysozyme adsorption at a silica surface using simulation and experiment: effects of pH on protein layer structure

“…Our MD simulations have indicated that hydrophobicity does have a role to play in adsorption, albeit a minor one at the lower pH7. We note that since electrostatics does not drive the adsorption at pH 4 10, the adsorbed protein may no longer be oriented according to its dipole moment, 35 and the dipole moment in any case will be different to that below the isoelectric point.…”

“…For the system SiO 2 V1 some additional simulations with ionic strength I =5Â 10 À2 M and I =7Â 10 À1 M were performed to further test the model. The silica surface model was constructed similarly to our recent work 35 using a (10% 1) slab of a-cristabolite (see ESI † for the details). The SiO 2 slab model (Fig.…”

“…This in turn creates an electric field above the surfaces, mimicking the environment above the charged surfaces observed experimentally. 35 Silica zeta potentials (shown below) reveal the surface charge density which produces an electric field above the surface, which strongly influences how the proteins will interact with the surface. In the case of pSiO 2 (Fig.…”

Locating the nucleation sites for protein encapsulated gold nanoclusters: a molecular dynamics and fluorescence study

“…24 To emulate the conditions found in the one pot method used to synthesize BSA-Au 11 the protein was solvated in a rectangular box of water of size 116 Å Â 89 Å Â 101 Å, and neutralized by adding NaCl at an ionic strength 0.05 M, yielding over 93 000 atoms in the system. 27), we believe these parameters provide a useful and simple model with which we can explore the growth of gold clusters within accessible protein surface regions. The protein was initially equilibrated for 300 ps at constant temperature of 300 K. Production simulations started by adding 25 gold atoms to the system with the protein.…”

Experimental and computational examination of anastellin (FnIII1c)–polymer interactions

“…Due to its relevance to biomaterials, 1 the adsorption of a number of Fn modules onto surfaces have been investigated. [31][32][33] These have shown that Fn adsorption is relatively nonspecific, with it readily adsorbing onto organic, 32 inorganic, 33 and graphite surfaces. 31 In comparison with experimental methods, molecular simulation can give significant insight into the early stages of protein adsorption and on the detailed microscopic information on the protein-surface interactions.…”