Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study

Abstract

Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.

Keywords: biomolecular simulation; diagnostics; staphylococcus protein A; therapeutics.

Figure 1

The SpA structure (PDB: 5H7A) illustrated using VMD 1.9.1 [9]. The protein is indicated as a ghost surface, and the secondary structural α-helices are coloured as follows. Helix 1: red ribbons (close to the N-terminus), helix 2: orange, helix 3: grey, helix 4: yellow, helix 5: light blue, helix 6: green, helix 7: dark blue, helix 8: brown, helix 9: black (close to the C-terminus). The purple needle indicates the dipole moment. The key Glu and Asp residues that interact with the Fc fragment of antibodies are indicated in the ‘liquorice’ representation [9].

Figure 2

RMSD of SpA in (a) water, (b) siloxide surface, (c) under-coordinated surface, (d) Au (111) surface simulations. The RMSD for the individual α-helices follows the colour scheme in Figure 1. The purple line represents the RMSD for the full protein, including the flexing between the α-helices.

Figure 2

RMSD of SpA in (a) water, (b) siloxide surface, (c) under-coordinated surface, (d) Au (111) surface simulations. The RMSD for the individual α-helices follows the colour scheme in Figure 1. The purple line represents the RMSD for the full protein, including the flexing between the α-helices.

Figure 3

Adsorption of SpA on the oxygen-rich surface. The protein colour scheme follows that in Figure 1. The outer layer of oxygen atoms in the silica model surface is shown as red spheres. Cl⁻ ions are shown as lime VdW spheres and Na⁺ as magenta. The adsorbing residues are also shown as VdW representation. The purple needle indicates the dipole moment, and water molecules are not shown for clarity.

Figure 4

Adsorption of SpA on the positively charged surface. The colour scheme is the same as in Figure 3. The purple needle indicates the dipole moment, and water molecules are not shown for clarity.

Figure 5

Adsorption of SpA on the hydrophobic gold surface. The colour scheme is the same as in Figure 3. The gold atoms are shown as pink VdW spheres (defined in VMD 1.9.4). The purple needle indicates the dipole moment, and water molecules are not shown for clarity.

Figure 6

The angles between the α-helix pairs (a) water, (b) siloxide, (c) Si under-coordinated, (d) Au (111).

Figure 6

The angles between the α-helix pairs (a) water, (b) siloxide, (c) Si under-coordinated, (d) Au (111).