Abstract
Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.
Highlights
The adsorption behavior of proteins on material surfaces serves an important role for numerous applications in the fields of biomaterials and biotechnology, including the design of implants for improved biocompatibility [1,2,3,4], drug delivery systems [5, 6], biosensors [7, 8], and surfaces used for bioseparations [9]
Adsorption free energies for a set of eight host–guest peptides over quartz (100) and amorphous silica surfaces were calculated from umbrella sampling and biasedREMD simulations using the CHARMM22/CMAP protein force field and CHARMM parameters previously published for both quartz and silica glass surfaces
Adsorption free energies were found to be overestimated for peptide adsorption to both of these surfaces by 5–9 kcal/mol relative to experimental values determined by atomic force microscopy (AFM)
Summary
The adsorption behavior of proteins on material surfaces serves an important role for numerous applications in the fields of biomaterials and biotechnology, including the design of implants for improved biocompatibility [1,2,3,4], drug delivery systems [5, 6], biosensors [7, 8], and surfaces used for bioseparations [9]. Because proteins mediate the adhesion of other biological entities to surfaces [12], including bacteria, viruses, and fungi, a molecular-level understanding of protein-surface interactions is important for the design of decontamination strategies for these types of biological agents as well. Over the past three decades, molecular dynamics (MD) simulations using empirical force field-based methods have been developed as a valuable tool for the prediction of the conformational behavior of proteins in aqueous solution. These methods have similar potential for use in predicting the orientation, conformation, and bioactivity of proteins when adsorbed on material surfaces. Before this potential can be realized, it is essential that these computational methods be first developed, evaluated, and Biointerphases (2012) 7:56 validated against experimental data in order to confirm that they are able to realistically represent protein–surface interactions
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