title: Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.
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.
authors.affiliation: Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, SC 29634, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Snyder
authors.forename: Tigran
authors.initials: T
authors.lastname: Abramyan
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Yancey
authors.forename: Aby A
authors.initials: AA
authors.lastname: Thyparambil
authors.forename: Yang
authors.initials: Y
authors.lastname: Wei
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Stuart
authors.forename: Robert A
authors.initials: RA
authors.lastname: Latour
mesh_terms: D000327:Adsorption; D003198:Computer Simulation; D005898:Glass / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012822:Silicon Dioxide / Q000737:chemistry* / Q000378:metabolism*; D013500:Surface Tension
chemical_list: D011506:Proteins; D012822:Silicon Dioxide