In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (ΔGads) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host-guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. ΔGads was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent ΔGads within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior.

14-mer α-helix and a 15-mer β-strand oligopeptides composed of leucine (L) and lysine (K) were used to investigate peptide adsorption and orientation onto well-defined methyl and carboxylic acid terminated self-assembled monolayer (SAM) surfaces with X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). XPS showed both peptides reached monolayer thickness on both SAMs, but significantly higher solution concentrations were required to reach this coverage on the methyl SAMs. This shows that the peptides adsorb more strongly onto the carboxyl-terminated SAMs. The excess oxygen detected by XPS and the H3O+ signal detected by ToF-SIMS for the SAMs with adsorbed peptides indicated that water molecules are associated with the adsorbed peptides, even under ultra-high vacuum conditions. Changes in the amount of L and K fragments detected by ToF-SIMS indicate the β-strand oriented differently on the two SAMs. The L side-chains were preferentially associated with the methyl-terminated SAM and the K side-chains were preferentially associated with the carboxyl SAM. In contrast, little change in the ToF-SIMS K/L ratio was observed for the α-helix peptide absorbed on the two SAMs, indicating ToF-SIMS was not as sensitive to orientation of the α-helix peptide.

All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with solid material surfaces. As a result, their applicability for representing the adsorption behavior of proteins with functionalized material surfaces should not be assumed. To address this issue, we conducted replica-exchange molecular dynamics simulations of the adsorption behavior of structured peptides to functionalized surfaces using three protein force fields that are widely used for the simulation of peptide adsorption behavior: CHARMM22, AMBER94, and OPLS-AA. Simulation results for peptide structure both in solution and when adsorbed to the surfaces were compared to experimental results for similar peptide-surface systems to provide a means of evaluating and comparing the performance of these three force fields for this type of application. Substantial differences in both solution and adsorbed peptide conformations were found amongst these three force fields, with the CHARMM22 force field found to most closely match experimental results.

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Fixed-charge empirical force fields have been developed and widely used over the past three decades for all-atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. While this is generally suitable for single-phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. While nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual-force-field approach (Dual-FF) to address this problem and implemented it in the CHARMM simulation package. This Dual-FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intra-phase interactions and a separate set to represent inter-phase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intra-phase and inter-phase molecular behavior to be accurately and efficiently modeled in the same simulation.