Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

• Published in: Biointerphases 2012-12, Vol.7 (1-4), p.24-24
• Main Authors: Collier, Galen, Vellore, Nadeem A., Yancey, Jeremy A., Stuart, Steven J., Latour, Robert A.
• Format: Article
• Language: English
• Subjects: Adsorption; Biological and Medical Physics; Biomaterials; Biomedical Engineering and Bioengineering; Biophysics; Chemistry and Materials Science; Materials Science; Molecular Dynamics Simulation; Physical Chemistry; Protein Binding; Proteins - chemistry; Surface and Interface Science; Surface Properties; Thin Films
• ISSN: 1934-8630; 1559-4106
• DOI: 10.1007/s13758-012-0024-z

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.