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A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF

Publication Type : Journal Article

Thematic Areas : Center for Computational Engineering and Networking (CEN)

Source : Langmuir, 2019

Url :

Campus : Coimbatore

School : Computational Engineering and Networking

Center : Center for Computational Engineering and Networking, Computational Engineering and Networking

Department : Center for Computational Engineering and Networking (CEN)

Verified : No

Year : 2021

Abstract : Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. To answer this question, we computed the adsorption free energies of peptides (representing eleven different amino acids) on a hydrophobic self-assembled monolayer (CH3-SAM) and compared them to the benchmark experimental data set. Our result revealed that existing biomolecular force fields, GAFF and AMBER ff14sb, cannot reproduce the experimental peptide adsorption free energies by Wei and Latour (Langmuir, 2009, 25, 5637-5646). To obtain the improved force fields, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the initial adsorption orientation of lysozyme on CH3-SAM. Two major orientations-face-down and face-up-were predicted. Our analysis on the protein structure, solvent accessible surface area, and binding of native ligand NAG3 suggested that lysozyme in the face-up orientation can remain active after initial adsorption. However, because of its weaker affinity (ΔΔG = 7.86 kcal/mol) for the ligand, the bioactivity of the protein is expected to reduce. Our work facilitates the use of MD for the study of protein-SAM systems. The refined force field compatible with GROMACS is available at

Cite this Research Publication : Pratiti Bhadra, Shirley W I Siu "Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF", Langmuir, 2019

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