Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations

Authors: Janani Sampath1, Jim Pfaendtner1*

  1. Department of Chemical Engineering, University of Washington, Seattle, WA, USA
  • Corresponding author email:

DOI10.24435/materialscloud:2019.0043/v1 (version v1, submitted on 26 August 2019)

How to cite this entry

Janani Sampath, Jim Pfaendtner, Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations, Materials Cloud Archive (2019), doi: 10.24435/materialscloud:2019.0043/v1.


The leucine-lysine amphiphilic peptide LKα14 has been used to study fundamental driving forces in processes such as peptide-surface binding and biomineralization. Here, we employ molecular dynamics (MD) simulations in tandem with replica exchange metadynamics to probe the binding mechanism and thermodynamics of LKα14 on silica. We also investigate the effect that the nature of the silica surface – crystalline vs. amorphous, has on the binding properties and peptide-surface conformations. We find that water adsorbs differently on both surfaces; it forms a denser interfacial layer on the crystalline surface, compared to the amorphous surface. This causes the peptide to bind more strongly on the amorphous surface than the crystalline surface. Cluster analysis shows that the peptide adopts a helical conformation at both surfaces, with a greater distribution of states on the crystalline surface. Peptide binding is primarily through lysine interactions, in line with prior experimental results.

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File name Size Description
MD5MD5: cae5dfb0779813d40b25d5d0f5890525
9.6 MiB plumed*.dat files correspond to the input used for Parallel-Tempering Metadynamics in the Well-Tempered Ensemble simulations
HILLS* files correspond to the Gaussian hills deposited during the simulation, used to construct free energy profiles


Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.

External references

Journal reference
J.Sampath,J.Pfaendtner, Mol.Phys., 2019 doi:10.1080/00268976.2019.1657192


Enhanced Sampling Molecular Dynamics Simulations Peptide Surface Interactions

Version history

26 August 2019 [This version]