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

Janani Sampath1, Jim Pfaendtner1*

1 Department of Chemical Engineering, University of Washington, Seattle, WA, USA

* Corresponding authors emails: jpfaendt@uw.edu
DOI10.24435/materialscloud:2019.0043/v1 [version v1]

Publication date: Aug 26, 2019

How to cite this record

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


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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:

2019.0043/v1 (version v1) [This version] Aug 26, 2019 DOI10.24435/materialscloud:2019.0043/v1