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

JSON Export

{
  "revision": 1, 
  "id": "185", 
  "created": "2020-05-12T13:53:05.795471+00:00", 
  "metadata": {
    "doi": "10.24435/materialscloud:2019.0043/v1", 
    "status": "published", 
    "title": "Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations", 
    "mcid": "2019.0043/v1", 
    "license_addendum": "", 
    "_files": [
      {
        "description": "plumed*.dat files correspond to the input used for Parallel-Tempering Metadynamics in the Well-Tempered Ensemble simulations\r\nHILLS* files correspond to the Gaussian hills deposited during the simulation, used to construct free energy profiles", 
        "key": "LKA14.zip", 
        "size": 10106965, 
        "checksum": "md5:cae5dfb0779813d40b25d5d0f5890525"
      }
    ], 
    "owner": 46, 
    "_oai": {
      "id": "oai:materialscloud.org:185"
    }, 
    "keywords": [
      "Enhanced Sampling", 
      "Molecular Dynamics Simulations", 
      "Peptide Surface Interactions"
    ], 
    "conceptrecid": "184", 
    "is_last": true, 
    "references": [
      {
        "type": "Journal reference", 
        "doi": "10.1080/00268976.2019.1657192", 
        "url": "", 
        "comment": "", 
        "citation": "J.Sampath,J.Pfaendtner, Mol.Phys., 2019"
      }
    ], 
    "publication_date": "Aug 26, 2019, 00:00:00", 
    "license": "Creative Commons Attribution 4.0 International", 
    "id": "185", 
    "description": "The leucine-lysine amphiphilic peptide LK\u03b114 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 LK\u03b114 on silica. We also investigate the effect that the nature of the silica surface \u2013 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.", 
    "version": 1, 
    "contributors": [
      {
        "affiliations": [
          "Department of Chemical Engineering, University of Washington, Seattle, WA, USA"
        ], 
        "familyname": "Sampath", 
        "givennames": "Janani"
      }, 
      {
        "email": "jpfaendt@uw.edu", 
        "affiliations": [
          "Department of Chemical Engineering, University of Washington, Seattle, WA, USA"
        ], 
        "familyname": "Pfaendtner", 
        "givennames": "Jim"
      }
    ], 
    "edited_by": 98
  }, 
  "updated": "2019-08-26T00:00:00+00:00"
}