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Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations

Janani Sampath1*, Jim Pfaendtner2*

1 Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

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

* Corresponding authors emails: janani26@uw.edu, jpfaendt@uw.edu
DOI10.24435/materialscloud:2020.0048/v1 [version v1]

Publication date: Apr 30, 2020

How to cite this record

Janani Sampath, Jim Pfaendtner, Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations, Materials Cloud Archive 2020.0048/v1 (2020), doi: 10.24435/materialscloud:2020.0048/v1.

Description

Titania (TiO2) is used extensively in biomedical applications; efforts to boost the biocompatibility of TiO2 include coating it with the titania binding hexamer, RKLPDA. To understand the binding mechanism of this peptide, we employ molecular dynamics simulations enhanced by metadynamics to study three amino acids present in the peptide – arginine (R), lysine (K), and aspartate (D), on four TiO2 variants that have different degrees of surface hydroxyl groups. We find that binding is a function of both sidechain charge and structure, with R binding to all four surfaces, whereas the affinity of K and D is dependent on the distribution of hydroxyl groups. Informed by this, we study the binding of the titania binding hexamer and 12mer (RKLPDAPGMHTW) on two of the four surfaces, and we see strong correlations between the binding free energy and the primary binding residues, in agreement with prior experiments and simulations. We propose that the discrepancies observed in prior work stem from distribution of surface hydroxyl groups that may be difficult to precisely control on the TiO2 interface.

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Files

File name Size Description
TBP.zip
MD5md5:87b7407bb9e468f5166042977623e788
255.6 MiB Input files to reproduce all the free energy profiles and convergence plots in the paper
README.txt
MD5md5:08ed795782ee73928f1d44aa40c3cf2c
962 Bytes Text describing contents of the files provided

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

Keywords

Biomaterials Metal Oxide Surface hydroxylation

Version history:

2020.0048/v1 (version v1) [This version] Apr 30, 2020 DOI10.24435/materialscloud:2020.0048/v1