Efficient conformational sampling at peptide-mineral interfaces: Insights from a quartz-binding peptide. — ASN Events
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  2. Session Five - Poster Session A
  3. Efficient conformational sampling at peptide-mineral interfaces: Insights from a quartz-binding peptide.

Efficient conformational sampling at peptide-mineral interfaces: Insights from a quartz-binding peptide. (#143)

Louise B. Wright 1 , Tiffany R. Walsh 2
  1. Dept. of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, West Midlands, U.K.
  2. Institute for Frontier Materials, Deakin University, Waurn Ponds, Vic, Australia

Harnessing the properties of biomolecules, such as peptides, adsorbed on inorganic surfaces is of interest to many cross-disciplinary areas of science, ranging from biomineralisation to nanomedicine. Key to advancing research in this area is determination of the conformation(s) of a peptide in its adsorbed state, at the aqueous interface. Despite recent breakthroughs1 , this can be challenging for experimental approaches. Molecular simulation can play a complementary role in accomplishing this goal, but also faces difficulties, chiefly due to the extensive conformational lability typical of mineral-binding peptides. To address this challenge, temperature-based replica exchange molecular dynamics (T-REMD) can yield enhanced sampling of interfacial conformations, but does so at great computational expense. Here, we investigate a number of more economical variations of REMD, based on Replica Exchange with Solvent Tempering (REST)23 4 using the aqueous quartz-binding peptide S1-(100) a-quartz interfacial system as a benchmark. We also test a number of additional implementation details specifically targeted at improving sampling of biomolecules at mineral interfaces. We find the REST-based variants yield configurational sampling of the peptide–surface system comparable with T-REMD, at a fraction of the computational time and resource. Our findings also deliver novel insights into the binding behaviour of the S1 peptide at the quartz (100) surface that are consistent with available experimental data.

  1. P. A. Mirau, R. R Naik and P. Gehring, J. Amer. Chem. Soc., (2011), 133, p18243
  2. Moors, S.L.C. et al., J. Chem. Theory Comput., (2011), 7, p231
  3. Terakawa, T. et al., J. Comput. Chem., (2011), 32, p1228
  4. Wang, L. et al, J. Phys. Chem. B, (2011), 115, p9431