Solution study of engineered quartz binding peptides using replica exchange molecular dynamics

Biomacromolecules. 2010 Dec 13;11(12):3266-74. doi: 10.1021/bm100646z. Epub 2010 Oct 22.


We use replica-exchange molecular dynamics (REMD) to interrogate molecular structures and properties of four engineered dodecapeptides (in solution, in the absence of a surface) that have been shown to bind to quartz with different propensities. We find that all of the strong-binding peptides feature some polyproline type II secondary structure, have less conformational freedom, and feature fewer intrapeptide hydrogen bonds compared with the weak binder. The regions of contiguous proline content in a given sequence appear to play a role in fostering some of these properties of the strong binders. For preliminary insights into quartz binding, we perform lattice-matching studies between a grid corresponding with the quartz (100) surface and the strong-binding peptide REMD structures. Our findings indicate a commonality among the putative contact residues, even for peptide structures with very different backbone conformations. Furthermore, interpeptide interactions in solution are studied. Our preliminary findings indicate that the strong-binder interpeptide contacts are dominated by weak, nonspecific hydrophobic interactions, while the weak-binding peptide shows more variable behavior due to the distribution of charged residues. In summary, the solution structures of peptides appear to be significant. We propose that these differences in their intra- and interpeptide interactions can influence their propensity to bind onto a solid substrate.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Molecular Dynamics Simulation
  • Peptides / chemistry*
  • Protein Binding
  • Protein Engineering*
  • Quartz*
  • Solutions


  • Peptides
  • Solutions
  • Quartz