The binding mechanism of an experimentally identified platinum-binding peptide by molecular dynamics simulation

Abstract

The technological potential of proteins that recognize specific fluid/solid interfaces is immense [1] – just a few examples of relevance here are the use of designed peptides for the fractionation of carbon nanotubes and the assembly of nanoscale building blocks to form complex nanostructured materials and electronic circuits. Despite this potential, elucidation of the structure and behaviour of proteins at such interfaces and the design of associated systems is still dominated by experiment and trial-and-error. We at Adelaide are developing computational tools that will complement this experimental effort. In this contribution, we will report results for very long (20 ns) molecular dynamics simulations of two experimentally identified platinum-binding peptides at various solvated face-centred cubic platinum surfaces with a view to identifying the binding mechanisms involved. In each case, the key residues responsible for the binding will be identified along with the balance between the various driving forces (hydrophobic, torsional, entropy, etc). Comparison with experimental results will be undertaken to validate the MD simulations. Analysis of the bound conformation and the mobility of the bound peptides in the plane parallel to the surface will also be undertaken to determine whether the ‘polypod’ molecular architecture predicted by previous molecular mechanics simulations [2] restricts the diffusion across the platinum surface in some circumstances.