Modelling of the interaction between peptides and graphitic surfaces

Abstract

The aim of this thesis is to understand the interactions of peptides with graphitic surfaces such as carbon nanotubes and graphite, in order to help establish guiding principles for the design of peptide sequences with controllable affinity to graphitic surfaces. Atomistic molecular dynamics (MD) simulations with our extended polarisable AMOEBAPRO force-field, which includes parameters for graphitic surfaces is used throughout. The peptide sequences studied were identified by phage-display experiments for their strong affinity to CNTs, and are rich in tryptophan and histidine residues [94]. The importance of the tryptophan residues on the binding affinity to CNTs is investigated by mutating each tryptophan by either tyrosine and phenylalanine. In addition, the effect of the surface curvature on the binding affinity is also explored. It is found that sequences containing tryptophan residues have more affinity to graphitic surfaces than those containing tyrosine or phenylalanine. Furthermore, it is suggested that these peptide sequences were selected for interfacial shape, since in the case of graphite, a compromise between having all the aromatic residues close to the surface and also allowing the non-aromatic residues to approach the surface is found. Following this study, the interaction of peptide sequences with CNTs is again studied, but this time with the aim to investigate the order of the residues, on the binding affinity to CNTs. The influence of the peptide sequence on the binding affinity to CNTs is studied by scrambling the sequence (HWKHPWGAWDTL). This study suggests that binding affinity is strongly dependent on the order of the content of the peptide sequences and gives some useful insights to the identification of principles that may help in the design of peptide sequences with controllable binding affinity to CNTs. For instance, it is found that strong binding may be due to the presence of isolated pairs of tryptophans, while weaker binding may be due to the presence of two tryptophan residues intercalated by another residue. The interactions of water with graphitic surfaces – CNTs, fullerenes and graphite – are also considered and it is found that the water structuring at the interface is weak and that there are no more than tree layers of structured water on the graphitic surfaces. Finally, the effect of the presence of OH defects on CNTs on the binding affinity to peptides is investigated. The results show that the binding affinity is not significantly affected by the presence of OH defects, but a general increase in the peptide mobility is noticed, giving insights for the applications of real CNTs with peptides. The work described in this thesis helps to understand what are the key residues involved in the interaction with CNTs, why do these key residues bind better to CNTs and provide insights on the mechanisms of peptided binding to CNTs, by demonstrating the role of peptide conformation