Tomasio, Susana de Miranda (2010) Modelling of the interaction between peptides and graphitic surfaces. PhD thesis, University of Warwick.

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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.

Item Type:	Thesis or Dissertation (PhD)
Subjects:	Q Science > QD Chemistry
Library of Congress Subject Headings (LCSH):	Peptides, Graphite -- Surfaces, Tryptophan, Nanotubes
Official Date:	July 2010
Dates:	Date Event July 2010 Submitted
Institution:	University of Warwick
Theses Department:	Department of Chemistry
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Walsh, Tiffany
Sponsors:	University of Warwick
Extent:	xxx, 233 p. : ill., charts
Language:	eng
URI:	http://wrap.warwick.ac.uk/id/eprint/34619

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