Name: Susana De Tomasio
Institution: University of Warwick
Research: Modelling the effect of the peptide sequence on the binding affinity to carbon nanotubes
The extraordinary physical and mechanical properties of carbon nanotubes (CNTs) means that they have promising applications in the fields of nanotechnology and medicine. However, for biological and biomedical applications, the extreme hydrophobicity and lack of dispersion of CNTs constitutes a big limitation to the accomplishment of these applications. In addition, due to the difficulty of purifying and separating CNTs, it has been hard to assemble them into practical structures.
The ability of biomolecules, such as peptides, to non-covalently bind to CNTs gives rise to new expectations for its selective dispersion and manipulation. Furthermore, peptides are well-known for their high specificity for other biomolecules and materials and for their ability to self-assemble into a wide diversity of complex functional structures.
Despite the large number of experiments in this area, the nature of the peptide-CNT interaction is not yet fully understood. Recent studies on the adsorption of peptides on inorganic surfaces pointed out the importance of the conformational structure of the peptides on the binding affinity. The purpose of this study is, therefore, to better understand how the order of the residues in a peptide affects interactions with a CNT.
This research is important because it may help to understand the relation between structure and binding at peptide-CNT interfaces. The purpose of Susana’s research was to try and better understand how the order of the residues of the peptide sequences may affect interactions with CNTs.
To achieve this, Susana used a tryptophan-rich peptide with strong affinity to CNTs selected by phage-display experiments and mixed the amino acid content of the sequence. Fifteen peptide sequences with the same content as the original sequence but in a different order were created. Interestingly, Susana found two peptide sequences with stronger affinity to the CNT than the original sequence. None of the scrambled sequences reached the lower binding affinity supported by a weak-binder control peptide but some of the sequences supported a decrease in the binding affinity comparable to mutations of the tryptophan content by either tyrosine or phenylalanine. These observations draw some useful insights into the possible mechanisms by which peptides bind to CNTs and represent a first step in the identification of the rules of design for peptide-CNT interfaces. Her findings show that the binding affinity to CNTs is strongly dependent on the order of the content of the peptide sequences.
MD simulations have been performed with the TINKER package locally installed on the NGS Leeds resource. Susana said “The biggest advantage of using NGS is that we can submit several jobs, which is very convenient since I need to simulate several initial configurations for each peptide sequence and I am studying 15 peptide sequences!”. Depending on the equilibration period, each simulation was run for 2-10 ns. In addition, Susana considered 5 to 7 different starting configurations for each sequence, yielding a total of around 100 distinct peptide-CNT simulations. According to Susana, these simulations were computationally expensive since she was using a polarisable force-field and Tinker is not parallel, so 1 ns of simulation could take up to 20 days.
Funding body – University of Warwick
Supervisor – Dr. Tiffany R. Walsh who said “The NGS is a wonderful and much-needed mid-range computing resource for UK-based researchers, especially those interested in modelling and simulation of advanced materials.”
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