Bioinformatics Protocols

The Bioinformatics-Protocols website contains a protocol, plus links to associated websites, that has been developed to use bioinformatics in the identification of novel protein-protein interactions. Protein-protein interactions play central roles in the physiological functions of proteins and many of the interactions that naturally occur are still unknown. An understanding of such interactions has potential for development of both diagnostic and therapeutic tools. The protocol detailed has been developed by Dr Nat Milton alongside the Neurodelta research group to allow in silico identification of novel protein-protein interactions. The methods presented all use website linked software freely available to academics alongside standard word-processing plus spreadsheet programs. The protocol is based on the idea that proteins coded by the sense and antisense strands of DNA interact. Antisense peptide sequences can also be used as potential ligands in laboratory based protein-protein interactions studies.

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An example of the use of these techniques was a study to identify Alzheimer's amyloid-ß (Aß) binding peptides that could block both neurotoxicity and fibril formation of Aß. The binding peptides were developed based on generating antisense peptides using the messenger RNA (mRNA) sequence for the Aß 1-43 peptide as a template [1],[2] that would specifically bind the Aß 1-43 peptide. The Aß antisense peptide sequences and data from their generation plus characterisation were the subject of published patent applications [2]. Subsequent studies by other groups demonstrated that similar Aß antisense peptides were able to prevent the toxicity of Aß [3], confirming the original observations.