Disease Motifs
Investigating the Biomechanics of Disease
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If you are interested in sponsoring some further research here are some more details.

The main aim will be to explore the nature of a disease by doing proteomic analysis of the proteins that are associates with that disease. There is no guarantee that anything will be found that will cure the disease definitively but hopefully a better understanding of the disease process will be made. This work is solely concerned with the theoretical and computational work.

The minimum time that is required to make any headway is one year but realistically to find some significant results may take longer, possibly five to ten years, but a five-year period might form some absolute limit if you would perfer that to be the case. Ideally, funding for a five year period would allow me the time to complete a reasonable amount of work on any one project without having to worry about looking for other funding. Hopefully some scientific ‘papers’ will get published in some renowned scientific journals but if these were not accepted by mainstream science journals, the work will be made available on here or elsewhere (see below).

One year would need to be supported by £35,000 and this will have to be paid in advance. For private individuals wanting to sponsor some research, but wishing to remain anonymous, your privacy WILL be respected. If you are interested in sponsorship please email me so that we can have a discussion about the details involved.

For further details or to just make some general (non-sponsorship related) enquiries about the work please feel free to email me

Journal of Alzheimers Disease & Parkinsonism

Preliminary set theory-type analysis of proteins associated with Parkinson's disease
- published paper 2014


In an attempt to create a model of Parkinson's disease (PD) eighty-three proteins were extracted from the Swiss-Prot protein database that had some casual mention of PD. These were split up into various subsets of proteins of which three are focused on here: PARK, made up of proteins that had some indication that polymorphisms in the protein might increase a person's susceptibility to develop PD; MITOCHOND, proteins which had some association with the mitochondria; and MT-C1D, proteins that were implicated in mitochondrial complex 1 deficiency. The PARK subset had 21 out of 83 proteins (21/83); MITOCHOND 33 out of 83 proteins (33/83); and MT-C1D 17 out of 83 proteins (17/83). The results could be used to build up a basic model of PD creating phenotypes based on sets of proteins. The main phenotypes established here are; non-mitochondrial PD (50/83) and mitochondrial PD (33/83). Further division is possible dependant on whether proteins have polymorphisms which increase susceptibility to develop PD. MT-C1D seems to be independent of the PARK set. This is a very simplistic attempt at trying to model Parkinson's disease at the proteomic level and will need further work to build up the more complex and realistic PD proteomic disease model.

Proteomic Analysis of the Amyloid Precursor A4 Protein Proteomic Analysis of the Amyloid Precursor A4 Protein

Not published in scientific journal but this paper is available as an e-paper for £3.99 exVAT. This is just a five page article or paper but will help fund my work.


This work demonstrates the principle of using sequence similarity to link possible causative microbial pathogens to particular parts of proteins that are associated with a particular disease. A small 10 amino acid sequence of amyloid precursor protein, including residues 711 and 713, were matched against the viral Swiss-Prot protein database for sequences of close similarity. This was conducted in the amino-carboxyl direction (NC) but also in the reversed direction (CN) i.e. the sequence was reversed. In the reversed (CN) direction two small three amino-acid (Valine-Isoleucine-Alanine and Valine-Glycine-Glycine) motifs were found in the capsid protein from the Venezuelan equine encephalitis virus (VEEV) and Eastern equine encephalitis virus (EEEV). This possibly suggests that there might be some link between these viral proteins and the amyloid precursor protein which may be more apparent in people who become infected with either of these two viruses e.g. People who die from infection of the virus may have an increased level of beta amyloid 40 or 42.

Theoretical Biological Switch With a Possible Important Role In Parkinson's Disease, Schizophrenia, Hyposmia and the Onco-Parkinson's Mechanism

Self-published on Lulu for £3.99 exVAT


Antagonists for the Histamine Receptor H2 (HRH2_HUMAN) protein may have some efficacy in reducing levodopa-induced dyskinesia in Parkinson's disease. Using short sequence proteomic analysis on the histamine receptor 2 which involves splitting this protein sequence into smaller fragments of ten amino acids and contrasting (using BLAST) against the human protein database.

Three main motifs were found; with the initial two being named the CW-motif and the NxxxNP-motif, with the adjacent amino acid residues being important. The third motif NPxxY overlays the end of the NxxxNP-motif and may form part of a rhodopsin NPxxY(x)5,6F type motif but in this case, it is a variant form NPxxY(x)6,7F present in many of the serotonin and dopamine receptors found here. Using the variants of NPxxY found in the dopamine and serotonin receptors, as a specific amino acid search-term (non-BLAST), it was found that a high proportion of the proteins returned were olfactory proteins.

This small region of similarity amongst dopamine, serotonin and olfactory receptors might be suggestive of a biological switch which might play an important role in Parkinson's disease, schizophrenia and the onco-Parkinson's effect seen in people with Parkinson's disease (who may have raised or lower risk of developing certain types of cancer).

There is more data available on the Project 3 page