Applied Bimatics - An Informatics & eHealth Blog

I am a clinician with a passion for informatics. This blog is about my eHealth journey exploring interoperability in Electronic Medical Records (EMR/EHR), Patient Safety, Pharmacovigilance, Data Analytics, Clinical Research and Bioinformatics in a clinical context. Comparing Canadian, Indian and Middle Eastern healthcare systems and services. Join our open facebook group here: https://www.facebook.com/groups/clinical.bioinformaticians/


Best peptides for women


In continuation with my previous posts here and in skin deep, let me add few more things I found recently.

Peptide Synthesis Deprotection
Peptide Synthesis Deprotection (Photo credit: Beige Alert)
The article titled “Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks “ published recently in PLOS Biology ( full text at : http://dx.plos.org/10.1371/journal.pbio.0030405 ) describes the signalling by short peptide segments. Short peptide segments interact with globular protein domains that share a common sequence pattern (e.g., SH3 binding to PxxP). They also point out that sequence comparison experiments are unlikely to discover the optimum short motif. They recommend using data from genome-scale interaction studies. So the methodology adopted by the designers of peptide-21 may not be robust.

OK, now I am going to do something here that I rarely ever do on my blogs: I am going to shamelessly self promote me without actually giving away much information. My plan is to get noticed by the cosmetic tycoons and make some money out of this incessant babbling about beauty peptides :-)

English: Example of mechanism of direct penetr...
English: Example of mechanism of direct penetrating peptide (Photo credit: Wikipedia)
I used a newly published algorithm (not mine) for bioinformatics analysis and found some interesting information.

The most commonly occurring tetra peptide in collagen is in fact GXXG and PXXP the commonest being GPPG.

The commonest tetra peptide repeats were GERG, GEKG, GFPG, GENG, GPRG, GHRG.

This is what terapeptide-21 is based on and there is nothing new till here.

But here comes the most surprising part!

The highest scoring short peptide of probable biological (signal) function does not belong to the above list!!

Hey, Do I hear my phone ringing?????


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Beauty born out of Bioinformatics


The beauty and the anti-ageing industry is focused on finding ways to augment the fibrillar proteins collagen and elastin embedded in an extracellular matrix in the dermal layer of the skin. A pentapeptide KTTKS, within the carboxy terminal propeptide of type I collagen is extensively used as an anti-ageing cosmetic ingredient. The proposed mechanism of action is tricking the body into believing that there is excessive collagen degradation so that collagen biosynthetic pathway is stimulated. I have blogged about the potential limitations in Skin Deep .
B0005968 Collagen fibril forming in vitro
B0005968 Collagen fibril forming in vitro (Photo credit: wellcome images)

Yet another peptide called tetrapeptide - 21 is claimed to be superior to KTTKS in anti-ageing properties. They claim to have discovered this by using bioinformatics methodology.

Let me quote from a product brochure:

We used bioinformatic methods to identify highly repetitive amino acid motifs in several human ECM proteins to identify sequences with inherent anti-aging activities.  Using the amino acid sequences of collagen I, II, III, IV, V, elastin, and proelastin, tetra-peptide sequences were identified by their frequency of occurrence. 

Beauty box1886
Beauty box1886 (Photo credit: Wikipedia)
The methodology has never been published. Their patent application states that they found GXXG and PXXP as the common motif among all collagens and elastin. They tried various combinations and found GEKG as the most biologically active one. At the sequence level all collagens are quite similar. It is also well known that the most common motifs in all types of collagen is GPX. So finding GXXG as the commonest tetrapeptide motif is hardly surprising.

So dear biochemicians:

1. Where does the MMPs cleave collagen?
2. How many amino acid residues are there in collagen degradation fragments?
3. Do you think GXXG can mimick collagen fragment?

and dear bioinformaticians:
1. If we consider Collagen I & III into consideration (more relevant for skin) which are the commonest penta and hexa peptide motifs. Do they converge?
Susan Anton
Susan Anton (Photo credit: Wikipedia)
2. How does adding an H to the carboxy terminal of such a penta/hexapeptide affect the polarity? Will it increase the skin penetration as described here? http://www.ncbi.nlm.nih.gov/pubmed/22452335

and finally dear cell biologists:
1. Do all collagen degradation fragments stimulate UVB induced hyaluronic acid degradation as described here: http://www.ncbi.nlm.nih.gov/pubmed/21454612

I have added a wiki page for this to summarise the findings. Feel free to add your thoughts here.

Resources:

collagen alpha-1(I) chain preproprotein [Homo sapiens] : http://www.ncbi.nlm.nih.gov/protein/NP_000079.2

collagen alpha-2(I) chain precursor [Homo sapiens]
http://www.ncbi.nlm.nih.gov/protein/NP_000080.2

collagen alpha-1(III) chain preproprotein [Homo sapiens]
http://www.ncbi.nlm.nih.gov/protein/4502951



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Importing ONTODerm Ontology

Map of Colombia with Departments
Map of Colombia with Departments (Photo credit: Wikipedia)
Two engineering students from Colombia are using ONTODerm for a noble cause. They are planning to take dermatology to the poor and the underprivileged. They started a teledermatology project, but discontinued it because of lack of support. Now they are working on an Ontology based diagnostic application using semantic web technologies.

One of the problems they have encountered may be important to be addressed here. They could not import ONTODerm into Sesame. The URL provided in the ONTODerm home page is protege specific. However you can export the latest ONTODerm version in the native format from the project page on knoodl. Just request for a free membership to ONTODerm community.

Please keep me posted if you are using ONTODerm or DermKnowledgeBASE for any such projects and I wish both of them all the very best.

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A Biochemical challenge!

Dear Reader

I am back again with a challenge this time. My last challenge got excellent response and I finally published the findings here. This challenge is probably more to do with biochemistry and I hope the Biochemicians facebook group under Prof. PTS would find this problem interesting.

Before I define the problem, please read the posts here to know about the clinical context.

1. The Big Bang Theory

2. Beauty of dark hair.
Molecule Man
Molecule Man (Photo credit: rizkapb)

In brief, Afamelanotide is a peptide drug being developed by Clinuvel pharmaceuticals for tanning. It is a synthetic alpha-MSH analog. (Click here for details)

A new patented molecule claims to have similar mechanism of action. (Click here for details)

The challenge is to find out:

1. How similar is the patented molecule to Afamelanotide?

2. Do you think the new molecule is designed for binding to cysteine rich keratin family in the hair cuticle? Can we improve this binding further by structural alterations?

3. Is the structure optimized for cutaneous penetration? In other words, what is the polarity and other relevant chemical and physical properties of the new molecule?

Please refer to the patented molecule as 'The bang' in your comments.

Thanks

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About Me

As a Dermatologist and Informatician my research mainly involves application of bioinformatics techniques and tools in dermatological conditions. However my research interests are varied and I have publications in areas ranging from artificial intelligence, sequence analysis, systems biology, ontology development, microarray analysis, immunology, computational biology and clinical dermatology. I am also interested in eHealth, Health Informatics and Health Policy.

Address

Bell Raj Eapen
Hamilton, ON
Canada