Sunday, September 22, 2019

Protein function observations - WCG - Protein Interactions : Prions

Protein function observations

"Help Cure Muscular Dystrophy Researcher Developing New Methods for Deciphering Protein-Protein Interactions"

https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=606

https://onlinelibrary.wiley.com/doi/full/10.1002/prot.25757

Docking poses of a single protein pose significant processing time consumption ..

" ∼50 000 docking poses for each protein pair. Thus, for a given protein P, we considered about 50 000 × 262 = 13 100 000 docking poses."
"23 642 ISs, which were merged into 370 IRs to define our second “extended” dataset, PPI‐262" (Interaction Sites IR)
Limited computation time demonstrates how complex life is; Being billions of interaction for more complex life forms.

In this example we see that probability of a pose being relevant compared to for example vain size & shape.. Or the particular acid/base/alkaline & Chemical composure of the environments of function..
Also temperature ranges need to be born in mind as bodies function though a set range of temperatures..  18|31

In beings living in for example geothermic vents.. The environmental pressure upon proteins is rather more challenging for most of the life on our planet; Proteins are a key reason for challenge & survival.

Available interaction points also count as potential attack vectors for acids; Oxides .. Ozone and other functioning chemical interactions & changers; Decomposer's or modifiers.

Trypsin in the diagram (Figure 2) brings a memory of the influence large amounts of brain fluid in Creutzfeldt-Jakob disease (CJD).. and the bovine version.. however this will have to be examined.

"both SCcons and SCnotLig are designed to target conserved sites, their predictions often overlap substantially.24 By contrast, SCgeom disregards conservation and uses only physicochemical properties and local geometry to capture highly protruding interfaces not necessarily conserved through evolution."

Conservation of binding sites though evolution denotes stable evolution over time,
Binding sites appear to have sudden modifiers that lead to large changes in the dynamics of shape; Chemical interaction & evolved function,
In this rule conservation of function does indicate smaller changes to the evolution of species,
Larger & sudden shifts in function have large dynamic shifts in pattern though-out a biological systems function & design,
Deliberate or random changes.. Have sweeping effects on function & biodiversity,
Large changes or small the complex interaction of dynamic chemical interactions have large effects on biological function & these need to be studied.

Small shifts in chemical composition of proteins have varied effects upon the function of the bio ecosystem..
Such an example is left & right handed prions in Creutzfeldt-Jakob disease (CJD), Smaller changes could potentially produce astonishingly large changes or almost unnoticed effects.

Some examples:
Ebola
Zika
eating disorders
Auto Immune diseases

https://www.ninds.nih.gov/Disorders/Patient-Caregiver-Education/Fact-Sheets/Creutzfeldt-Jakob-Disease-Fact-Sheet

Regards Rupert S https://science.n-helix.com

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