User:Linnikh/sandbox

Sources for Hydrophobic Collapse edit:

http://www.sciencedirect.com/science/article/pii/S1476927106000296

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218722/

Hydrophobic Collapse
Basic description of Hydrophobic collapse. Along the side here, I'd like to include a diagram of the "Folding Funnel" which shows multiple configurations and kinetically accessible levels, as well as energy states.

https://upload.wikimedia.org/wikipedia/commons/thumb/9/91/Folding_funnel_schematic.svg/2000px-Folding_funnel_schematic.svg.png

I have various articles ready which discuss the order and time taken for a protein to form hydrophobic aggregates,

http://www.sciencedirect.com/science/article/pii/S0006349507712742

Energetics
Hydrophobic aggregation in polar solvents is largely driven by favourable changes in entropy. In this section I'd like to discuss the mechanisms behind nonpolar aggregation in the context of amino acid composition. In this case, I would reference the degrees of freedom of the solvent, the interactions between the solvent and the unfolded polypeptide, as well as the interactions after aggregation. A discussion of entropy and thermodynamics may be necessary

Localized Secondary Structures
Here I would like to talk about localized regions of nonpolar residues, for instance the formation of an alpha-helix with a nonpolar side and a polar side, as well as beta sheets and precedence of polarity or lack thereof on each face. Voet has good information on this.

Methionine edits
Methionine (abbreviated as Met or M; encoded by the codon AUG) is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated -+NH3 form under biological conditions), an α-carboxylic acid group (which is in the deprotonated –COO- form under biological conditions), and an S-methyl thioether side chain, classifying it as a non-polar, aliphatic amino acid. It is essential in humans, meaning the body cannot synthesize it and thus it must be obtained from the diet.

Methionine is coded for by the initiation codon meaning it indicates the start of the coding region and is the first amino acid produced in a nascent polypeptide during mRNA translation.