Talk:Hydrophobic collapse

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Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 00:07, 17 January 2022 (UTC)[reply]

wrong statement

commonly misunderstood: "While the entropy of the polypeptide has decreased as it enters a more ordered state, the overall entropy of the system increases, contributing to the thermodynamic favourability of a folded polypeptide." This is false. Protein folding is entropically disfavoured, due to the great loss in chain entropy while folding which exceeds gain through hydophobic effect largely. Folding is spontaneous becouse of enthalpy effects. Example for the protein Lyzosym: Delta(S)*T = 167 kcal/mol Delta(H) = -198 kcal/mol Dehydration of Residues that a buried in folded Protein = 17 kcal/mol source: http://n.ethz.ch/~dcadosch/download/Glockshuber/Vorlesungsskript.pdf --2001:67C:10EC:52C6:8000:0:0:F9C (talk) 17:39, 9 December 2016 (UTC) pscl[reply]

Needs work

I feel like this article is not properly cited for a majority of its description. Furthermore, the material is dense and run-on. I intend to make edits to go into more detail regarding the mechanisms of hydrophobic collapse (More detail regarding molten globules and folding funnel models) as well as adding some graphics.--Linnikh (talk) 22:35, 27 October 2015 (UTC)[reply]

Outline

Here are some proposed edits (still in their infancy) that I would like to add to this page

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

Surface Secondary Structures

The formation of a hydrophobic core requires the surface structures of this aggregate to maintain contact with both the polar solvent as well as the internal structures. In order to do this, these surface structures usually express amphipathic properties. The surface structure expressed by an alpha helix may have nonpolar residues in an N+3, N+4 dynamic, allowing the alpha-helix to nonpolar properties on on side when split longitudinally along the axis. Similarly, beta strands can also adopt this property with simple alternation of polar and nonpolar residues. Every N+1 side chain will occupy space on the opposite side of the beta strand.^[1]

http://www.fasebj.org/content/10/1/75.full.pdf http://onlinelibrary.wiley.com/doi/10.1002/prot.20459/full

--Linnikh (talk) 23:08, 3 November 2015 (UTC)[reply]

References

^ Sharadadevi, Ambure; Sivakamasundari, Chandrasekaran; Nagaraj, Ramakrishnan (8 April 2005). "Amphipathic ɑ-helices in proteins: Results from Analysis of Protein Structures". Proteins: Structure, Function, and Bioinformatics. 59 (4): 791-801. doi:10.1002/prot.20459. Retrieved 10 November 2015. {{cite journal}}: More than one of |pages= and |page= specified (help)

[1] Sharadadevi, Ambure; Sivakamasundari, Chandrasekaran; Nagaraj, Ramakrishnan (8 April 2005). "Amphipathic ɑ-helices in proteins: Results from Analysis of Protein Structures". Proteins: Structure, Function, and Bioinformatics. 59 (4): 791-801. doi:10.1002/prot.20459. Retrieved 10 November 2015. {{cite journal}}: More than one of |pages= and |page= specified (help)

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