Intrinsically Disordered Protein: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eran Hodis (talk | contribs) |
Eric Martz (talk | contribs) →Protein disorder predictors: reorganized section |
||
| Line 33: | Line 33: | ||
== Protein disorder predictors == | == Protein disorder predictors == | ||
=== Principles Used in Prediction === | |||
<table align='right'><tr valign='top'><td> | <table align='right'><tr valign='top'><td> | ||
[[Image:FoldIndex.jpeg | thumb | FoldIndex<ref>PMID: 15955783</ref> output for three protein sequences (a) Cat-Muscle Pyruvate Kinase (b) The human p53 tumor suppressor protein (c) Chicken gizzard caldesmon; green is folded and red is unfolded]]</td><td>[[Image:DisorderAA.jpg | thumb | Content of order-promoting and disorder-promoting amino acids in the ''Drosophila'' proteome (black) and in the cytoplasmic domain of gliotactin that was shown to be IUP (gray) <ref>PMID: 14579366</ref>]] | [[Image:FoldIndex.jpeg | thumb | FoldIndex<ref name="foldindex">PMID: 15955783</ref> output for three protein sequences (a) Cat-Muscle Pyruvate Kinase (b) The human p53 tumor suppressor protein (c) Chicken gizzard caldesmon; green is folded and red is unfolded]]</td><td>[[Image:DisorderAA.jpg | thumb | Content of order-promoting and disorder-promoting amino acids in the ''Drosophila'' proteome (black) and in the cytoplasmic domain of gliotactin that was shown to be IUP (gray) <ref>PMID: 14579366</ref>]] | ||
</td></tr></table> | </td></tr></table> | ||
Led by the assumption that “since amino acid sequence determines 3-D structure, amino acid sequence should also determine lack of 3-D structure” <ref name='Dunker2001'>PMID: 11533628</ref> specific sequence features shared by IUPs have been evaluated and algorithms for their identification formulated. | Led by the assumption that “since amino acid sequence determines 3-D structure, amino acid sequence should also determine lack of 3-D structure” <ref name='Dunker2001'>PMID: 11533628</ref> specific sequence features shared by IUPs have been evaluated and algorithms for their identification formulated. | ||
The low hydrophobicity and high net charge of naively unfolded proteins result in a difference in amino acid composition between them and naively folded proteins <ref>PMID: 11093259</ref>. | |||
Compared to sequences of ordered proteins, disordered protein sequences are substantially depleted in I, L, V, W, F, Y, and C, which were therefore designated as “order promoting” amino acids, and enriched in E, K, R, G, Q, S, P, and A, which have been designated as “disorder promoting”. The under representation of hydrophobic amino acids in a protein diminishes one of the basic thermodynamic forces known to be important for protein folding, namely, the hydrophobic interaction. Because a hydrophobic core does not form, such proteins have large hydrodynamic dimensions. | |||
=== Prediction Servers === | |||
* [http://bip.weizmann.ac.il/fldbin/findex/ FoldIndex]<ref name="foldindex" /> makes predictions based on the observation that IUPs occupy the low hydrophobicity/ high net-charge portion of charge-hydrophobicity phase space. (See Figure above.) | |||
* [http://bioinf.cs.ucl.ac.uk/disopred/ DISOPRED] | |||
* [http://www.pondr.com/ PONDR] | |||
* [http://iupred.enzim.hu/ IUPred] | |||
The | ''The above list is incomplete. Addition of other servers is welcome, and summaries of methods, pros and cons for each server would be useful.'' | ||
== Biological implications of IUPs == | == Biological implications of IUPs == | ||
