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Review
. 2013 Apr 1;1(1):e24684.
doi: 10.4161/idp.24684. eCollection 2013 Jan-Dec.

The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins

Vladimir N Uversky  1   2
Affiliations
Review

The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins

Vladimir N Uversky. Intrinsically Disord Proteins. .

Abstract

The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their "disorder promoting potencies," which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue.

Keywords: glutamic acid; intrinsically disordered protein; protein function; protein structure; protein-protein interaction.

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Figures

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Figure 1. Amino acid determinants defining structural and functional differences between the ordered and intrinsically disordered proteins. (A) Fractional difference in the amino acid composition (compositional profile) between the typical IDPs from the DisProt database and a set of completely ordered proteins calculated for each amino acid residue. The fractional difference was evaluated as (CDisProt-CPDB)/CPDB, where CDisProt is the content of a given amino acid in a DisProt databse, and CPDB is the corresponding content in the data set of fully ordered proteins. Positive bars correspond to residues found more abundantly in IDPs, whereas negative bars show residues, in which IDPs are depleted. Amino acid types were ranked according to their decreasing disorder-promoting potential. (B). Amino acid compositions of several data sets discussed in the text (DisProt, UniProt, PDB Select 25 and surface residues48).
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Figure 2. Structural properties of glutamic acid. (A) Chemical structure of the glutamic acid residue. (B) Ramachandran plots for backbone conformations of the 18 non-glycine and non-proline amino acids. Marked regions of density correspond to the right-handed α-helix region (α), mirror image of α (αL), region largely involved in β-sheet formation (βS), and region associated with extended polyproline-like helices, but also observed in β-sheet (βP).
See this image and copyright information in PMC

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