Binary classification of protein molecules into intrinsically disordered and ordered segments.
Understanding of human proteins is doubtlessly essential for both basic and applied sciences. With protein structures accumulating and protein structure prediction improving, it is becoming increasingly accurate to assign structural domains (SDs) to amino acid sequences. Although structural domains in proteins (SDs) are important,
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half of the regions in the human proteome are currently left with no SD assignments. These unassigned regions consist not only of novel SDs, but also of intrinsically disordered (ID) regions since proteins, especially those in eukaryotes; generally contain a significant fraction of ID regions. As ID regions can be inferred from amino acid sequences, a method that combines SD and ID region assignments can determine the fractions of SDs and ID regions in any proteome.The discovery of intrinsically disordered proteins (IDPs) has brought a paradigm change to structural biology. IDPs are those that do not assume any stable 3D structure by themselves under physiological conditions.
The conventional prediction methods only identify possible ID regions, without assigning the remainder as SDs. In order to remedy this defect, we developed the DICHOT method which divides the entire amino acid sequence of a query protein into SDs and ID regions. In addition to conventional methods of SD assignment and ID prediction, the DICHOT system introduces sequence conservation as a third factor, based on the observation that ID regions are less conserved than structural regions are.
Using the DICHOT system, the present study has revealed, for the first time, the concrete ratio of intrinsically ordered and disordered segments in the human proteome: on the average 65% of human protein residues are in SDs, while the remaining 35% fall within ID regions.
Authors: Satoshi Fukuchi1, Kazuo Hosoda, Keiichi Homma, Takashi Gojobori and Ken Nishikawa.
Source: Fukuchi et al. BMC Structural Biology 2011, 11:29
Publication date: 22nd june, 2011.
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