Comparing and combining predictors of mostly disordered proteins.
Intrinsically disordered proteins and regions carry out varied and vital cellular functions. Proteins with disordered regions are especially common in eukaryotic cells, with a subset of these proteins being mostly disordered, e.g., with more disordered than ordered residues. Two distinct methods have been previously described for using amino acid sequences to predict which proteins are likely to be mostly disordered. These methods are based on the net charge-hydropathy distribution and disorder prediction score distribution. Each of these methods is reexamined, and the prediction results are compared herein. A new prediction method based on consensus is described. Application of the consensus method to whole genomes reveals that approximately 4.5% of Yersinia pestis, 5% of Escherichia coli K12, 6% of Archaeoglobus fulgidus, 8% of Methanobacterium thermoautotrophicum, 23% of Arabidopsis thaliana, and 28% of Mus musculus proteins are mostly disordered. The unexpectedly high frequency of mostly disordered proteins in eukaryotes has important implications both for large-scale, high-throughput projects and also for focused experiments aimed at determination of protein structure and function.
Oldfield
Christopher J
CJ
Molecular Kinetics, Inc., 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA.
Cheng
Yugong
Y
Cortese
Marc S
MS
Brown
Celeste J
CJ
Uversky
Vladimir N
VN
Dunker
A Keith
AK
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019843:Archaeal Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D016384:Consensus Sequence; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D019277:Entropy; D005189:False Positive Reactions; D006801:Humans; D051379:Mice; D008956:Models, Chemical; D011237:Predictive Value of Tests; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism; D012372:ROC Curve; D055672:Static Electricity
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D011506:Proteins