Map of Genetically Constrained Regions in Human Intrinsically Disordered Proteins

Abstract

Intrinsically disordered proteins (IDPs) and regions (IDRs) are pivotal for biological processes like signaling, recognition, and regulation, and have been found to be implicated in many diseases. Evolutionary selection of IDPs thus has been extensively investigated through multiple sequence alignment (MSA) methods. Recent large-scale catalogues of human genome sequences have enabled the detection of constrained regions depleted of genetic variation. Here, we aim to identify the prevalence, characteristics, and functions of genetically constrained IDRs. We mapped the missense tolerance ratio (MTR), quantifying the depletion of amino acid substitutions in genome aggregation database (a sample of 138,632 individuals) on 210 human IDPs from DisProt7.0 database. We identified 63 IDRs (length<100 residues) having 25th percentile MTR, indicating these IDRs are >75% constrained. For further verification, we annotated IDRs using MPC (Missense badness, PolyPhen-2, and Constraint) score to identify regions in genes that are depleted of substitutions. We found 70 more IDRs with MPC < 1.0 (lower observed versus expected substitutions). We then investigated the functions and interactions of the 133 missense constrained IDRs (mcIDRs). We spotted 25 mcIDRs carrying molecular recognition features (assemblers or effectors), 14 acting as flexible linkers/spacers, 51 to have disordered state and 45 involved in protein-protein interactions. Looking further into the cross-species MSA (BLAST search, 50% identity cut-off), we found 53 mcIDRs with >90% and 26 mcIDRs with <30% conserved residues. We further examined the enrichment of disease-associated loci in mcIDRs, and found 645 rare singletons (new mutations in evolution) and 635 pathogenic missense mutations. We exploited two genetic constraint metrics to identify IDRs that are restricted against substitutions. The observed functional diversity of the constrained IDRs, their contrast with evolutionary conservations, and their accumulation of disease-associated loci will advance our understanding of IDP-based regulations in human pathology.