Unexpected features of the dark proteome

Abstract

We surveyed the "dark" proteome-that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology. structure prediction | protein disorder | transmembrane proteins | secreted proteins | unknown unknowns T he Protein Data Bank (PDB) (1) of experimentally determined macromolecular structures recently surpassed 110,000 entries-a landmark in understanding the molecular machinery of life. Structure determination lags far behind DNA sequencing, but high-throughput computational modeling (2, 3) can leverage the PDB to provide accurate structural predictions for a large fraction of protein sequences. Thus, structural data now scale with se-

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

“…15 Traditional ordered proteins have a relatively stable 3-D structure possess Ramachandran angles that vary only slightly around their equilibrium positions with occasional cooperative conformational switches. On the other hand, IDPs/ IDPRs, despite being biologically active, fail to form specific 3D structures and exist as highly dynamic structural ensembles, either at the secondary or at the tertiary level.…”

Visualization of Biomedical Data

“…On average, each protein sequence matches to ∼200 PDB structures (63) but contains several dark regions, with no detectable similarity to any known 3D structure (66). (e) A stacked bar chart showing the total fraction of protein residues that map to any PDB structure (either directly or via homology modelling); the remaining fraction (dark proteome) is divided into dark regions (d ) and dark proteins (where a single dark region spans an entire sequence) (66). Stacked bar charts have been used to achieve moderate data density, and axes replaced by two shaded regions (indicating 25%, 50%, and 75%).…”

“…Interestingly, much of the remaining dark proteome currently cannot be explained (e.g., Figure 6f ). Exploring this dark protein structure universe is an important data science challenge (65) in which visualization is playing a key role (66). High-throughput approaches are also being applied to molecular dynamics (67), generating increasingly large, complex trajectories; these data can give insights into key events (e.g., binding with ligands or other proteins).…”

Novel function discovery through sequence and structural data mining

“…These sequences include so-called ORFans [59], domains of unknown function (DUFs) [60,61], and protein 'dark matter' [62,63 ]. Many apparent ORFan proteins are likely highly divergent homologs of known structural families [60,64].…”