Discovery and Visualization of the Hidden Relationships among N-Glycosylation, Disulfide Bonds, and Membrane Topology

Abstract

Membrane proteins (MPs) are functionally important but structurally complex. In particular, MPs often carry three structural features, i.e., transmembrane domains (TMs), disulfide bonds (SSs), and N-glycosylation (N-GLYCO). All three features have been intensively studied; however, how the three features potentially correlate has been less addressed in the literature. With the growing accuracy from computational prediction, we used publicly available information on SSs and N-GLYCO and analyzed the potential relationships among post-translational modifications (PTMs) and the predicted membrane topology in the human proteome. Our results suggested a very close relationship between SSs and N-GLYCO that behaved similarly, whereas a complementary relation between the TMs and the two PTMs was also revealed, in which the high SS and/or N-GLYCO presence is often accompanied by a low TM occurrence in a protein. Furthermore, the occurrence of SSs and N-GLYCO in a protein heavily relies on the protein length; however, TMs seem not to possess such length dependence. Finally, SSs exhibits larger potential dynamics than N-GLYCO, which is confined by the presence of sequons. The special classes of proteins possessing extreme or unique patterns of the three structural features are comprehensively identified, and their structural features and potential dynamics help to identify their susceptibility to different physiological and pathophysiological insults, which could help drug development and protein engineering.

A quest for cytosolic sequons and their functions

“…These results demonstrated that the sequon-poor regions of a protein are occupied by other PTMs, which agreed with our previous studies 13 in which we observed a complementarity between N-glycosylation, ɑ-helix TM domains, and disulfide bridges, suggesting the generalization of this rule. Such observations may be resolved from steric and spatial constraints in protein structure, in which the poor presentation of one type of PTM often gives space to the other PTMs.…”

“…In the case of TM and secreted proteins, the complementary PTMs to N-glycosylation-poor proteins were TM domains (Fig. 7 ), similar to what we discovered before 13 . We also discovered here that the secreted sequon-poor proteins, disulfide bridges and O-glycosylation were complementary to N-linked sequons (Fig.…”

“…The distribution of sequon conflicts following an exponential decrease (Fig. 2 ), similar to those in the TM N-glycoproteins 13 .

Figure 2 The distribution of sequon conflicts in transmembrane (TM) proteins.

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“…Our results were similar to a previous study on SwissProt glycoproteins 9 , in which a previous report had hypothesized that the sequons in the majority of the glycosylated proteins were utilized for glycosylation. From our recent studies analyzing the conflicts between the predicted ectodomains and the N-glycan and sequon locations in N-glycosylated TM proteins 13 , it is clear that most N-glycans in TM proteins were located in the ectodomain (i.e. ecto-sequons).…”