Intrinsic disorder and the human tear film proteome

Abstract

Purpose : We aimed to characterize the proteome of the human tear film and assess for the presence of intrinsically disordered proteins (IDPs). IDPs are proteins that lack a fixed, 3D structure, yet retain biological functionality. The presence of these proteins may provide insight into the molecular interactions occurring within the milieu of tears.

Methods : A bioinformatics proteomics study of 1,481 previously published proteins in the tear film of four healthy subjects. The amino acid sequences of the proteins were subject to a suite of computational tools, including the Compositional Profiler (CP), the Predictor of Natural Disordered Regions (PONDR), and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING).

Results : The CP analysis showed 1/10 order-promoting amino acid residues and 5/10 disorder-promoting amino acid residues were significantly enriched (p-value < 0.05). The PONDR classification system labeled 401 (27.2%) proteins as highly disordered. STRING predicted that the protein-protein interaction network (PIN) has 1,624 nodes (proteins) and 11,578 edges (interactions; p-value < 1.0 x 10^-16).

Conclusions : Our findings suggest that the human tear film proteome is intrinsically disordered. IDPs were abundant in our query sample of proteins. Additionally, our set of proteins was enriched in many disorder-promoting residues. The highly complex PIN is likely secondarily to the large proportion of IDPs in the proteome. These findings develop our understanding of the molecular interactions within the human tear proteome.

This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.

 

Amino acid composition profile of the human tear film. The fractional difference is calculated as (C_x – C_order)/C_order, where C_x is the content of a given amino acid in the query set (tear film), and C_order is the content of a given amino acid in the background set of highly ordered proteins. Positive values indicate enrichment, and negative values indicate depletion of amino acids. * represents significant enrichment or depletion (p-value < 0.05).

 

Prediction of Natural Disordered Regions (PONDR®) VSL2 output for 1481 tear film proteins. PONDR® VSL2 score is the average disorder score for a protein. PONDR® VSL2 (%) is the percent of residues with disorder scores above 0.5. Color blocks indicate regions in which proteins are mostly ordered (blue and light blue), moderately disordered (pink and light pink), or mostly disordered (red). Color block classifications are conventions in disorder-based proteomics.