Dark Proteome Database: Studies on Disorder.

Agostinho Rosa,João Manuel R. S. Tavares,Cátia Rocha,Pedro M. C. Pina,Nelson Perdigão

doi:10.3390/ht9030015

Abstract

There is a misconception that intrinsic disorder in proteins is equivalent to darkness. The present study aims to establish, in the scope of the Swiss-Prot and Dark Proteome databases, the relationship between disorder and darkness. Three distinct predictors were used to calculate the disorder of Swiss-Prot proteins. The analysis of the results obtained with the used predictors and visualization paradigms resulted in the same conclusion that was reached before: disorder is mostly unrelated to darkness.

Highlights

With this work, we explored the difference between disorder and darkness (i.e., the distinction between intrinsically disordered proteins (IDP’s) [1] and their relationship with the dark proteome (DP) [2])
As defined, disordered regions are those with evidence of structural heterogeneity [3] where some become well-structured in particular contexts, and “dark” regions, as defined in 2015 [2], are those that do not match any Protein Data Bank (PDB) [4] entry, where some PDB entries, which are frequently obtained from electron microscopy (EM) or nuclear magnetic resonance (NMR) [5], are highly disordered
Dataset: The set of protein sequences selected for this work study is from the Swiss-Prot release of July 2016, together with the protein structures extracted from PDB on July 2016, including the predictions from Aquaria [14], Protein Model Portal [15], and Predict Protein [16], according to their versions of July 2016 [6]

Summary

Introduction

We explored the difference between disorder and darkness (i.e., the distinction between intrinsically disordered proteins (IDP’s) [1] and their relationship with the dark proteome (DP) [2]).

Results

Conclusion