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

Philippe Lieutaud; François Ferron; Alexey V Uversky; Lukasz Kurgan; Vladimir N Uversky; Sonia Longhi

doi:10.1080/21690707.2016.1259708

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

Intrinsically Disord Proteins. 2016 Dec 21;4(1):e1259708. doi: 10.1080/21690707.2016.1259708. eCollection 2016.

Authors

Philippe Lieutaud¹, François Ferron¹, Alexey V Uversky², Lukasz Kurgan³, Vladimir N Uversky⁴, Sonia Longhi¹

Affiliations

¹ Aix-Marseille Université, AFMB UMR, Marseille, France; CNRS, AFMB UMR, Marseille, France.
² Center for Data Analytics and Biomedical Informatics, Department of Computer and Information Sciences, College of Science and Technology, Temple University , Philadelphia, PA, USA.
³ Department of Computer Science, Virginia Commonwealth University , Richmond, VA, USA.
⁴ Department of Molecular Medicine and USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.

Abstract

In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins lack a stable 3D structure, are ubiquitous and fulfill essential biological functions. Their conformational heterogeneity is encoded in their amino acid sequences, thereby allowing intrinsically disordered proteins or regions to be recognized based on properties of these sequences. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray crystallization. This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved in induced folding. It also provides a set of detailed instructions that should be followed to perform computational analysis of disorder.

Keywords: disorder databases and metaservers; induced folding; intrinsic disorder; intrinsically disordered proteins; intrinsically disordered regions; prediction methods.