WARIO: Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins

Abstract

Characterizing the structure of flexible proteins, particularly within the realm of intrinsic disorder, presents a formidable challenge due to their high conformational variability. Currently, their structural representation relies on (possibly large) conformational ensembles derived from a combination of experimental and computational methods. The detailed structural analysis of these ensembles is a difficult task, for which existing tools have limited effectiveness. This study proposes an innovative extension of the concept of contact maps to the ensemble framework, incorporating the intrinsic probabilistic nature of disordered proteins. Within this framework, a conformational ensemble is characterized through a weighted family of contact maps. To achieve this, conformations are first described using a refined definition of contact that appropriately accounts for the geometry of the inter-residue interactions and the sequence context. Representative structural features of the ensemble naturally emerge from the subsequent clustering of the resulting contact-based descriptors. Importantly, transiently-populated structural features are readily identified within large ensembles. The performance of the method is illustrated by several use cases and compared with other existing approaches, highlighting its superiority in capturing relevant structural features of highly flexible proteins. An open-source implementation of the method is provided together with an easy-to-use Jupyter notebook, available at https://gitlab.laas.fr/moma/WARIO.