Description of conformational ensembles of disordered proteins by residue-local probabilities. Issue 15 (29th March 2023)

• Record Type: Journal Article
• Authors: Bastida, Adolfo; Zúñiga, José; Miguel, Beatriz; Soler, Miguel A.
• Is Part Of: Physical chemistry chemical physics. Volume 25:Issue 15(2023)
• Page Start: 10512
• Page End: 10524
• Publication Date: 2023-03-29
• Subjects: Chemistry, Physical and theoretical -- Periodicals; 541.3
• DOI: 10.1039/d2cp05970c
• Languages: English
• ISSNs: 1463-9076

Abstract

Abstract : Neighbour-dependent probability expressions describe accurately the conformational ensembles of disordered proteins from short MD trajectories. Abstract : The study of proteins with intrinsically disordered regions (IDRs) has emerged as an active field of research due to their intriguing nature. Although IDRs lack a well-defined folded structure, they play important functional roles in cells, following biological mechanisms different from those of the traditional structured proteins. Consequently, it has been necessary to re-design experimental and theoretical methods in order to face the challenges introduced by the dynamic nature of IDRs. In this work, we present an accurate and cost-effective method to study the conformational dynamics of IDRs based on the use of residue-local probabilistic expressions that characterize the conformational ensembles obtained from finite-temperature molecular dynamics (MD) simulations. It is shown that the good performance and the high convergence rates achieved with our method are independent of the IDR lengths, since the method takes advantage of the major influence of the identity and conformation of the nearest residue neighbors on the amino-acid conformational preferences to evaluate the IDR conformational ensembles. This allows us to characterize the conformational space of IDRs using a reduced number of probabilities which can be obtained from comparatively short MD simulations or experimental databases. To exemplify the usefulness of our approach, we present an application to directly detect Molecular Recognition Features (MoRFs) in an IDR domain of the protein p53, and to follow the time evolution of the thermodynamic magnitudes of this system during its exploration of the conformational space.