Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions

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Abstract

In this study, we have used the coarse-grained model developed for the intrinsically disordered saliva protein (IDP) Histatin 5, on an experimental selection of monomeric IDPs, and we show that the model is generally applicable when electrostatic interactions dominate the intra-molecular interactions. Experimental and theoretically calculated small-angle X-ray scattering data are presented in the form of Kratky plots, and discussions are made with respect to polymer theory and the self-avoiding walk model. Furthermore, the impact of electrostatic interactions is shown and related to estimations of the conformational ensembles obtained from computer simulations and “Flexible-meccano.” Special attention is given to the form factor and how it is affected by the salt concentration, as well as the approximation of using the form factor obtained under physiological conditions to obtain the structure factor.

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Subject classification (UKÄ) – MANDATORY

  • Theoretical Chemistry

Keywords

  • coarse-grained modeling, electrostatic interactions, intrinsically disordered proteins, Monte Carlo simulations, small-angle X-ray scattering
Original languageEnglish
Pages (from-to)2478-2492
JournalJournal of Molecular Biology
Volume430
Issue number16
Early online date2018 Mar 21
Publication statusPublished - 2018
Publication categoryResearch
Peer-reviewedYes