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

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T1 - Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions

AU - Cragnell, Carolina

AU - Rieloff, Ellen

AU - Skepö, Marie

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - coarse-grained modeling

KW - electrostatic interactions

KW - intrinsically disordered proteins

KW - Monte Carlo simulations

KW - small-angle X-ray scattering

UR - http://www.scopus.com/inward/record.url?scp=85044773582&partnerID=8YFLogxK

U2 - 10.1016/j.jmb.2018.03.006

DO - 10.1016/j.jmb.2018.03.006

M3 - Article

VL - 430

SP - 2478

EP - 2492

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 1089-8638

IS - 16

ER -