Conformational analysis of the IQSEC2 protein by statistical thermodynamics

• Published in: Current research in structural biology Vol. 8; p. 100158
• Main Authors: Shokhen, Michael, Albeck, Amnon, Borisov, Veronika, Israel, Yonat, Levy, Nina S., Levy, Andrew P.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-01-2024; Elsevier
• Subjects: Accelerated molecular dynamics; Ensemble method of Gibbs; Protein dimerization; Protein folding; Statistical thermodynamics; Protein dimerization; Statistical thermodynamics; Accelerated molecular dynamics; Ensemble method of Gibbs; Protein folding
• ISSN: 2665-928X; 2665-928X
• DOI: 10.1016/j.crstbi.2024.100158

Mutations in the IQSEC2 gene result in severe intellectual disability, epilepsy and autism. The primary function of IQSEC2 is to serve as a guanine exchange factor (GEF) controlling the activation of ARF6 which in turn mediates membrane trafficking and synaptic connections between neurons. As IQSEC2 is a large intrinsically disordered protein little is known of the structure of the protein and how this influences its function. Understanding this structure and function relationship is critical for the development of novel therapies to treat IQSEC2 disease. We therefore sought to identify IQSEC2 conformers in unfolded and folded states and analyze how conformers differ when binding to ARF6 and thereby influence GEF catalysis. We simulated the folding process of IQSEC2 by accelerated molecular dynamics (aMD). Following the ensemble method of Gibbs, we proposed that the number of microstates in the ensemble replicating a protein macroscopic system is the total number of MD snapshots sampled on the production MD trajectory. We divided the entire range of reaction coordinate into a series of consecutive, non-overlapping bins. Thermal fluctuations of biomolecules in local equilibrium states are Gaussian in form. To predict the free energy and entropy of different conformational states using statistical thermodynamics, the density of states was estimated taking into account how many MD snapshots constitute each conformational state. IQSEC2 dimers derived from the most stable folded and unfolded conformers of IQSEC2 were generated by protein-protein docking and then used to construct IQSEC2-ARF6 encounter complexes. We suggest that IQSEC2 folding and dimerization are two competing processes that may be used by nature to regulate the process of GDP exchange on ARF6 catalyzed by IQSEC2.
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•Conformational analysis of IQSEC2 is presented using statistical thermodynamics based on the Gibbs ensemble method.•We describe the folding energy landscape of IQSEC2 and identify 7 folded and 4 unfolded conformers of IQSEC2.•IQSEC2 conformers differ in their ability to interact with ARF6.•IQSEC2 can form an encounter complex with ARF6 only in an unfolded state.•The N terminal fragment of IQSEC2 plays a critical role in the Ca2+ induced self-association (dimerization) of IQSEC2.