UNDERSTANDING THE CONFORMATIONAL LANDSCAPE OF APO CALX-CBD12 VIA STRUCTURE BASED MODEL WITH GAUSSIAN POTENTIAL

The Drosophila Na⁺/Ca²⁺ exchanger (CALX) is fundamentally regulated by its two-domain region,
CALX-CBD12. Previous studies[1] have shown that, unlike mammalian NCXs, CALX is inhibited by
the highly cooperative binding of four Ca²⁺ ions to the CBD1 domain. Structural characterizations
using NMR and SAXS revealed that CALX-CBD12 exhibits significant flexibility in the apo state,
sampling an ensemble of compact and extended conformations, but becomes rigid and
predominantly adopts an extended conformation in the presence of Ca²⁺. Understanding in detail the
conformational landscape of the apo state and the transition pathways toward the Ca²⁺-bound state is
essential for elucidating the mechanism of allosteric regulation of CALX. In this work, we employ a
Structure-Based Model (SBM) with Gaussian potentials, built upon previously published structural
and experimental data, to simulate the dynamics of CALX-CBD12 in the apo state. Our simulations
reveal the free energy landscape of the system in the apo state, identifying multiple minima
corresponding to distinct conformational arrangements, ranging from more compact to more
extended conformations. To further characterize these transitions, we visualized the energy funnel
associated with the conformational changes using the Energy Landscape Visualization Method
(ELViM). Our approach demonstrates the utility of SBMs with Gaussian potentials in exploring
complex conformational landscapes and uncovering transition mechanisms in flexible multidomain
proteins.
This work was supported by Coordination for the Improvement of Higher Education Personnel
(CAPES) and São Paulo Research Foundation (FAPESP 022/07231-7).
[1] Cardoso et al., Biophys. J. 2020; Degenhardt et al., Biophys. J. 2021