Calcium Induced Regulation of Skeletal Troponin — Computational Insights from Molecular Dynamics Simulations

<div><p>The interaction between calcium and the regulatory site(s) of striated muscle regulatory protein troponin switches on and off muscle contraction. In skeletal troponin binding of calcium to sites I and II of the TnC subunit results in a set of structural changes in the troponin complex, displaces tropomyosin along the actin filament and allows myosin-actin interaction to produce mechanical force. In this study, we used molecular dynamics simulations to characterize the calcium dependent dynamics of the fast skeletal troponin molecule and its TnC subunit in the calcium saturated and depleted states. We focused on the N-lobe and on describing the atomic level events that take place subsequent to removal of the calcium ion from the regulatory sites I and II. A main structural event - a closure of the A/B helix hydrophobic pocket results from the integrated effect of the following conformational changes: the breakage of H-bond interactions between the backbone nitrogen atoms of the residues at positions 2, 9 and sidechain oxygen atoms of the residue at position 12 (N²-OE¹²/N⁹-OE¹²) in sites I and II; expansion of sites I and II and increased site II N-terminal end-segment flexibility; strengthening of the β-sheet scaffold; and the subsequent re-packing of the N-lobe hydrophobic residues. Additionally, the calcium release allows the N-lobe to rotate relative to the rest of the Tn molecule. Based on the findings presented herein we propose a novel model of skeletal thin filament regulation.</p> </div

The core domain of the troponin molecule.

<p>The Ca²⁺ sensor troponin consist of 3 subunits. The TnI subunit is shown in blue, the TnC subunit is shown in red and the TnT subunit is show in yellow. Ca²⁺ ions located in sites I through IV are shown as green vdW spheres. Sites III and IV located in the IT arm have a higher affinity to Ca²⁺ and do not serve a regulatory role. The N-terminal of TnT, the C-terminal of TnT and the C-terminal of TnI are not present in the crystal structure and are not displayed herein. Molecular coordinates were obtained from 1YTZ.pdb.</p

Hydrophobic core and hydrophobic residue re-packing following release of Ca²⁺.

<p>In all panels the saturated, open state N-lobe TnC is shown in red and the depleted, closed state N-lobe TnC is shown in blue. <b>A.</b> A hydrophobic PHE scaffold remains undisturbed in the open to closed transition. Residues PHE74, PHE77 and PHE25 are shown as vdW spheres. Top panel shows the TnC open state, bottom panel shows the TnC closed state. Green arrows point to PHE74 in each panel. <b>B.</b> Expulsion of residue PHE28 into the solvent and sliding of VAL44 into the hydrophobic core in the open to closed transition. Top panel shows the TnC open state, bottom panel shows the TnC closed state. Orange arrows point to PHE28 in each panel. <b>C.</b> Tight repacking of MET81, MET80 and MET45, which finish in a tight formation upon closure of the hydrophobic pocket, takes place in the open to closed transition. Top panel shows the TnC open state, bottom panel shows the TnC closed state. Violet arrows point to MET80 and MET81 in each panel.</p