Binding Energy and Free Energy of Calcium Ion to Calmodulin EF-Hands with the Drude Polarizable Force Field

Abstract

Calcium ions are important messenger molecules in cells, which bind calcium-binding proteins to trigger many biochemical processes. We constructed four model systems, each containing one EF-hand loop of calmodulin with one calcium ion bound, and investigated the binding energy and free energy of Ca2+ by the quantum mechanics symmetry-adapted perturbation theory (SAPT) method and the molecular mechanics with the additive CHARMM36m (C36m) and the polarizable Drude force fields (FFs). Our results show that the explicit introduction of polarizability in the Drude not only yields considerably improved agreement with the binding energy calculated from the SAPT method but is also able to capture each component of the binding energies including electrostatic, induction, exchange, and dispersion terms. However, binding free energies computed with the Drude and the C36m FFs both deviated significantly from the experimental measurements. Detailed analysis indicated that one of main reasons might be that the strong interactions between Ca2+ and the side chain nitrogen of Asn/Gln in the Drude FF caused the distorted coordination geometries of calcium. Our work illustrated the importance of polarization in modeling ion–protein interactions and the difficulty in generating accurate and balanced FF models to represent the polarization effects.

Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin

“…Parameters for all atoms within the simulation were determined from the Charmm36 force field . Although previous studies have detailed difficulties of modeling Ca 2+ ion interactions and Ca 2+ -binding free energies in MD simulations involving biomolecules, the Charmm36 force field has been shown as a reliable force field option for producing experimental-like configurations of proteins in simulations where Ca 2+ is bound to an EF-hand protein (i.e., troponin) . The TMD simulations were conducted using an NPT ensemble at 310 K with Langevin temperature and pressure dampening.…”

Assessments of Variational Autoencoder in Protein Conformation Exploration

“…Calmodulin (CaM) is a regulatory Ca 2+ -binding protein involved in the regulation of many important biological processes. [43][44][45] The calcium-binding motif in CaM is a helix-loop-helix structure named EF-hand comprising 12 residues. The binding of calcium ions causes the conformation transition of EF-hand loops and induces substantial rearrangement.…”

“…The binding of calcium ions causes the conformation transition of EF-hand loops and induces substantial rearrangement. 43,45 EF-loops I to IV of CaM comprise residue numbers 20-31, 56-67, 93-104, and 129-140, respectively. Many studies have been conducted to determine the binding affinity and selectivity of four EF-hand loops, experimentally and computationally.…”

“…Many studies have been conducted to determine the binding affinity and selectivity of four EF-hand loops, experimentally and computationally. [44][45][46][47] Ye et al reported EF-loops I-IV to have dissociation constants with the order I > III ≈ II > IV. 46 Ca 2+ ions were removed sequentially with the reverse order of binding affinity (IV, II, III, I).…”

Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation

“…Among the other techniques for the BFE calculations, techniques including the free energy perturbation method, thermodynamic integration, and umbrella sampling have been used for rigorous estimates of Ca 2+ affinity for a variety of CBPs. However, results are often not consistent with experimental findings. − The prediction of the correct order of binding of Ca 2+ to different proteins is even more challenging. Recent work, which describes the impact of troponin C mutations on calcium binding affinity using adaptive steered molecular dynamics, illustrates this point.…”