posted on 2024-03-08, 15:34authored byRui Lai, Guohui Li, Qiang Cui
High binding affinity and selectivity of metal ions are
essential
to the function of metalloproteins. Thus, understanding the factors
that determine these binding characteristics is of major interest
for both fundamental mechanistic investigations and guiding of the
design of novel metalloproteins. In this work, we perform QM cluster
model calculations and quantum mechanics/molecular mechanics (QM/MM)
free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and
its mutant. While a nonpolarizable MM model (CHARMM36) does not lead
to the correct experimental trend, treatment of the metal binding
site with the DFTB3 model in a QM/MM framework leads to relative binding
free energies (ΔΔGbind) comparable
with experimental data. For the wild-type (WT) protein, the calculated
ΔΔGbind is ∼6.6 kcal/mol
in comparison with the experimental value of 5.6 kcal/mol. The good
agreement highlights the value of a QM description of the metal binding
site and supports the role of electronic polarization and charge transfer
to metal binding selectivity. For the D51A/E101D/F102W mutant, different
binding site models lead to considerable variations in computed binding
affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant
coordination number for the mutant, the calculated relative binding
affinity is ∼4.8 kcal/mol, in fair agreement with the experimental
value of 1.6 kcal/mol. The WT protein is observed to feature a flexible
binding site that accommodates a range of coordination numbers for
Ca2+, which is essential to the high binding selectivity
for Ca2+ over Mg2+. In the mutant, the E101D
mutation reduces the flexibility of the binding site and limits the
dominant coordination number of Ca2+ to be seven, thereby
leading to reduced binding selectivity against Mg2+. Our
results highlight that the binding selectivity of metal ions depends
on both the structural and dynamical properties of the protein binding
site.