Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ

Abstract

CopZ is a copper chaperone from Bacillus subtilis. It is an important part of Cu(I) trafficking. We have calculated pK(a) values for the CXXC motif of this protein, which is responsible for the Cu(I) binding, and the Cu(I) binding constants. Polarizable and fixed-charges formalisms were used, and solvation parameters for the both models have been refitted. We had to partially redevelop parameters for the protonated and deprotonated cysteine residues. We have discovered that the polarizable force field (PFF) is qualitatively superior and allows a uniformly better level of energetic results. The PFF pK(a) values for cysteine are within about 0.8-2.8 pH units of the experimental data, while the fixed-charges OPLS formalism yields errors of up to tens of units. The PFF magnitude of the copper binding energy is about 10 kcal/mol or 50% higher than the experimental value, while the using the refitted OPLS parameters leads to an overall positive binding energy, thus predicting no thermodynamically stable complex. At the same time, the agreement of the polarizable S···Cu(I) distances with the experimental results is within 0.08 Å range, and the nonpolarizable calculations lead to an error of about 0.4 Å. Moreover, the accuracy of the PFF has been achieved without any explicit fitting to either pK(a) or CopZ···Cu(I) binding energies. We believe that this makes our polarizable technique a choice method in reproducing protein-copper binding and further supports the notion that explicit treatment of electrostatic polarization is crucial in many biologically relevant studies, especially ion binding and transport.

Figure 1

Processes considered in this work. Cyx stands for a deprotonated Cys residue with a charge of −1e⁻.

Figure 2

Complexes of CH₃SH (a) and CH₃S⁻ (b) particles with one water molecule used in fitting the sulfur and hydrogen parameters.

Figure 3

The part of the CopZ protein molecule used in the simulations. HID stands for histidine-delta (hydrogen on the delta-nitrogen), ACE is −C(=O)−CH₃ and NMA denotes −N(−H)−CH₃.

Figure 4

The part of the CopZ protein molecule used in the simulations. The system conformation is from the PDB data for the apo-structure.

Figure 5

Protonated form of cysteine dipeptide used in calculating Cys pKa shift.

Figure 6

Deprotonated form of cysteine dipeptide used in calculating Cys pKa shift.

Figure 7

Positions of Cys13 and Cys16 residues in the apo-form of CopZ. The latter is coordinated by oxygen atoms of the Asp66 residue.

Figure 8

OPLS complex of CopZ with Cu(I).

Figure 9

PFF complex of CopZ with Cu(I).