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. 2013 Jan;13(1):207-222.
doi: 10.4208/cicp.170911.131011s.

In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor

Lin Wang  1 , Shawn Witham  1 , Zhe Zhang  1 , Lin Li  1 , Michael E Hodsdon  2 , Emil Alexov  1
Affiliations

In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor

Lin Wang et al. Commun Comput Phys. 2013 Jan.

Abstract

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa's of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that the main reason for pH-dependence of the binding of hPRL-hPRLr-ECD is a number of salt- bridges across the interface of the complex, while no salt-bridges are formed in the hGH-hPRlr-ECD. Specifically, most of the salt-bridges involve histidine residues and this is the reason for the pH-dependence across a physiological range of pH. The analysis not only revealed the molecular mechanism of the pH-dependence of the hPRL-hPRLr-ECD, but also provided critical insight into the underlying physic-chemical mechanism.

Keywords: electrostatics; human growth hormone; human prolactin; human prolactin receptor; pH-dependence; pKa calculations.

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Figures

Figure 1
Figure 1
Calculated pH-dependence of proton uptake/release (ΔQ(binding)) with dielectric constant 4 and 8 (left panel, in the range pH=0 to 14). The corresponding binding energies for hPRL-hPRLr-ECD and experimental energy (right panel, in the range pH=5 to 8). The energies are adjusted to be zero at pH=5.
Figure 2
Figure 2
Proton uptake/release ΔQ (binding) as a function of pH for hGH-hPRLr-ECD complex with different reference energy for Zn2+ ion (left panel, in pH range from 0 to 14). The corresponding pH-dependent component of the binding free energy and experimental energy (right panel, in the pH range from 5 to 8). The energies are adjusted to be zero at pH=5. The “rxn” stands for “reference energy” in Kcal/mol units.
Figure 3
Figure 3
Global amino acid count of hGH and hPRL for polar and non-polar residues. The wide slanted hatches represent hGH while horizontal hatches represent hPRL.
Figure 4
Figure 4
Interfacial amino acid count of hGH and hPRL for polar and non-polar residues. The wide slanted hatches represent hGH while horizontal hatches represent hPRL.
Figure 5
Figure 5
Salt bridge analysis: (A) The interface of hPRLr-ECD taken from the complex with hPRL. (B) The interface of hPRLr-ECD taken from the complex with hGH. (C) The interface of hPRL taken from the complex with hPRLr-ECD. (D) The interface of hGH taken from the complex with hPRLr-ECD. (E) Interfacial salt-bridges within hPRLr-ECD and hPRL complex. (F) Interfacial salt bridges within hPRLr-ECD and hGH complex. Yellow bonds between atoms represent salt bridges; In figure A, B, C, D, interface residues are white, non-interface residues are green; In figure E, F, hPRL receptors are green, ligands are white.
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