Do Halide Motifs Stabilize Protein Architecture?

Halide anions are traditionally recognized as the structure maker and breaker of bulk water to indirectly influence the physicochemical and biological properties of biomacromolecules immersed in electrolyte solution, but here we are more interested in whether they can be structured in the protein interior, forming that we named “halide motifs”, to stabilize the protein architecture through direct noncovalent interactions with their context. In the current work, we present a systematical investigation on the energy components in 782 high-quality protein halide motifs retrieved from the Protein Data Bank (PDB), by means of the continuum electrostatic analysis coupled with nonelectrostatic considerations, as well as hybrid quantum mechanical/molecular mechanical (QM/MM) examination. We find that most halide motifs (91.6%) in our data set are substantially stabilizing, and their average stabilization energy is significantly larger than that previously obtained for sophisticated protein salt bridges (−15.16 vs −3.66 kcal/mol). Strikingly, nonelectrostatic factors, especially the dispersion potential, rather than the electrostatic aspect, dominate the energetic profile of the pronouncedly charged halide motifs, since the expensive cost for electrostatic desolvation penalty requires being paid off using the income receiving from the favorable Coulomb interactions during the motif formation. In addition, all the energy terms involved in halide motifs, regardless of their electrostatic or nonelectrostatic nature, highly depend on the degree of the motif’s burial in the protein, and the buried halide motifs are generally associated with a high stability. The results presented herein should be of valuable use in establishing a knowledge framework toward understanding the functional implications underlying anion structured in a biological molecule.