In the context of the near neighbor quasi component hierarchy there are universal descriptors of the density distribution between water molecules and the protein atom types across hundreds of globular proteins. We can pre-compute the proximal or perpendicular distribution functions (pRDFs) as a solvent density around any globular protein atom. These can then be used to reconstruct the solvent distribution with modest relative error. In this study, we extended the calculations of solute-water pair pRDFs to more solute atom categories and considered them within the context of two different solute types: the corresponding side chain analogs and the whole protein. This work computed the proximal radial distribution around charged and sulfur-containing amino acid side chain atoms. The pRDFs around sulfur atom and charged side chain atoms maintained their universality in both cases. Solvent reconstruction from the additional charged amino acid side chain atom pRDFs revealed the effect of protein surface charge distribution on solvent density, particularly in regions less dense than bulk water. Solvent reconstruction from the additional pRDF for sulfur atom prevented bubble formation where there are sulfur-containing residues on the protein surface. Ultimately the addition of more solute atom categories improves reconstruction errors relative to simulation. Solvent density reconstructions from the solute-water pair pRDFs, where the solutes are the side chain analogs, show better errors relative to that from molecular dynamics simulations than reconstruction from the protein-water pRDFs. Effect of excluded voronoi configuration space within the different solute contexts is discussed.

Improving reconstruction of the solvent density from proximal radial distribution functions

248th National Meeting (2014)

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