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. 2020 Nov 6;3(6):1111–1143. doi: 10.1021/acsptsci.0c00089

Figure 7.

Figure 7

Stereo views of the WATMD annotations described in the text, exemplified for monomeric Mpro (2QCY). In general, solvation shells are loosely organized into three major strata (demarcated by yellow lines) spanning between the protein surface and bulk solvent (noting that bulk solvent per se is omitted from WATMD analyses), as follows: (1) Stratum 1: ULOVs that are largely or fully devoid of protein H-bond partners, which reside directly adjacent to nonpolar protein surface patches, as well as HOVs residing directly adjacent to polar protein surface patches comprised of multiple donors and/or acceptors; (2) Stratum 2: weaker, partially H-bond depleted LOVs that bridge between strata 1 and 3; (3) Stratum 3: BLOVs and H/O-agnostic SBLOVs that bridge between bulk solvent and the outer reaches of the solvation shell (putatively dominated by lateral water–water H-bonding). Voxels are denoted by spheres, which are scaled in proportion to their relative time-averaged H and O occupancies, and color-coded according to relative preference for O versus H (red and blue, respectively), or lack thereof (white). (A) Full WATMD grid, viewed toward the protein surface in the direction of strata 3 to 1. A crystallized Mpro substrate extracted from 2Q6G (magenta) is overlaid on the active site for reference. Bulk solvent surrounding the solvation shell has been removed, resulting in an irregular grid boundary. (B) AS of Mpro viewed approximately parallel to the pocket. Stratum 3 voxels typically consist of BLOVs (yellow spheres) and SBLOVs (white spheres). (C) Same as B, except zoomed into stratum 2 voxels, which typically consist of LOVs occupied by solvation that is weakly H-bonded to a single protein donor or acceptor (small dark blue spheres). (D) Same as B, except zoomed into stratum 3 voxels, which typically consist of HOVs occupied by solvation that is strongly H-bonded to multiple protein donor(s) and/or acceptor(s) (large spheres) or ULOVs occupied by solvation that is largely or fully devoid of H-bonds (dot-sized spheres). UHOVs corresponding to trapped water within buried channels/cavities are not shown.