Fig. 4.

Structured and unstructured waters coordinating bryostatin in the shallow binding mode. Waters are highlighted for clarity. Note the coordination of a water with C9 and C3 OH groups, as well as SER10 side chain and a lipid carbonyl oxygen. The C3 OH is also hydrogen bonding with the SER10 backbone amide proton. A structured water also coordinates with C19 OH. Unstructured waters from bulk solvent hydrogen bond as well with the C13 Z-enoate. Solvation of both of these moieties provides stabilization of shallow orientation and a barrier to insertion more deeply into the membrane. Other PKC-binding ligands lack such water-coordinating moieties, and therefore only favor the deeply inserted state. Conversely, altering substitution at deeply embedded C7 and C8 can substantially abrogate binding activity altogether (see Supplementary Fig. 5). The conformation shown of bryostatin is the predominant one of the simulations; see Supplementary Figs. 6 and 7 and Supplementary Discussion for more discussion of bryostatin’s conformations