Section 23.2.5.3. Non-complementary negative electrostatic surface potential of protein sites specific for anions

The presence of an uncompensated negatively charged Asp56 is unusual for an anion-binding site, as observed in PBP. In fact, a related discovery of profound ramification is that the binding-cleft region of PBP has an intense negative electrostatic surface potential (Fig. 23.2.5.3a) (Ledvina et al., 1996). Non-complementarity between the surface potential of a binding region and an anion ligand is not unique to PBP. We have reported similar findings for SBP, a DNA-binding protein, and, even more dramatically, for the redox protein flavodoxin (Fig. 23.2.5.3b) (Ledvina et al., 1996). Evidently, for proteins such as these, which rely on hydrogen-bonding interactions with only uncharged polar residues for anion binding and electrostatic balance, a non-complementary surface potential is not a barrier to binding. This conclusion is supported by very recent fast kinetic studies of binding of phosphate to PBP and the effect of ionic strength on binding (Ledvina et al., 1998).

Figure 23.2.5.3| top | pdf | Electrostatic surface potential of (a) the phosphate-binding protein and (b) flavodoxin. The molecular surface electrostatic potentials, calculated and displayed using GRASP (Nicholls et al., 1991), are −10 kT (red), neutral (white) and +10 kT (blue) [see Ledvina et al. (1996) for more details]. (a) Wild-type phosphate-binding protein based on the X-ray structure of the open cleft, unliganded form (Ledvina et al., 1996). The phosphate-binding site is located in the cleft (with negative surface potential) in the middle of the molecule and between the two domains. (b) Flavodoxin with bound flavin mononucleotide (FMN). The phosphoryl group (P) of the FMN is bound in a pocket with intense negatively charge surface potential. The surface potential was calculated without the bound flavin mononucleotide using the structure from the Protein Data Bank (PDB code: 2fox).