Table 2

Electrostatic calculations. pK(1/2) values for titratable residues were estimated from electrostatic calculations with the quasi-macroscopic model in MEAD, version 1.1.8 (39). Hydrogen atoms and partial charges were added from the DISCOVER force field (Molecular Simulations); the hydroxyls of Ser, Thr, Tyr, and waters were oriented by PROTEUS [distributed as part of the GRASP package (46, 47)] with recommended parameters. Partial charges for the Schiff base-retinal moiety used the parameter set from Tavan et al. (48). Multiple site titration used Monte Carlo sampling as performed by the program xmcti (49). pK a values for the Schiff base that were determined in the dark are shown in parentheses (25).

ResiduepK(1/2), with ClpK(1/2), w./o. Cl
Arg103 11.011.0
Arg108 15.013.0
Asp141 11.712.7
Glu219 2.52.6
Asp238 4.8−2.0
Schiff base19.8 (8.9)7.3 (7.4)
Palmitate4.54.5