Two phenylalanine residues from TmPurQ, Phe51 and Phe110, proposed to be the entrance of the ammonia channel and located in first shell of the TmPurQ active site, are also found at this interface.
Clams are laid in first, shells opened to the katsuobushi-rich stock.
Analysis of >2800 Co-hArgI variants revealed a sizable number of amino acid substitutions in second-shell residues that confer appreciable catalytic activity at physiological pH, a few even resulting in a higher kcat/ Km relative to that of the parental enzyme.
Of >2800 double mutants of first- and second-shell residues analyzed, we found more than 80 unique amino acid substitutions, of which four were in first-shell residues.
This is reflected in change in first-shell oxygen distance (Sn−O) from ±2.05 Å in SnO2 to 1.95 Å in 5 Sn-β, which is fully consistent with a change in geometry from octahedral to tetrahedral.
The ions located in the first shell exhibit an extremely long residence, in the order of 2.5 ns, while ions in the second shell dwelled in the layer with time constant of ∼200 ps.
The intensity of the electrostatic potential in the second shell is in the order of 4 kBT, explaining the restriction on the translational motion of the ions at that distance from the protein.
They found that nearly all EMI+ ions show a concentrated orientation in the first shell, i.e., parallel to the surface, but a nearly isotropic orientation in the second shell, as shown in Fig. 12c.
Structures in the second shell are compared in batches of 100, selecting those with the strongest connections first.
The minimum in the first shell (In O) and the second shell (In–In) bond distances coincides with the maximum in mobility and can be a contributing factor to a small effective mass.
This is an important finding as it also influences ordering in the second shell as will be discussed in detail below.
