One can specify the cation type, the number of cation positions expected to bind to the query structure, the minimal distance between predicted cations, width of the cubic grid, the ionic radius of the cation or use default values.
The default number of predicted ions is calculated on the basis of the number of residues in the target structure; the minimal default distance between predicted cations is the one observed in known structures (Supplementary Table S1), and the default width of the cubic grid C is 0.5Å.
Thus, to distinguish between the two evolutionary scenarios, we constructed a phylogenetic tree of the catalytic subunits of the V- and F-ATPase and superimposed on it the known or predicted cation specificity, based on the available experimental data and presence or absence of the complete set of Na+-binding ligands (Fig. 5).
There is also no evidence of a change in major groove dimension because of the collapse of the phosphate backbone onto the tethered cation, as has been predicted for divalent cations as a source of DNA bending.
This crude sampling (see Figure 8A and Supplementary Movie SI1) reveals that it is at the same time possible to shift the maximum predicted density for cations in the pore and to reduce energy barriers between energy wells by choosing an appropriate sequence of orientations for the Oγ Hγ dipole of Ser6′ (Supplementary Figure S9A) as the ion flows down the pore.
According to the computational results, the ligand conformational transition is predicted, under an excess of sodium cations, between [Na2(H2L)]6– and [Na3 HL ]6–.
In the case of the V1F mutant, one cation-pi interaction was predicted between Phe1 and Arg344.
This reveals that the macroscopic zero shear rate viscosities combined with the Stokes Einstein equation would not correctly predict the values of the cation diffusion coefficients.
The optimized networks were able to precisely predict the concentrations of the three cations in synthetic mixtures.
The czcABCRD operon encoding a cation-proton antiporter, which is responsible for cobalt, zinc, and cadmium resistances [ 98], was predicted in the genomes of GP72 and Pf-5.
