Figure 1.
The electrostatic iso-potential surfaces of Apo-CaB.
The electrostatic potential as calculated for the protein in ionic strength of 150 mM. The dielectric constant of the protein was set as εp = 2 and εw = 78. (A) 1 kBT surface, (B) 4 kBT surface and (C) 10 kBT surface.
Figure 2.
The variation of the Ca2+ ion's diffusion coefficient in the successive shells of Apo-CaB.
The bulk columns (either from simulations or measured experimentally) refer to Ca2+ in protein-free solutions. * The calculated value is comparable to that of a globular protein of the same size [24], [25]. ** The calculated value is comparable with the experimental diffusion coefficient of free Ca2+ ions [26].
Table 1.
Residence time of Ca2+ ions near the CaB protein.
Figure 3.
Ca2+ distribution around Apo-CaB.
A histogram of the percentage of time a Ca2+ ion spends at a specific distance from the Apo-CaB, out of the total time it is within a distance of 1.2 nm from the protein (black curve). The accumulation of the histogram is presented in the red curve.
Figure 4.
The main frame kinetics of Ca2+ ions residence in the 2nd (top panel) and 3rd (bottom panel) shell of Apo-CaB. The inset depicts the dynamics on a semi log scale. The residence time decay curves are in black. One exponential fits are in green and a bi-exponential fits are in blue.
Figure 5.
The diffusion mobility of Ca2+ ions on the surface of the protein.
The figure relates the translational motion of Ca+2 ions expressed by the MSD of a Ca2+ ion as a function of the time the ion remained with the first (solid line) or the second (dashed line) shell of Apo-CaB. The translational motion of the ion was corrected for the rotation and translation of the protein. Straight lines indicate events where MSD > = 1 nm2.
Figure 6.
The structure of Holo Calbindin D9k.
The CaB (backbone cartoon) with two bound Ca2+ ions (blue VDW) as taken from the crystal structure 3ICB. The binding residues are denoted as lines. Protein atoms closer than 0.3 nm are denoted as CPK (oxygens in red, carbons in cyan). Frame A depicts the whole protein. Frame B depicts the binding sites with the names of the binding residues. The E60 hydrogen bonded water oxygen that coordinate site I Ca2+ is also shown (in CPK) along with the relevant distances.
Table 2.
Total binding times, primary hit count and secondary hit count of Ca2+ ion to Apo-CaB residues, calculated from ten 100 ns WT and ten 100 ns E60D simulations.
Figure 7.
The Ca2+ binding characteristics of specific anionic residues Associated with the Ca+2 binding sites.
(A) Total binding time, (B) number of primary hits and (C) number of secondary hits. Data is presented for the WT (blue) and E60D (red).
Figure 8.
Number of Ca2+ transfers between residues 58 and 60 with residues 54 and 65. The top panel counts the Ca2+ transfer between the whole residues where the bottom panel counts the Ca2+ transfer between the carboxylates. All events, in any direction were counted for both the WT (blue) and E60D (red) simulations.
Table 3.
Simulations' details and composition.