The viable defect sites of MCM-41 for the binding of the divalent nickel ions were determined from exploring the available pairs of vicinal and close non-vicinal silanol groups.
In this simple scheme, adapted for the NikR case, the binding of the ligand (nickel) induces (1) a change in the electrostatic potential of the protein (i.e., making the overall net charge of the protein more positive) and/or (2) a conformational change in the protein that leads to the formation of a structure that is complementary to the nik operon.
A possible mechanism explaining how the binding of excess nickel ions stabilizes the NikR−DNA complex could be the ability of excess nickel to further stabilize helix α3.
In general, the binding of excess nickel ions does not induce significant conformational changes in NikR, although the change in cell dimension for the NikR−DNA complex indicates that the crystal lattice can accommodate rearrangements.
The pH adjustment from pH 5.0 to pH 8.0, which was required for the binding of DIII to the nickel (Ni) IMAC resin, did not cause any significant change in protein profile and 3(b), Lane 4).
It shows very few bands in the silver-stain gel from material bound to the nickel-nitrilotriacetic acid (Ni-NTA) beads compared to the STOMP sample, confirming that nonspecific photo-tagging and nonspecific binding of proteins to the nickel affinity beads is minimal.
The binding of vanadium and nickel porphyrins to γ-Al2O3, SiO2-Al2O3 MoO3/andO3, NiO/Al2O3, and to Co- and Ni-Mo/Al2O3 catalysts in their oxide and sulfide forms, and their subsequent decomposition reactions when heated in nitrogen or exposed to hydrogen and thiophene in catalytic hydrodesulfurisation, have been studied by electron spin resonance.
X-ray elemental mapping profiles and graphical data recorded using transmission electron microscopy (TEM) showed binding of both nickel and lead to Bacillaceae bacteria, but most importantly preferential binding of lead; FTIR spectroscopy depicted involvement of active groups such as hydroxyl, amine, and carboxyl in the uptake of both metals.
The water meniscus acted as a nanoscale electrochemical cell, causing ionisation of the nickel surface and localised binding of the poly-histidine-tagged peptides and proteins.
As a potential mutagen, nickel can cause chromosome damage both in vitro and in vivo; and on a molecular basis, nickel is found to induce DNA damage (DNA strandbreaks and crosslinks, infidelity of DNA replication, inhibition of DNA repair, and the helical transition of B-DNA to Z-DNA) by binding of nickel ions to DNA and nuclear proteins.
