Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6

Zymography assisted quick purification, characterization and inhibition analysis of K. pneumoniae alkaline phosphatase by mercury and thiohydroxyal compounds

In-gel hydrolysis of para-nitrophenyl phosphate (p-NPP) to yellow colored para-nitrophenol was used to locate precisely the K. pneumoniae alkaline phosphatase (Kp-ALKP) on 7% native PAGE. Subsequent removal of the yellow-stained band and electroelution yielded a 54 kDa, Kp-ALKP with K_m, V_max and k_cat values of (0.7 ± 0.02) mM, (80 ± 4.5) μmol min^-1 and (39.2 ± 2.2) × 10⁴ s^-1 respectively for p-NPP. Kp-ALKP was optimally active at 70 °C and pH 7.2 that was activated by Mg²⁺, Ca²⁺, Co²⁺ and inhibited by EDTA, PO₄, Pb²⁺, Cu²⁺ and Hg²⁺. The enzyme was trypsin resistant and retained 75% activity in presence of 10 mM PO₄ and 65% activity at 3 mM Hg²⁺ showing it's PO₄^3- irrepressibility and Hg²⁺-tolerance. Molecular dynamics simulation revealed increased structural stability of Kp-ALKP at 70 °C that accounts for it's optimal temperature. Zymography revealed that both DTT and β-mercaptoethanol induced activity loss accompanied by mobility retardation of Kp-ALKP on 7% native PAGE. These results and in Silico analysis shows that both DTT and βME reduce the C³⁰⁸-C³⁵⁸ disulfide bond, leading to an open conformation of the enzyme. However, Hg²⁺ had negligible effect on the in-gel mobility of Kp-ALKP indicating it's plausible non-covalent interaction with surface-accessible amino-acids without significant conformational change. For the first time our study reveals the zymography as an easy, inexpensive and convenient tool for quick purification, characterization and conformational analysis of K. pneumoniae alkaline phosphatase.

DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method

To extend the value of biosensor-SPR in the characterization of DNA recognition by nucleoproteins, we report a comparative analysis of DNA-facilitated target search by two ETS-family transcription factors: Elk1 and ETV6. ETS domains represent an attractive system for developing biosensor-based techniques due to a broad range of physicochemical properties encoded within a highly conserved DNA-binding motif. Building on a biosensor approach in which the protein is quantitatively sequestered and presented to immobilized cognate DNA as nonspecific complexes, we assessed the impact of intrinsic cognate and nonspecific affinities on long-range (intersegmental) target search. The equilibrium constants of DNA-facilitated binding were sensitive to the intrinsic binding properties of the proteins such that their relative specificity for cognate DNA were reinforced when binding occurred by transfer vs. without nonspecific DNA. Direct measurement of association and dissociation kinetics revealed ionic features of the activated complex that evidenced DNA-facilitated dissociation, even though Elk1 and ETV6 harbor only a single DNA-binding surface. At salt concentrations that masked the effects of nonspecific pre-binding at equilibrium, the dissociation kinetics of cognate binding were nevertheless distinct from conditions under which nonspecific DNA was absent. These results further strengthen the significance of long-range DNA-facilitated translocation in the physiologic environment.