Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor

Insights into the Allosteric Response to Acidity by the Helicobacter pylori NikR Transcription Factor

“…Values higher than 1, despite HpNikR binding DNA with a 1:1 stoichiometry, are thought to be due to a cooperative two-step DNA-binding process. , We note that the Hill coefficients for several mutants are noticeably lower than those for WT HpNikR at pH 6.0. However, this has also been exhibited for other mutants at pH 7.6 and does not necessarily indicate that cooperativity has been affected. Nevertheless, the largely reduced affinities indicate that the histidine residues are important for the response to acidity.…”

“…We also attempted to investigate two lysine residues from the MBD (Lys64 and Lys140) that form a pocket around Trp54, since they were shown in our previous work to be part of the allosteric response to nickel . We were unable to examine the single alanine mutants, double alanine mutant, and double methionine mutant that we had previously studied, because each of them precipitated during exchange into the pH 6.0 buffer. Precipitation of these mutants at pH 6.0 implies that these lysine residues are important for HpNikR solubility at pH 6.0.…”

“…At low pH, while Trp54 does seem to be important for facilitating the formation of the DNA-bound state (albeit to a lesser extent than that observed at pH 7.6 with nickel), the linker residues do not appear to play a critical role. It has been speculated that the allosteric response of HpNikR to nickel binding might involve changes in internal dynamics, analogous to the responses of CzrA from Staphylococcus aureus and AdcR from Streptococcus pneumoniae. ,, For both those metalloregulators, zinc binding influences DNA binding in part by modulating the internal dynamics of the protein. , Examining how the internal dynamics of HpNikR change at lower pH levels would provide more information about the impact of acidity on this protein.…”

Beyond the Active Site: The addition of a remote loop reveals a new complex biological function for chitinase enzymes

“…To assess whether residues in the scaffold have long-range effects on rigidity and conformational modifications of loop II, we utilized rigidity transmission allostery (RTA) algorithms 16 . RTA is a computational approach based on mathematical rigidity theory 17,18 and graph theory, which analyzes long-range communication and allosteric networks within protein structures [19][20][21][22] . RTA measures whether local mechanical perturbation of rigidity at one site propagates and modifies rigidity and conformational degrees of freedom at distant site(s) in protein structure.…”

“…The RTA method utilizes graph and rigidity theory 17,18 techniques to identify allosteric networks within structures of proteins and protein complexes [19][20][21][22] . Starting with protein structures of Anc4 + Loop II and Anc5LoopI, we applied the RTA algorithm by sequentially perturbing rigidity of individual residues and monitoring changes in conformational degrees of freedom in loop II.…”