Effect of DNA Binding on Geminate CO Recombination Kinetics in CO-sensing Transcription Factor CooA

Abstract

Background: CooA proteins are CO-sensing transcription factors. Results: DNA binding to CooA-CO speeds up geminate rebinding of CO. Conclusion: DNA binding reduces heme heterogeneity and CO rebinding barrier. This along with distal pocket trapping maintains the "on" state long enough for transcription to take place. Significance: This work provides a deeper understanding of the allosteric transition in CooA proteins.

Dynamics of the Heme-binding Bacterial Gas-sensing Dissimilative Nitrate Respiration Regulator (DNR) and Activation Barriers for Ligand Binding and Escape

“…These findings are also in agreement with similar experiments in C. hydrogenoformans CooA, concluding no enthalpy barrier from the distal heme pocket (29). In the latter work, a modest temperature dependence was attributed to changes in the distribution of the heme configuration, whereas in the systems studied in our work, the temperature predominantly influences the ligand escape yield.…”

“…The decay of the amplitude of the transient spectra implies that CO partially recombines on the picosecond-nanosecond time scale. The kinetics of rebinding are qualitatively similar to those of CooA (29,30), but the amplitude of the recombination phase is much lower and as much as ϳ35% of the dissociated CO escapes the heme pocket. The rebinding kinetics can be well described by two exponential phases of ϳ100 (30%) and ϳ900 (35%) ps.…”

“…3B, inset) and from Carboxydothermus hydrogenoformans (29). Unfortunately in CooA, a quantitative analysis similar to the one performed for DNR is complicated by the very low escape yield of CO.…”

“…Effect of DNA Binding on Ligand Recombination-Recent work by Champion and co-workers (29) has shown that binding of DNA to the CooA-CO complex leads to kinetically more homogeneous heme-CO rebinding, an observation that was interpreted in terms of DNA-induced stabilization of a specific protein configuration. For the DNR-NO complex, in the absence or presence of bound DNA, we observed identical, mono-exponential, kinetics within experimental error ( Fig.…”

Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c

“…Doming is typically observed in oxygen storage or transport proteins such as hemoglobin (7,8) and myoglobin (9). Moreover, the coupling of heme doming to the protein conformational substates has been shown to be functionally significant in a variety of heme protein systems (10)(11)(12). However, heme ruffling, which is the primary topic of this paper, is the dominant OOP deformation found in c-type cytochromes (4-6, 13) and nitrophorins (14)(15)(16), which are involved in electron and NO transport, respectively.…”