Viscosity-Dependent Dynamics of CO Rebinding to Microperoxidase-8 in Glycerol/Water Solution

Rebinding dynamics of NO to microperoxidase-8 probed by time-resolved vibrational spectroscopy

Femtosecond vibrational spectroscopy was used to probe the rebinding kinetics of NO to microperoxidase-8 (Mp), an ideal model system for the active site of ligand-binding heme proteins, including myoglobin and hemoglobin, after the photodeligation of MpNO in glycerol/water (G/W) solutions at 294 K. The geminate rebinding (GR) of NO to Mp in viscous solutions was highly efficient and ultrafast and negligibly dependent on the solution viscosity, which was adjusted by changing the glycerol content from 65% to 90% by volume in G/W mixtures. The kinetics of the GR of NO to Mp in viscous solutions was well represented by an exponential function with a time constant of ca. 11 ps. Although the kinetic traces of the GR of NO to Mp in solutions with three different viscosities (18, 81, and 252 cP) almost overlap, they show a slight difference early in the decay process. The kinetic traces were also described by the diffusion-controlled reaction theory with a Coulomb potential. Since the ligand is deligated in a neutral form, an ionic pair of NO(-) and Mp(+) may be produced before forming the Mp-NO bond by an electron transfer from Mp to NO as the deligated NO is sufficiently near to the Fe atom of Mp. The strong reactivity between NO and ferrous heme may arise from the Coulomb interaction between the reacting pair, which is consistent with the harpooning mechanism for NO binding to heme.

Dynamics of geminate rebinding of CO to cytochrome c in guanidine HCl probed by femtosecond vibrational spectroscopy

Femtosecond vibrational spectroscopy was used to probe the rebinding dynamics of CO to cytochrome c (Cytc) in 1.8 and 7 M guanidine HCl (GdnHCl) after photodeligation of the corresponding CO-bound protein in D2O buffer (pD = 7.4) at 283 K. Geminate rebinding (GR) dynamics of CO to the folded Cytc in 1.8 M GdnHCl (nCytc) is similar to that to chemically modified cytochrome c (cCytc), suggesting that the overall conformations of nCytcCO and cCytcCO are similar. About 86% of the dissociated CO molecules were geminately rebound to nCytc nonexponentially within 1 ns. The efficient GR of CO to the folded Cytc can be attributed to the organized protein matrix near the active site of nCytc that provides an efficient trap for the diffusing CO ligand after photodissociation. Although the concentration of nCytc did not affect its GR yield of CO, GR yield of CO to the unfolded Cytc in 7 M GdnHCl (uCytc) increased from 5 to 30% as the protein concentration increased from 0.3 to 9 mM. Time-resolved spectra of the (13)CO dissociated from both 9 mM nCytc(13)CO and 9 mM uCytc(13)CO showed a growing band with a peak at 2090 cm(-1) on the picosecond time scale, which was assigned to (13)CO in D2O solvent. At 1 ns, the fraction of the CO band in the solvent was about 10% of the nascent photodeligated protein in nCytc and more than 50% in the concentrated uCytc. Whereas a small opening in the active site of nCytc is responsible for the ultrafast escape of CO to solution in the folded protein, a large fraction of the CO escape to the solvent in uCytc results from the denatured structure of the active site in the unfolded protein. The spectrum of the CO dissociated from the concentrated uCytcCO contained a band that decayed as efficiently as that for the folded protein, suggesting that some fraction of uCytcCO might form aggregates even in 7 M denaturant, such that the aggregate acts as an efficient trap for the diffusing CO after deligation. No hint of precipitate in the concentrated uCytcCO and protein refolding upon dilution of the GdnHCl indicate that the aggregate does not grow continuously but remains as a soluble oligomer. The delayed appearance of the solvated CO and the inefficient GR of CO in uCytcCO suggest that the monomeric unfolded CytcCO so loosely arranged that the protein matrix cannot trap CO efficiently but the bound CO is still buried within hydrophobic residues even under the harsh denaturation condition.

Effect of DNA binding on geminate CO recombination kinetics in CO-sensing transcription factor CooA

Carbon monoxide oxidation activator (CooA) proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding in two CooA homologues, Rhodospirillum rubrum (RrCooA) and Carboxydothermus hydrogenoformans (ChCooA). The effects of DNA binding and the truncation of the DNA-binding domain on the CO geminate recombination kinetics were specifically investigated. The CO rebinding kinetics in these CooA complexes take place on ultrafast time scales but remain non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the time scale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in the CooA proteins relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Comparison of the CO rebinding kinetics of RrCooA, truncated RrCooA, and DNA-bound RrCooA proteins reveals that the uncomplexed and inherently flexible DNA-binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases, and the distribution of the conformations available in the heme domain becomes restricted. The kinetic studies also offer insights into how the architecture of the heme environment can tune entropic barriers in order to control the geminate recombination of CO in heme proteins, whereas spin selection rules play a minor or non-existent role.