Relaxation dynamics of myoglobin in solution

Tian, Wei; Sage, J. Timothy; Šrajer, V.; Champion, P. M.

doi:10.1103/physrevlett.68.408

Cited by 129 publications

(209 citation statements)

References 19 publications

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“…These observations led us to conclude that the large effect of the water entry signal noted above on the geminate time scale evolution of the visible band spectrum probably interfered with an accurate analysis of changes in the geminate yield in terms of changes in the underlying geminate rebinding and escape rate constants. Moreover, because of the well known nonexponential character of the room temperature geminate rebinding kinetics of MbCO, the kinetic treatment in terms of a single geminately dissociated ligand state used here clearly oversimplified a complex process (40). In any event, the important quantity in the present kinetic analysis was the geminate yield, and the g values found here (Table 2) were in reasonable agreement with those obtained from Soret absorption photolysis measurements (31).…”

Section: Effect Of Ph On Observed Geminate and Bimolecular Recombinatsupporting

confidence: 82%

The pH Dependence of Heme Pocket Hydration and Ligand Rebinding Kinetics in Photodissociated Carbonmonoxymyoglobin

Esquerra

Jensen

Bhaskaran

et al. 2008

Journal of Biological Chemistry

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We monitored the occupancy of a functionally important non-coordinated water molecule in the distal heme pocket of sperm whale myoglobin over the pH range 4.3-9.4. Water occupancy was assessed by using time-resolved spectroscopy to detect the perturbation of the heme visible band absorption spectrum caused by water entry after CO photodissociation (Goldbeck, R. A., Bhaskaran, S., Ortega, C., Mendoza, J. L., Olson, J. S., Soman, J., Kliger, D. S., and Esquerra, R. M. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 1254 -1259). We found that the water occupancy observed during the time interval between ligand photolysis and diffusive recombination decreased by nearly 20% as the pH was lowered below 6. This decrease accounted for most of the concomitant increase in the observed CO bimolecular recombination rate constant, as the lower water occupancy presented a smaller kinetic barrier to CO entry into the pocket at lower pH. These results were consistent with a model in which the distal histidine, which stabilizes the water molecule within the distal pocket by accepting a hydrogen bond, tends to swing out of the pocket upon protonation and destabilize the water occupancy at low pH. Extrapolation of this model to lower pH suggests that the additional increase in ligand association rate constant observed previously in stopped-flow studies at pH 3 may also be due in part to reduced distal water occupancy concomitant with further His 64 protonation and coupled protein conformational change.

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Section: Effect Of Ph On Observed Geminate and Bimolecular Recombinatsupporting

confidence: 82%

The pH Dependence of Heme Pocket Hydration and Ligand Rebinding Kinetics in Photodissociated Carbonmonoxymyoglobin

Esquerra

Jensen

Bhaskaran

et al. 2008

Journal of Biological Chemistry

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“…The value of k 0 is 1.5 ϫ 10 11 s Ϫ1 , which is two orders of magnitude larger than what is found for Mb (23,25). This strongly suggests that, in addition to the distal enthalpic barrier (H 0 Ϸ 7 kJ/mol), there are significant entropic barriers that are presented by the protein, which are absent in the model systems.…”

Section: Discussionmentioning

confidence: 57%

“…Kinetic studies of MbCO have suggested that the enthalpic barrier for CO binding to the heme in Mb is Ϸ18 kJ/mol near room temperature (23,24), whereas analysis of kinetic data below the glass transition (T Ͻ T g ) suggest that the average barrier is Ϸ11 kJ/mol (25). In either temperature range, the corresponding Arrhenius prefactor for MbCO is found to be ϳ10 9 s Ϫ1 (1,(23)(24)(25).…”

mentioning

confidence: 99%

“…In either temperature range, the corresponding Arrhenius prefactor for MbCO is found to be ϳ10 9 s Ϫ1 (1,(23)(24)(25). The increase in the enthalpic rebinding barrier for T Ͼ T g is thought to be due to the relaxation (or diffusion) of Mb from its bound state conformation (frozen in at low temperature) to its unbound conformation after ligand photolysis (2,19,22).…”

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confidence: 99%

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Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates

Ionascu

Gruia

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

195

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We present temperature-dependent kinetic measurements of ultrafast diatomic ligand binding to the ''bare'' protoheme (L 1-FePPIX-L 2, where L1 ‫؍‬ H2O or 2-methyl imidazole and L2 ‫؍‬ CO or NO). We found that the binding of CO is temperature-dependent and nonexponential over many decades in time, whereas the binding of NO is exponential and temperature-independent. The nonexponential nature of CO binding to protoheme, as well as its relaxation above the solvent glass transition, mimics the kinetics of CO binding to myoglobin (Mb) but on faster time scales. This demonstrates that the nonexponential kinetic response observed for Mb is not necessarily due to the presence of protein conformational substates but rather is an inherent property of the solvated heme. The nonexponential kinetic data were analyzed by using a linear coupling model with a distribution of enthalpic barriers that fluctuate on slower time scales than the heme-CO recombination time. Below the solvent glass transition (T g Ϸ 180 K), the average enthalpic rebinding barrier for H 2O-PPIX-CO was found to be Ϸ1 kJ/mol. Above T g, the barrier relaxes and is Ϸ6 kJ/mol at 290 K. Values for the first two moments of the heme doming coordinate distribution extracted from the kinetic data suggest significant anharmonicity above T g. In contrast to Mb, the protoheme shows no indication of the presence of ''distal'' enthalpic barriers. Moreover, the wide range of Arrhenius prefactors (10 9 to 10 11 s ؊1 ) observed for CO binding to heme under differing conditions suggests that entropic barriers may be an important source of control in this class of biochemical reactions.heme proteins

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“…The results can be crosschecked by noting that the sum of the two contributions H BA = H P + H D ≈ 20 kJ/mol is very close to independent measurements 80,81 of the MbCO rebinding barrier (H BA = 18 ± 2 kJ/mol) and to the room temperature barrier predicted by an early model. 32,80 Transient absorption spectra of photolyzed FePPIX-CO. Panel A shows a sample in 80% (v/ v) glycerol solution. Panel B shows data for a sample in 1% (w/v) CTAB solution, the dashed line in B is the scaled equilibrium difference spectra between the deoxy and CO bound sample (from Figure 1B Table 1.…”

Section: Proximal and Distal Contributions To The Rebinding Barriermentioning

confidence: 99%

CO Rebinding to Protoheme: Investigations of the Proximal and Distal Contributions to the Geminate Rebinding Barrier

et al. 2005

J. Am. Chem. Soc.

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The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imidazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imidazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, H p , to be 11 ± 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: ΔG D ≈ 12 ± 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin (~3 kJ/mol), then lead to a distal pocket enthalpic barrier of H D ≈ 9 ± 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements (Tian et al. Phys. Rev. Lett. 1992, 68, 408) of the enthalpic MbCO rebinding barrier (18 ± 2 kJ/mol).

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Relaxation dynamics of myoglobin in solution

Cited by 129 publications

References 19 publications

The pH Dependence of Heme Pocket Hydration and Ligand Rebinding Kinetics in Photodissociated Carbonmonoxymyoglobin

The pH Dependence of Heme Pocket Hydration and Ligand Rebinding Kinetics in Photodissociated Carbonmonoxymyoglobin

Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates

CO Rebinding to Protoheme: Investigations of the Proximal and Distal Contributions to the Geminate Rebinding Barrier

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