Water Penetration and Binding to Ferric Myoglobin

Cao, Wenxiang; Christian, James F.; Champion, P. M.; Rosca, and Florin; Sage, J. Timothy

doi:10.1021/bi010067e

Cited by 82 publications

(181 citation statements)

References 70 publications

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“…where (1 Ϫ n w ) is the distal water molecule vacancy factor and kЈ in CO , the microscopic bimolecular rate constant, was close to the diffusion-controlled value for heme-ligand binding, ϳ1 ϫ 10 8 M Ϫ1 s Ϫ1 (43,44). We now report that the agreement observed previously at neutral pH between obs Ϫ1 and the kЈ value calculated from water occupancy extends over the pH range examined in the present study, pH 4.3-9.4 (see Table 2).…”

Section: Discussionmentioning

confidence: 56%

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: Discussionmentioning

confidence: 56%

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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“…When BHA binds it stabilizes the water molecule and suppresses the 750 cm −1 mode. 43,44 A direct comparison of the open band coherence spectra of ferric species of Mb and HRP with and without BHA is shown in the upper three panels of Figure 3 (measured at 418 nm). The frequencies of Mb and HRP are summarized in Table 1 and Table 2.…”

Section: Resultsmentioning

confidence: 99%

“…To interrogate the five-coordinate species of the native enzyme, which probably absorbs near 390 nm 43 (as seen in Figure 1C), we also carried out coherence measurements with 405 nm excitation (lower panels of Figure 3). The strongest oscillations in the HRP spectrum appear at 77 and 196 cm −1 , which is conspicuously different from the data recorded with 418 nm excitation.…”

Section: Resultsmentioning

confidence: 99%

“…As can be seen in Figure 1C, a five-coordinate ferric Mb absorption spectrum, with no distal water, has been measured for the H64L mutant. 43,44 It displays a broad Soret band that peaks near 390 nm, which is suggestive of the possibility that the shoulder near 390 nm in native HRP represents the population of the five-coordinate ferric heme, while the peak near 403 nm reflects the presence of water-bound six-coordinate material. The five/six-coordinate equilibrium is shifted by the addition of benxhydroxamic acid (BHA), a substrate-like inhibitor of HRP, which favors a six-coordinated water-bound species.…”

Section: Discussionmentioning

confidence: 99%

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Coherence Spectroscopy Investigations of the Low-Frequency Vibrations of Heme: Effects of Protein-Specific Perturbations

et al. 2008

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Femtosecond coherence spectroscopy is used to probe the low-frequency (20-200 cm −1 ) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the lowfrequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above ~50 cm −1 and very weak activity below ~50 cm −1 . Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm −1 , while HRPCN displays a strong oscillation at higher frequency (96 cm −1 ) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays lowfrequency coherence spectra that contain strong modes near 30 and 80 cm −1 , probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm −1 that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T ≲ 50 K, as pure dephasing processes due to the protein-solvent phonon bath are frozen out.

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“…The H64L mutation replaces the E7 distal histidine with a leucine resulting in a DHP that is apolar and in loss of the steric and dynamic contributions of the large mobile imidazole side chain. The 64L side chain has been shown to be essentially neutral with respect to steric hindrance (Quillin et al, 1993) and in the H64L single mutant eliminates the entry of water into the DHP subsequent to ligand photodissociation (Cao et al, 2001). The H64L series of double mutants in which the second mutation is at the residue 68(E11) site has been shown to be an effective series for exposing the role of the E11 side chain in modulating the CO recombination in the absence of the strong influence of the H64 side chain and of the H64 mediated entry of water into the vacated DHP (Dantsker et al, 2005a).…”

Section: Examples Illustrating the New Formalismmentioning

confidence: 99%

Ligand recombination and a hierarchy of solvent slaved dynamics: The origin of kinetic phases in hemeproteins

Samuni

Dantsker

Roche

et al. 2007

Gene

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Ligand recombination studies play a central role both for characterizing different hemeproteins and there conformational states but also for probing fundamental biophysical processes. Consequently, there is great importance to providing a foundation from which one can understand the physical processes that give rise to and modulate the large range of kinetic patterns associated with ligand recombination in myoglobins and hemoglobins. In this work, an overview of cryogenic and solution phase recombination phenomena for COMb is first reviewed and then a new paradigm is presented for analyzing the temperature and viscosity dependent features of kinetic traces in terms of multiple phases that reflect which tier(s) of solvent-slaved protein dynamics is(are) operative on the photoproduct population during the time course of the measurement. This approach allows for facile inclusion of both ligand diffusion among accessible cavities and conformational relaxation effects. The concepts are illustrated using kinetic traces and MEM populations derived from the CO recombination process for wild type and mutant myoglobins either in sol-gel matrices bathed in glycerol or in trehalose derived glassy matrices. Keywords myoglobin; carbonmonoxide; sol-gel; trehalose; geminate recombination; Xe cavities Ligand recombinationStudies utilizing ligand recombination subsequent to photodissociation continue to provide basic insight into the functional properties of the many varieties of hemoglobin and myoglobin like molecules that are found through out the animal and plant worlds. Such studies are significant for several reasons all of which stem from the sensitivity of the recombination process to global structure, site specific effects and dynamics. Ligand recombination data at ambient temperatures are often useful in establishing potential functions of a newly described hemeproteins as well as routinely being used in exploring structure-function correlations in well characterized molecules such as human hemoglobin and mammalian myoglobins. Ligand recombination in myoglobin in particular has provided biophysics with a process that has allowed for dramatic advances in understanding: i) protein dynamics, ii) the role of protein dynamics in modulating protein reactivity and iii) the interplay between the dynamical properties of the protein and the surrounding solvent. Despite the heavy focus on understanding Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author ManuscriptGene. Author manuscript; available in PMC 2008 August 15. Published in final edited form as:Gene. 200...

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Water Penetration and Binding to Ferric Myoglobin

Cited by 82 publications

References 70 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

Coherence Spectroscopy Investigations of the Low-Frequency Vibrations of Heme: Effects of Protein-Specific Perturbations

Ligand recombination and a hierarchy of solvent slaved dynamics: The origin of kinetic phases in hemeproteins

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