Rebinding and relaxation in the myoglobin pocket

Ansari, Anjum; Berendzen, Joel; Braunstein, D.; Cowen, B. R.; Frauenfelder, Hans; Hong, Mineui; Iben, Icko; Johnson, Jerald B.; Ormos, Pál; Sauke, Todd B.; Scholl, Reinhard; Schulte, Alfons; Steinbach, Peter; Vittitow, J.; Young, Robert D.

doi:10.1016/0301-4622(87)80034-0

Cited by 366 publications

(475 citation statements)

References 45 publications

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“…The CO stretching frequency at equilibrium is shown in the top spectrum. Difference spectra are shown at 125 µs, 250 µs, 375 µs, 500 µs, 1 ms, and 4 ms. quency of 507 cm -1 and corresponding CO stretching frequency of 1945 cm -1 are consistent with a histidine-ligated species (8,15,(29)(30)(31). Since the proximal histidine H93 is absent, there are two strong candidates for histidine ligation: H64 on the distal side and H97 on the proximal side.…”

Section: Discussionsupporting

confidence: 56%

A Photolysis-Triggered Heme Ligand Switch in H93G Myoglobin

et al. 2001

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Resonance Raman spectroscopy and step-scan Fourier transform infrared (FTIR) spectroscopy have been used to identify the ligation state of ferrous heme iron for the H93G proximal cavity mutant of myoglobin in the absence of exogenous ligand on the proximal side. Preparation of the H93G mutant of myoglobin has been previously reported for a variety of axial ligands to the heme iron (e.g., substituted pyridines and imidazoles) [DePillis, G., Decatur, S. M., Barrick, D., and Boxer, S. G. (1994) J. Am. Chem. Soc. 116,[6981][6982]. The present study examines the ligation states of heme in preparations of the H93G myoglobin with no exogenous ligand. In the deoxy form of H93G, resonance Raman spectroscopic evidence shows water to be the axial (fifth) ligand to the deoxy heme iron. Analysis of the infrared C-O and Raman Fe-C stretching frequencies for the CO adduct indicates that it is six-coordinate with a histidine trans ligand. Following photolysis of CO, a time-dependent change in ligation is evident in both step-scan FTIR and saturation resonance Raman spectra, leading to the conclusion that a conformationally driven ligand switch exists in the H93G protein. In the absence of exogenous nitrogenous ligands, the CO trans effect stabilizes endogenous histidine ligation, while conformational strain favors the dissociation of histidine following photolysis of CO. The replacement of histidine by water in the five-coordinate complex is estimated to occur in <5 µs. The results demonstrate that the H93G myoglobin cavity mutant has potential utility as a model system for studying the conformational energetics of ligand switching in heme proteins such as those observed in nitrite reductase, guanylyl cyclase, and possibly cytochrome c oxidase.

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Section: Discussionsupporting

confidence: 56%

A Photolysis-Triggered Heme Ligand Switch in H93G Myoglobin

et al. 2001

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“…39 Under normal conditions in WT, A 1 is the dominant conformer, A 0 is a minor presence, and A 2 -A 3 are hardly present. 39 At low pH, the relative population of A 0 increases relative to that of A 1 . It has been suggested by several authors 40 that, among other differences, the A 1 state is characterized by H64 down in the heme pocket and A 0 is characterized by H64 up out of the pocket.…”

Section: Methodsmentioning

confidence: 99%

Vibrational Dynamics of Carbon Monoxide at the Active Site of Myoglobin: Picosecond Infrared Free-Electron Laser Pump-Probe Experiments

Hill¹,

Tokmakoff²,

Peterson³

et al. 1994

J. Phys. Chem.

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Picosecond mid-IR pump-probe measurements of vibrational relaxation (VR) of CO bound to the active sites of wild-type and mutant myoglobins (Mb) reveal that an approximately linear relationship exists between the protein matrix-induced CO frequency shift and the VR rate. This relation parallels a similar linear relationship seen in a series of heme model compounds where Fe was replaced by Ru and Os. The VR rate of CO in the Mb is sensitive only to the magnitude of protein-induced carbonyl frequency shifts and apparently is not sensitive to the specific details of how the shift is induced, e.g., hydrogen bonding to CO or electrostatic interactions in the heme pocket. CO VR is insensitive to substantial changes in protein structure that do not affect the CO vibrational frequency. These observations suggest that the mechanism of carbon monoxide VR in heme proteins such as Mb occurs by through-π-bond anharmonic coupling, which, as shown in prior work, is also the dominant coupling in the model compounds. The experiments indicate that differing protein structures influence VR of CO bound at the active site not by opening and closing channels for vibrational energy flow from CO to the protein but by affecting the rate of energy flow from CO to heme. The rates are determined by the extent of back-bonding, which determines the magnitude of through-π-bond anharmonic coupling between CO and heme. The back-bonding and, therefore, the extent of anharmonic coupling are influenced by the electric fields in the heme pocket, which likely differ in the proteins studied here.

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“…Carbonmonoxy-myoglobin (MbCO) has been extensively studied both experimentally [47][48][49][50][51][52][53][54][55][56] and computationally. [57][58][59][60] Myoglobin (Mb) is a small globular heme protein weighing approximately 17 kDa that is found in mammalian muscle tissue.…”

Section: D Vibrational Echo Experiments a Illustration Of The mentioning

confidence: 99%

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

148

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Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.

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Rebinding and relaxation in the myoglobin pocket

Cited by 366 publications

References 45 publications

A Photolysis-Triggered Heme Ligand Switch in H93G Myoglobin

A Photolysis-Triggered Heme Ligand Switch in H93G Myoglobin

Vibrational Dynamics of Carbon Monoxide at the Active Site of Myoglobin: Picosecond Infrared Free-Electron Laser Pump-Probe Experiments

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

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