Real space refinement of neutron diffraction data from sperm whale carbonmonoxymyoglobin

Hanson, Jonathan C.; Schoenborn, Benno P.

doi:10.1016/0022-2836(81)90530-1

Cited by 163 publications

(95 citation statements)

References 25 publications

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“…In MbCO there are 98 atom-atom contacts (18). Thus, there are substantial differences in the number of van der Waals contacts between the heme and the amino acid residues of the protein when comparing the deoxy Mb to the Biophysics: Rousseau (19) and MbCO (18). Weak interactions between the heme and these residues or water molecules could perturb heme vibrational frequencies, and the frequency shifts we detect could reflect the differences between the MbCO heme contacts and the deoxy Mb contacts.…”

Section: Discussionmentioning

confidence: 93%

“…In addition, a water molecule, with partial occupancy, has been observed to lie over (-3.0 A) an a-methine bridge carbon atom in the deoxy crystal (17). In MbCO there are 98 atom-atom contacts (18). Thus, there are substantial differences in the number of van der Waals contacts between the heme and the amino acid residues of the protein when comparing the deoxy Mb to the Biophysics: Rousseau (19) and MbCO (18).…”

Section: Discussionmentioning

confidence: 99%

“…We obtain this distance from the reported core-size correlation (21) (23). We take the iron-to-center-of-pyrrole-nitrogenplane distance as 0.1 A, the value reported for MbCO from a neutron diffraction analysis (18). For (27,28).…”

Section: Discussionmentioning

confidence: 99%

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Metastable photoproducts from carbon monoxide myoglobin.

Rousseau¹,

Argade²

1986

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

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The photoproduct of carbon monoxide myoglobin generated at 4 K and lower has a resonance Raman spectrum characteristic of a high-spin heme but in which the high-frequency core size-sensitive lines are at lower frequency than those in the deoxy preparation. Such differences are not detected in the photoproduct generated at higher temperatures (50 K) or in that generated at room temperature with 10-nsec pulses. The data indicate that at the low temperature (4 K), the heme in the photoproduct is not fully relaxed, and from the data we conclude that the photoproduct has an expanded porphyrin core. We infer that the core size exceeds that in deoxymyoglobin because the rigid protein prevents the highspin iron atom from moving to its full out-of-plane displacement at the very low temperatures.To gain an understanding of the basic mechanisms of ligand association in heme proteins, the elementary steps in the ligand binding and release process must be uncovered. An approach to the elucidation of these steps is to photodissociate a bound ligand and follow the relaxation of the deoxy heme that has been generated. At room temperature the evolution of this photoproduct occurs over a wide temporal scale ranging from the subpicosecond absorption of the photon (1) to structural relaxation of the protein residues, which may occur on a time scale of 10s of microseconds (2,3). The specific relaxation pathway of the photoproduct is very complex and depends on the protein as well as the ligand.An alternate approach in the identification of the intermediate structures in the photoproduct relaxation is through the use of cryogenic temperatures, where metastable states may be isolated (4). By this method changes in the properties of photodissociated heme proteins were detected many years ago with optical absorption techniques (4-6), and studies of the metastable species have been since extended with many other techniques. The relationship between the structure, as inferred from the resonance Raman spectra, of the lowtemperature photoproduct and the transient photoproduct generated at 300 K was discussed recently, and in carbon monoxide hemoglobin, HbCO, it was observed that the differences in the Raman spectra between the stabilized photoproduct and the deoxy preparation at 80 K were the same as those obtained transiently at room temperature with 10-nsec pulses (7). These findings led us to investigate the low-temperature (1.6-100 K) photodissociation of carbon monoxide myoglobin, MbCO, with resonance Raman scattering to determine the properties of the unrelaxed photoproduct and its relationship to the room-temperature transient photoproduct. The experiments were carried out by freezing CO-bound Mb to low-temperature and then directing a laser beam on the sample. The laser photodissociates the CO, resulting in a deoxy heme trapped in the frozen protein matrix. At the lowest temperatures we find significant differences in the resonance Raman spectra ofthe photoproduct and the equilibrium deoxy species. We interpret these results...

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

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Metastable photoproducts from carbon monoxide myoglobin.

Rousseau¹,

Argade²

1986

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

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“…It has long been recognized that neutrons provide an excellent probe to use in analyzing the atomic and molecular structure of proteins (Schoenborn, 1969;Hanson & Schoenborn, 1981) and other large complexes like nerve membranes, retinal rods, ribosomes, viruses, chromatin, etc. (Schindler, Langer, Engelman & Moore, 1979;Jacrot, 1976).…”

Section: Introductionmentioning

confidence: 99%

Peak-shape analysis for protein neutron crystallography with position-sensitive detectors

Schoenborn¹

1983

Acta Cryst Sect A

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In neutron protein crystallography, the use of positionsensitive detectors controlled by a modern dataacquisition system permits new approaches to datacollection strategies. Instead of dealing with conventional scans, like the 0-20 scan, that provide an integrated intensity as a function of a rotational parameter, the computer-linked counter can be used to produce a three-dimensional reflection profile. As the crystal steps (AoJ) through a reflection, the observed data for each step are stored in an external memory as a function of extent in 20 and height (y) of a reflection. In this space, the reflection will be a three-dimensional distribution with dimensions determined by such basic geometrical conditions as A2, crystal size, mosaic spread, counter-resolution, and beam-collimation parameters. Knowledge of the interaction of these basic parameters will allow the design of optimal beam optics and will permit the delineation of the reflection from the background and permit, therefore, an accurate intensity determination.

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“…The linear least-square fitting of the plots for P. catodon MbCN yields the relaxation rate of 4.85 s -l ( T I = 206 ms) at 35°C for a proton spin which is 0.61 nm away from the heme iron and relaxes purely by paramagnetic dipolar relaxation. The distances between the heme iron and the protons of the IleFG5 and PheCDl residues in P. catodon MbCN have been estimated from their T I values and are compared with the corresponding distances calculated from the crystal coordinates of its carbonmonoxy form [36] in Table 4. The distances determined from T1 are smaller compared with the corresponding data calculated from the X-ray coordinates and there is a systematic error between them, i.e.…”

Section: Determination Of the Distance Between A Proton And The Heme mentioning

confidence: 99%

NMR study of Galeorhinus japonicus myoglobin

Yamamoto¹,

Iwafune²,

Nanai³

et al. 1991

European Journal of Biochemistry

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The molecular structure of the active site of myoglobin from the shark, Galeorhinusjaponicus, has been studied by 'H-NMR. Some hyperfine-shifted amino acid proton resonances in the met-cyano form of G. japonicus myoglobin have been unambiguously assigned by the combined use of various two-dimensional NMR techniques; they were compared with the corresponding resonances in Physter catodon myoglobin. The orientations of ThrElO and IleFG.5 residues relative to the heme in G. japonicus met-cyano myoglobin were semiquantitatively estimated from the analysis of their shifts using the magnetic susceptibility tensor determined by a method called MATDUHM ( Mol. Biol. 153, 117-1241. In spite of a substantial difference in shift between the corresponding amino acid proton resonances for the two proteins, the orientations of these amino acid residues relative to the heme in the active site of both myoglobins were found to be highly alike.NMR of paramagnetic hemoproteins has provided a wealth of information about the structural properties of their active sites [l-61. 'H-NMR resonances arising from heme peripheral groups and amino acid residues near the heme have been effectively used as a useful structural probe in the NMR study of hemoprotein because these resonances are resolved well outside the poorly resolved diamagnetic envelope in the chemical shift region of 0 -10 ppm and they are quite sensitive to the heme molecular environments. Additionally, the observation of the nuclear Overhauser effect (NOE) [7], even in the presence of paramagnetic relaxation, allows not only the signal assignments of hyperfine-shifted resonances [3, 8 -101 but also the determination of internal mobility of specific groups in the heme pocket [ l l -141.As far as the structural determination of the active site in hemoprotein is concerned, resonances of non-coordinated amino acid protons are of particular importance because of their extremely high sensitivity to the spatial position of the nuclei relative to the heme [I5 -171. Their hyperfine shifts are purely pseudo-contact shifts (dPJ and hence can be interpreted quantitatively in terms of the dipolar interaction between Correspondence to Y. Yamamoto,

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Real space refinement of neutron diffraction data from sperm whale carbonmonoxymyoglobin

Cited by 163 publications

References 25 publications

Metastable photoproducts from carbon monoxide myoglobin.

Metastable photoproducts from carbon monoxide myoglobin.

Peak-shape analysis for protein neutron crystallography with position-sensitive detectors

NMR study of Galeorhinus japonicus myoglobin

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