Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin

Chu, K.R.; Vojtchovský, Jaroslav; McMahon, Benjamin H.; Sweet, Robert M.; Berendzen, Joel; Schlichting, Ilme

doi:10.1038/35002641

Cited by 245 publications

(231 citation statements)

References 28 publications

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“…Two propanoate side chains of all tetrapyrrole chromophores in allophycocyanin are accessible from the surface of the protein molecule (51). The two propanoic side chains of the heme in cytochromes (52), myoglobin (53), and hemoglobin (54) also are exposed from the heme pocket, but those of mitochondrial cytochrome c are buried in a crevice (50). In this regard, PhyB appears to resemble the mitochondrial cytochrome c. The phytochrome protein seems therefore to differ from other Table 1).…”

Section: Discussionmentioning

confidence: 99%

In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore

Hanzawa

Inomata

Kinoshita

et al. 2001

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

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Phytochrome B (PhyB), one of the major photosensory chromoproteins in plants, mediates a variety of light-responsive developmental processes in a photoreversible manner. To analyze the structural requirements of the chromophore for the spectral properties of PhyB, we have designed and chemically synthesized 20 analogs of the linear tetrapyrrole (bilin) chromophore and reconstituted them with PhyB apoprotein (PHYB). The A-ring acts mainly as the anchor for ligation to PHYB, because the modification of the side chains at the C2 and C3 positions did not significantly influence the formation or difference spectra of adducts. In contrast, the side chains of the B-and C-rings are crucial to position the chromophore properly in the chromophore pocket of PHYB and for photoreversible spectral changes. The side-chain structure of the D-ring is required for the photoreversible spectral change of the adducts. When methyl and ethyl groups at the C17 and C18 positions are replaced with an n-propyl, n-pentyl, or n-octyl group, respectively, the photoreversible spectral change of the adducts depends on the length of the side chains. From these studies, we conclude that each pyrrole ring of the linear tetrapyrrole chromophore plays a different role in chromophore assembly and the photochromic properties of PhyB.

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Section: Discussionmentioning

confidence: 99%

In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore

Hanzawa

Inomata

Kinoshita

et al. 2001

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

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“…The Inset shows a cross section through part of Mb with a heme group situated in the heme cavity and a major cavity called Xe-1 and labeled D. Small ligands such as carbon monoxide (CO) bind covalently at the heme iron. We denote the position of the CO by S if it is in the solvent, by A if it is bound covalently to the iron, by B if it is still in the heme pocket but not covalently bound (9)(10)(11), and by D (11)(12)(13) (5,(14)(15)(16). Fluctuations between these substates are denoted by k 01 (T) and k 13 (T).…”

Section: The Dichotomy Of Motionsmentioning

confidence: 99%

Slaving: Solvent fluctuations dominate protein dynamics and functions

Fenimore

Frauenfelder

McMahon

et al. 2002

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

640

558

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Protein motions are essential for function. Comparing protein processes with the dielectric fluctuations of the surrounding solvent shows that they fall into two classes: nonslaved and slaved. Nonslaved processes are independent of the solvent motions; their rates are determined by the protein conformation and vibrational dynamics. Slaved processes are tightly coupled to the solvent; their rates have approximately the same temperature dependence as the rate of the solvent fluctuations, but they are smaller. Because the temperature dependence is determined by the activation enthalpy, we propose that the solvent is responsible for the activation enthalpy, whereas the protein and the hydration shell control the activation entropy through the energy landscape. Bond formation is the prototype of nonslaved processes; opening and closing of channels are quintessential slaved motions. The prevalence of slaved motions highlights the importance of the environment in cells and membranes for the function of proteins.. . . everything that living things do can be understood in terms of the jigglings and wigglings of atoms.R. P. Feynman (1) P roteins perform most of the functions of living things, from metabolism to thinking. Textbooks usually show proteins naked, neglect fluctuations, and take little notice of the protein environment. Real proteins, however, are wiggling and jiggling, dressed by the hydration shell, and embedded in a cell or cell membrane. Feynman (1) stated the central problem succinctly, namely understanding protein functions in terms of the atomic motions. We are still very far from this goal, but progress is being made. Here we consider the effect of solvent fluctuations on protein processes. We will show that protein motions can be nonslaved or slaved. Nonslaved motions are independent of the solvent fluctuations. Slaved motions have rates that are proportional to the fluctuation rate of the solvent, but are smaller. We introduce a model, based on the energy landscape of the protein, that suggests how the protein controls its slaved dynamics. We use myoglobin (Mb) as a prototype, but the concepts apply also to many other proteins. The Dichotomy of MotionsThe main result of the present article emerges when the temperature dependences of protein processes are compared with the dielectric relaxation rate coefficient k diel (T) (2) of the solvent, essentially the average tumbling rate of the solvent water molecules. Fig. 1 shows k diel (T) (2) and the rate coefficients for various processes in Mb embedded in a 3:1 (vol͞vol) glycerol͞ water solvent (3-7). [We do not consider vibrations here, which can be described by normal modes (8).] We characterize the rate coefficients for selected processes by using the Inset in Fig. 1. The Inset shows a cross section through part of Mb with a heme group situated in the heme cavity and a major cavity called Xe-1 and labeled D. Small ligands such as carbon monoxide (CO) bind covalently at the heme iron. We denote the position of the CO by S if it is in the solvent, by A i...

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“…In the A 1 and A 3 substates, the imidazole side chain is neutral and resides inside the distal pocket, whereas it is doubly protonated and pointed towards the solvent in the A 0 substate (67,68). After photodissociation, the CO ligand transiently occupies specific locations inside Mb, the primary docking site B on top of heme pyrrole C (14-16) and secondary sites C and D that coincide with two of four hydrophobic cavities in the protein interior, labeled Xe4 and Xe1 for their ability to bind Xe (17)(18)(19)69). In each of these sites, the CO ligand gives rise to specific photoproduct spectra, with the stretching frequency fine-tuned by the vibrational Stark effect, the interaction of the CO infrared transition dipole with the electric field at the site (31,63,70,71).…”

Section: The Active Site Of Wild-type Hbimentioning

confidence: 99%

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,

et al. 2007

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Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with x-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.The globin superfamily of proteins includes vertebrate hemoglobins (Hb), vertebrate myoglobins (Mb), invertebrate globins, plant globins, and bacterial and fungal flavohemoproteins (1). These proteins all bind oxygen and a variety of other small molecules at the central iron of a heme group enwrapped by the polypeptide chain in its characteristic 'globin' fold. Yet they are structurally highly diverse, ranging in size from the small monomeric mini-hemoglobin of the nemertean worm Cerebratulus lacteus with only 109 amino acid residues (2) to the giant erythrocruorin protein found in the annelid Lumbricus terrestris that consists of 144 hemoglobin subunits held together by 36 linker proteins (3). Globins perform a multitude of tasks in biological systems, including oxygen storage and transport, NO scavenging, enzyme action and small-molecule sensor function (4,5).The monomeric Mb is arguably the best studied member of the globin family. For many years, Mb has served as a model system for protein structural dynamics (6-13). A surprising complexity was discovered in its seemingly simple ligand binding reaction, which involves Address correspondence to G. Ulrich Nienhaus, Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Tel.: +49 731 5023050, Fax.: +49 731 5023059, Email: uli@uiuc.edu. ∥ Current Address: Department of Biochemistry and Molecular Biology, University of Texas, Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77551-1055, USA * The first two authors contributed equally. † G.U.N. was supported by the Deutsche Forschungsgemeinschaft (grant Ni 291/3) and the Fonds der Chemischen Industrie. W.E.R. was supported by the National Institutes of Health (grants DK43323 and GM66756). NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2008 December 11. Published in final edited form as:Biochemistry. (FTIR) cryospectroscopy to study the migration of carbon monoxide (CO) among cavities within the protein interio...

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Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin

Cited by 245 publications

References 28 publications

In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore

In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore

Slaving: Solvent fluctuations dominate protein dynamics and functions

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,

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Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin

Cited by 245 publications

References 28 publications

In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore

In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore

Slaving: Solvent fluctuations dominate protein dynamics and functions

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis,

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Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,