X-ray Structure Determination of the Cytochrome c2: Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides

Axelrod, Herbert L.; Abresch, Edward C.; Okamura, M. Y.; Yeh, Andrew; Rees, Douglas C.; Fehér, G.

doi:10.1016/s0022-2836(02)00168-7

Cited by 150 publications

(206 citation statements)

References 74 publications

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“…The coordinate axes were based on the x-ray cocrystal structure of Cyt and RC from Rb. sphaeroides obtained by Axelrod et al (19). Fig.…”

Section: Determining the Ts Ensemble By Using The Correlation Coefficmentioning

confidence: 83%

“…6a). In addition, the relatively small number of hydrophobic residues in the short-range binding domain (19) may be important in ensuring that when short-range van der Waals contacts do form, they lead to the bound state rather than to a trapped state. The processes that are important in the final steps of protein association and electron transfer are not well understood and require further study.…”

Section: Discussionmentioning

confidence: 99%

“…The structures of the native RC (19) and Cyt (33) were obtained from the crystallographic coordinates [Protein Data Bank (PDB) ID codes 1L9B and 1C2R]. Mutant structures were obtained by manually modeling the modified residues into the protein structure by using the program SWISS PDB VIEWER (35) followed by an energy-minimization procedure using the AMBER potential.…”

Section: Methodsmentioning

confidence: 99%

“…However, the fast-exchange regime has been observed in other cases (17,18). The structure of the Cyt͞RC complex has been obtained by cocrystallizing Cyt and RC and determining the x-ray crystal structure (19). The complex is active in the crystal and has the same electron-transfer rate in the crystal as in solution, demonstrating that the complex represents the active state.…”

Section: [1]mentioning

confidence: 99%

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Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Miyashita

Onuchic

Okamura

2004

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

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Electrostatic interactions strongly enhance the electron transfer reaction between cytochrome (Cyt) c 2 and reaction center (RC) from photosynthetic bacteria, yielding a second-order rate constant, k 2 Ϸ 10 9 s ؊1 ⅐M ؊1 , close to the diffusion limit. The proposed mechanism involves an encounter complex (EC) stabilized by electrostatic interactions, followed by a transition state (TS), leading to the bound complex active in electron transfer. The effect of electrostatic interactions was previously studied by Tetreault et al. electron transfer ͉ photosynthesis ͉ electrostatics ͉ site-directed mutagenesis ͉ correlation I ntermolecular electron-transfer reactions play important roles in many biological processes such as photosynthesis and respiration (1). In these reactions, two electron-transfer proteins associate to form an electron donor-acceptor complex in which electron transfer occurs (2). Electrostatic interactions can greatly enhance the rate of protein association by providing long-range guidance in the association process (3). For fast processes assisted by electrostatic interactions, a two-step association mechanism has been proposed (4, 5). The first step is the formation of a loosely bound encounter complex (EC), followed by a rate-limiting process through a transition state (TS), leading to the bound active state. In this paper we examine the association process for the reaction center (RC) and cytochrome (Cyt) c 2 that are involved in the electron-transfer chain in bacterial photosynthesis by using electrostatic calculations and experimental data to obtain a molecular description of the TS and the EC. The results of these calculations describe the ensemble of states that represent a roadmap for the association process and the interactions likely to be important in the dynamics. This approach is complementary to Brownian dynamics simulations (5-7) that yield the diffusional rate constant.The RC is the membrane protein involved in the primary light-induced electron-transfer step in bacterial photosynthesis (8,9). Light absorbed by RC pigments activates photooxidation of the primary donor, D, a bacteriochlorophyll dimer, leading to the reduction of a quinone molecule Q, DQ 3 D ϩ Q Ϫ . The electron from Q Ϫ cycles back to D ϩ through an electron-transfer chain involving the membrane-bound Cyt bc1 complex. The last step in the cycle involves a soluble Cyt c 2 molecule that shuttles the electron back to the RC to complete the cyclic electron-transfer process. This cyclic electron transfer is coupled to proton pumping across the membrane that drives ATP synthesis.The rates of electron transfer between isolated RCs and Cyt c 2 have been measured by using laser-flash techniques and shown to be well optimized for cyclic electron transfer by using the scheme below (refs. 10-13; reviewed in ref. 14).[1]Before the laser flash, the Cyt and RC (denoted DQ) are in equilibrium between a bound state and a free state with the dissociation constant K d Ϸ 10 Ϫ6 M at low ionic strength (Ϸ5 mM) (13). After a laser flash, t...

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“…The coordinate axes were based on the x-ray cocrystal structure of Cyt and RC from Rb. sphaeroides obtained by Axelrod et al (19). Fig.…”

Section: Determining the Ts Ensemble By Using The Correlation Coefficmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: [1]mentioning

confidence: 99%

See 2 more Smart Citations

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Miyashita

Onuchic

Okamura

2004

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

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“…These are the underlying reasons why there are so few crystal structures of redox complexes. Our search of the Protein Data Bank (PDB) gives nine unique crystal structures of noncovalent endogenous binary redox complexes: 2PCC (8), 2ZON (9), 2IAA (9), 1T9G (10), 2V3B (11), 2DE5 (12), 2H3X (13), 1L9B (14), 1KYO (15), and 2YVJ (16). Of these, one of the most extensively studied redox complexes is between yeast CCP and cytochrome c (Cytc) (17), which includes the crystal of the noncovalent (8) and a disulfide engineered covalent complex (18).…”

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confidence: 99%

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

Jasion

Doukov

Pineda

et al. 2012

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

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The causative agent of leishmaniasis is the protozoan parasite Leishmania major . Part of the host protective mechanism is the production of reactive oxygen species including hydrogen peroxide. In response, L. major produces a peroxidase, L. major peroxidase (LmP), that helps to protect the parasite from oxidative stress. LmP is a heme peroxidase that catalyzes the peroxidation of mitochondrial cytochrome c . We have determined the crystal structure of LmP in a complex with its substrate, L. major cytochrome c (LmCytc) to 1.84 Å, and compared the structure to its close homolog, the yeast cytochrome c peroxidase–cytochrome c complex. The binding interface between LmP and LmCytc has one strong and one weak ionic interaction that the yeast system lacks. The differences between the steady-state kinetics correlate well with the Lm redox pair being more dependent on ionic interactions, whereas the yeast redox pair depends more on nonpolar interactions. Mutagenesis studies confirm that the ion pairs at the intermolecular interface are important to both k cat and K M . Despite these differences, the electron transfer path, with respect to the distance between hemes, along the polypeptide chain is exactly the same in both redox systems. A potentially important difference, however, is the side chains involved. LmP has more polar groups (Asp and His) along the pathway compared with the nonpolar groups (Leu and Ala) in the yeast system, and as a result, the electrostatic environment along the presumed electron transfer path is substantially different.

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Long‐Range Electron Transfer in Biology

Winkler

2005

Encyclopedia of Inorganic Chemistry

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Electron‐transfer processes are vital elements of energy transduction pathways in living cells. A unique synergy between theory and experiment has produced an extraordinarily detailed understanding of the factors that regulate this ‘current of life’. Studies of Ru‐modified proteins have provided insights into the distance‐ and driving‐force dependences of intraprotein electron transfer rates. Electron transfer across protein–protein interfaces has been probed both in solution and in structurally characterized crystals. It is now clear that electrons tunnel between sites in biological redox chains, and that protein structures tune thermodynamic properties and electronic coupling interactions to facilitate these reactions. This research has produced an experimentally validated, electron tunneling timetable that predicts the time required for an electron to transfer across a specified distance in a protein. Many of the electron tunneling rates measured in cytochrome c oxidase and photosynthetic reaction centers agree well with timetable predictions, indicating that the natural reactions are highly optimized, both in terms of thermodynamics and electronic coupling.

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X-ray Structure Determination of the Cytochrome c2: Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides

Cited by 150 publications

References 74 publications

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

Long‐Range Electron Transfer in Biology

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X-ray Structure Determination of the Cytochrome c2: Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides

Cited by 150 publications

References 74 publications

Transition state and encounter complex for fast association of cytochrome c 2 with bacterial reaction center

Transition state and encounter complex for fast association of cytochrome c 2 with bacterial reaction center

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

Long‐Range Electron Transfer in Biology

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Product

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Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center

Transition state and encounter complex for fast association of cytochrome c ₂ with bacterial reaction center