The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics

Ubbink, Marcellus; Ejdebäck, Mikael; Karlsson, Bengt; Bendall, Derek S.

doi:10.1016/s0969-2126(98)00035-5

Cited by 305 publications

(442 citation statements)

References 67 publications

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“…Our calculations confirm the theory [21,30] which supposes that a decrease in the rate constant at low values of the ionic strength is caused by the shift of equilibrium to an ensemble of complexes that are not optimal for the electron transfer. At low ionic strength protein molecules spend more time in "wrong" orientations, which do not satisfy the docking conditions (in the computer simulation) or do not form a final complex capable of electron transfer.…”

Section: Resultssupporting

confidence: 83%

“…On the other hand, since electrostatic attraction is very strong at low ionic strength, the approach of two proteins can give rise to unproductive intermediates that do not meet the docking conditions and the proteins can remain "wrong" oriented for a long time that does not satisfy the docking conditions. The main hypothesis explaining the non-monotonic behavior consists in the formation of tight but nonproductive complexes due to the electrostatic interactions strength at low salt concentration [21,30]. Strong electrostatic attraction does not let the Brownian force break the "wrong" complex and try to make the productive complex again.…”

Section: Second Order Rate Constant Dependence On the Ionic Strengthmentioning

confidence: 99%

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Computer Simulation of Protein-Protein Association in Photosynthesis

Kovalenko

Abaturova

Diakonova

et al. 2011

Math. Model. Nat. Phenom.

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Abstract. The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in "wrong" orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.

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Section: Resultssupporting

confidence: 83%

Section: Second Order Rate Constant Dependence On the Ionic Strengthmentioning

confidence: 99%

Computer Simulation of Protein-Protein Association in Photosynthesis

Kovalenko

Abaturova

Diakonova

et al. 2011

Math. Model. Nat. Phenom.

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“…Because the orientation of the respective side chains at the protein surface is often disordered, a stabilizing effect seems unlikely. The conserved charged residues, which surround the actual recognition site, may be involved in electrostatic interactions that modulate intermediate states of binding and unbinding of CYC to QCR, similar to the proposed model of plastocyanin binding to cytochrome f (25).…”

Section: Resultsmentioning

confidence: 75%

Crystal structure of the yeast cytochrome bc ₁ complex with its bound substrate cytochrome c

Lange

Hunte

2002

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

342

351

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Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover. In respiration, the mobile electron carrier cytochrome c shuttles electrons from the cytochrome bc 1 complex to cytochrome c oxidase. Despite extensive studies of this fundamental step of energy metabolism, the structures of the respective electron transfer complexes were not known. Here we present the crystal structure of the complex between cytochrome c and the cytochrome bc 1 complex from Saccharomyces cerevisiae. The complex was crystallized with the help of an antibody fragment, and its structure was determined at 2.97-Å resolution. Cytochrome c is bound to subunit cytochrome c 1 of the enzyme. The tight and specific interactions critical for electron transfer are mediated mainly by nonpolar forces. The close spatial arrangement of the c-type hemes unexpectedly suggests a direct and rapid heme-to-heme electron transfer at a calculated rate of up to 8.3 ؋ 10 6 s ؊1 . Remarkably, cytochrome c binds to only one recognition site of the homodimeric multisubunit complex. Interestingly, the occupancy of quinone in the Qi site is higher in the monomer with bound cytochrome c, suggesting a coordinated binding and reduction of both electron-accepting substrates. Obviously, cytochrome c reduction by the cytochrome bc 1 complex can be regulated in response to respiratory conditions.

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“…Although other observables, such as pseudo-contact shifts and cross-correlation involving the Curie-spin relaxation, arising from unpaired electrons with an anisotropic g-tensor have been shown to be useful for the investigation of metal-binding proteins (2,(47)(48)(49)(50)(51), similar applications to macromolecules with an extrinsic paramagnetic group tend to problematic owing to various practical considerations (e.g. the presence of enantiomers in the EDTA coordination system and linker flexibility; cf.…”

Section: Discussionmentioning

confidence: 99%

Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules

Iwahara

Tang

Clore

2007

Journal of Magnetic Resonance

244

385

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The use of 1 H transverse paramagnetic relaxation enhancement (PRE) has seen a resurgence in recent years as method for providing long-range distance information for structural studies and as a probe of large amplitude motions and lowly populated transient intermediates in macromolecular association. In this paper we discuss various practical aspects pertaining to accurate measurement of PRE 1 H transverse relaxation rates (Γ 2 ). We first show that accurate Γ 2 rates can be obtained from a two time-point measurement without requiring any fitting procedures or complicated error estimations, and no additional accuracy is achieved from multiple time-point measurements recorded in the same experiment time. Optimal setting of the two time-points that minimize experimental errors is also discussed. Next we show that the simplistic single time-point measurement that has been commonly used in the literature, can substantially underestimate the true value of Γ 2 , unless a relatively long repetition delay is employed. We then examine the field dependence of Γ 2 , and show that Γ 2 exhibits only a very weak field dependence at high magnetic fields typically employed in macromolecular studies. The theoretical basis for this observation is discussed. Finally, we investigate the impact of contamination of the paramagnetic sample by trace amounts (≤5%) of the corresponding diamagnetic species on the accuracy of Γ 2 measurements. Errors in Γ 2 introduced by such diamagnetic contamination are potentially sizeable, but can be significantly reduced by using a relatively short time interval for the two time-point Γ 2 measurement.

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The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics

Cited by 305 publications

References 67 publications

Computer Simulation of Protein-Protein Association in Photosynthesis

Computer Simulation of Protein-Protein Association in Photosynthesis

Crystal structure of the yeast cytochrome bc ₁ complex with its bound substrate cytochrome c

Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules

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The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics

Cited by 305 publications

References 67 publications

Computer Simulation of Protein-Protein Association in Photosynthesis

Computer Simulation of Protein-Protein Association in Photosynthesis

Crystal structure of the yeast cytochrome bc 1 complex with its bound substrate cytochrome c

Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules

Contact Info

Product

Resources

About

Crystal structure of the yeast cytochrome bc ₁ complex with its bound substrate cytochrome c