Binding Hot Spot in the Weak Protein Complex of Physiological Redox Partners Yeast Cytochrome c and Cytochrome c Peroxidase

Volkov, Alexander N.; Bashir, Qamar; Worrall, J.A.R.; Ubbink, Marcellus

doi:10.1016/j.jmb.2008.10.091

Cited by 31 publications

(33 citation statements)

References 56 publications

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“…1B), amino acid residues located near the heme moiety such as Glu16, Thr28, Lys72, and Phe82 in the CcP interaction site (21,25) are not involved in interactions with CcO. The contribution of the N-and C-terminal helix regions to regulation of the binding orientation of Cyt c is more prominent in CcO than that in the interaction with CcP (Fig.…”

Section: Comparisons Of the Present Results With Other Electron Transmentioning

confidence: 94%

“…Thus, the electrostatic interactions between mammalian Cyt c and CcO are unlikely to represent the predominant interaction for stabilization of the complex as suggested by the previous molecular dynamics calculations for small model proteins (19). Although no direct ionic interaction was reported in the high resolution structure of the cross-linked Cyt c-CcP complex (20), the ET rate from Cyt c to CcP depends on the ionic strength (20) and thermodynamic parameters indicate significant contribution of the electrostatic interaction to the formation of the ET complex (21). Therefore, the present results strongly suggest that charged amino acid residues in the interaction site contribute to the process of adjusting the orientation of Cyt c with respect to CcO through their electrostatic interactions, in order to facilitate the strictly controlled ET reaction.…”

Section: Chemical Shift Perturbation Mapping Of Interaction Sites In mentioning

confidence: 84%

“…plexes Involving Cytochrome c. The Cyt c-cytochrome c peroxidase (CcP) complex has been the most extensively analyzed ET complex at present (20,21,24,25). The similarity in the complex formation mechanism in the CcO∕Cyt c and CcP∕Cyt c systems has been proposed, because the interaction sites for Cyt c in both CcP and CcO surfaces are surrounded by negatively charged amino acid residues.…”

Section: Comparisons Of the Present Results With Other Electron Transmentioning

confidence: 99%

See 2 more Smart Citations

NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase

Sakamoto

Kamiya²,

Imai³

et al. 2011

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

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The final interprotein electron transfer (ET) in the mammalian respiratory chain, from cytochrome c (Cyt c ) to cytochrome c oxidase (C c O) is investigated by 1 H- 15 N heteronuclear single quantum coherence spectral analysis. The chemical shift perturbation in isotope-labeled Cyt c induced by addition of unlabeled C c O indicates that the hydrophobic heme periphery and adjacent hydrophobic amino acid residues of Cyt c dominantly contribute to the complex formation, whereas charged residues near the hydrophobic core refine the orientation of Cyt c to provide well controlled ET. Upon oxidation of Cyt c , the specific line broadening of N-H signals disappeared and high field 1 H chemical shifts of the N-terminal helix were observed, suggesting that the interactions of the N-terminal helix with C c O are reduced by steric constraint in oxidized Cyt c , while the chemical shift perturbations in the C-terminal helix indicate notable interactions of oxidized Cyt c with C c O. These results suggest that the overall affinity of oxidized Cyt c for C c O is significantly, but not very much weaker than that of reduced Cyt c . Thus, electron transfer is gated by dissociation of oxidized Cyt c from C c O, the rate of which is controlled by the affinity of oxidized Cyt c to C c O for providing an appropriate electron transfer rate for the most effective energy coupling. The conformational changes in Lys13 upon C c O binding to oxidized Cyt c , shown by 1 H- and 1 H, 15 N-chemical shifts, are also expected to gate intraprotein ET by a polarity control of heme c environment.

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Section: Comparisons Of the Present Results With Other Electron Transmentioning

confidence: 94%

Section: Chemical Shift Perturbation Mapping Of Interaction Sites In mentioning

confidence: 84%

Section: Comparisons Of the Present Results With Other Electron Transmentioning

confidence: 99%

See 1 more Smart Citation

NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase

Sakamoto

Kamiya²,

Imai³

et al. 2011

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

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show abstract

“…In addition, paramagnetic effects have also been employed in the characterization of protein-protein complexes. For instance, pseudocontact shifts were used to characterize the interaction of yeast iso-cytochrome c with cytochrome c peroxidase [19,20], spin-labels to map the interaction between pseudoazurin and nitrite reductase [10] and paramagnetic relaxation enhancement [21].…”

Section: Introductionmentioning

confidence: 99%

Rubredoxin as a paramagnetic relaxation-inducing probe

Almeida

Pauleta

Moura

et al. 2009

Journal of Inorganic Biochemistry

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“…Despite the importance of encounter complex ensembles in protein-protein association, little is known of their structures and configurations because their populations are low, their lifetimes are short, and they are difficult to trap, rendering them essentially invisible to conventional structural and biophysical methods. Recently, however, the application of NMR paramagnetic relaxation enhancement (PRE), a technique that is exquisitely sensitive to the presence of lowly populated states in the fast exchange regime (12,13), has offered new insights into the physicochemical and structural nature of transient encounter complexes in protein-DNA (14) and protein-protein (15)(16)(17)(18)(19)(20) association. The mechanism, however, whereby the interacting molecules in the encounter complex ensemble find their final stereospecific structure, remains poorly understood.…”

mentioning

confidence: 99%

Mechanistic details of a protein–protein association pathway revealed by paramagnetic relaxation enhancement titration measurements

Fawzi

Doucleff

Suh

et al. 2010

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

113

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Protein-protein association generally proceeds via the intermediary of a transient, lowly populated, encounter complex ensemble. The mechanism whereby the interacting molecules in this ensemble locate their final stereospecific structure is poorly understood. Further, a fundamental question is whether the encounter complex ensemble is an effectively homogeneous population of nonspecific complexes or whether it comprises a set of distinct structural and thermodynamic states. Here we use intermolecular paramagnetic relaxation enhancement (PRE), a technique that is exquisitely sensitive to lowly populated states in the fast exchange regime, to characterize the mechanistic details of the transient encounter complex interactions between the N-terminal domain of Enzyme I (EIN) and the histidine-containing phosphocarrier protein (HPr), two major bacterial signaling proteins. Experiments were conducted at an ionic strength of 150 mM NaCl to eliminate any spurious nonspecific associations not relevant under physiological conditions. By monitoring the dependence of the intermolecular transverse PRE (Γ 2 ) rates measured on 15 N-labeled EIN on the concentration of paramagnetically labeled HPr, two distinct types of encounter complex configurations along the association pathway are identified and dissected. The first class, which is in equilibrium with and sterically occluded by the specific complex, probably involves rigid body rotations and small translations near or at the active site. In contrast, the second class of encounter complex configurations can coexist with the specific complex to form a ternary complex ensemble, which may help EIN compete with other HPr binding partners in vivo by increasing the effective local concentration of HPr even when the active site of EIN is occupied.enzyme I-histidine containing phosphocarrier protein complex | encounter complex | lowly populated states | NMR | phosphotransferase system S pecific protein-protein interactions underlie virtually every process in the cell. In general, specific protein-protein recognition proceeds via a two-step process (1-3): weak association via diffusion-controlled intermolecular collisions results in the formation of an ensemble of short-lived, encounter complexes located in multiple local free energy minima of a two-dimensional funnel-like energy landscape on the protein surface (4); subsequent rearrangement along the energy landscape, involving translations and rotations of the two partner proteins, permits the global free energy minimum to be located, resulting in the formation of a well-defined specific complex stabilized by a defined set of electrostatic and van der Waals interactions. From a functional perspective, encounter complex ensembles are thought to play a critical role in fine tuning reaction fluxes inside the cell (5), enhancing association on-rates by increasing the interaction crosssection and reducing the conformational search space on the path to the specific complex (6-11). Despite the importance of encounter complex ensembles in...

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Binding Hot Spot in the Weak Protein Complex of Physiological Redox Partners Yeast Cytochrome c and Cytochrome c Peroxidase

Cited by 31 publications

References 56 publications

NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase

NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase

Rubredoxin as a paramagnetic relaxation-inducing probe

Mechanistic details of a protein–protein association pathway revealed by paramagnetic relaxation enhancement titration measurements

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