Complex formation between methionine and a heme peptide from cytochrome c.

Harbury, Henry A.; Cronin, John R.; Fanger, Michael W.; Hettinger, Thomas P.; Murphy, Alexander J.; Myer, Yash P.; Vinogradov, Serge N.

doi:10.1073/pnas.54.6.1658

Cited by 169 publications

(93 citation statements)

References 11 publications

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“…At the same time, K O must be small (Ͻ Ͻ1) for any path, implying large, albeit different, values of K L (Ͼ ϾK R ) for both Im and MeIm, such that both very effectively exchange for methionine once in the heme site. This is fully consistent with the known affinities of ferric heme for thioethers and imidazoles (25).…”

Section: Journal Of Biological Chemistry 22527supporting

confidence: 77%

“…Because of the sigmoidicity of the concentration dependence, estimates of the second order rate constants for Im binding varied from 25 , indicating an implicit conformational step as seen in cyt c and c 2 but with a much longer transition time (1 s versus 30 ms). After reaching an intermediate plateau at 50 -100 mM, the rate of binding increased again at higher concentrations, with a parabolic dependence (n Ϸ 2 in the log(Rate) versus log[Im] plot).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Binding of Imidazole to the Heme of Cytochrome c1 and Inhibition of the bc1 Complex from Rhodobacter sphaeroides

Kokhan

Shinkarev

Wraight

2010

Journal of Biological Chemistry

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The kinetics of imidazole (Im) and N-methylimidazole (MeIm) binding to oxidized cytochrome (cyt) c 1 of detergentsolubilized bc 1 complex from Rhodobacter sphaeroides are described. The rate of formation of the cyt c 1 -Im complex exhibited three separated regions of dependence on the concentration of imidazole: (i) below 8 mM Im, the rate increased with concentration in a parabolic manner; (ii) above 20 mM, the rate leveled off, indicating a rate-limiting conformational step with lifetime ϳ1 s; and (iii) at Im concentrations above 100 mM, the rate substantially increased again, also parabolically. In contrast, binding of MeIm followed a simple hyperbolic concentration dependence. The temperature dependences of the binding and release kinetics of Im and MeIm were also measured and revealed very large activation parameters for all reactions. The complex concentration dependence of the Im binding rate is not consistent with the popular model for soluble c-type cytochromes in which exogenous ligand binding is preceded by spontaneous opening of the heme cleft, which becomes ratelimiting at high ligand concentrations. Instead, binding of ligand to the heme is explained by a model in which an initial and superficial binding facilitates access to the heme by disruption of hydrogen-bonded structures in the heme domain. For imidazole, two separate pathways of heme access are indicated by the distinct kinetics at low and high concentration. The structural basis for ligand entry to the heme cleft is discussed.The binding of small molecules to c-type hemes has been widely studied in type I cytochromes c and is known to result in displacement of the native methionine ligand and to cause significant conformational changes in the heme binding domain (1-4). The affinities and kinetics of binding reflect the interactions among the exogenous ligand, the heme, and the protein and provide a window into the static and dynamic properties of the heme domain.In cytochromes (cyts) 2 c and c 2 , the methionine ligand of the heme is located in the middle of a 12-18-residue linker connecting two ␣-helices of the conserved cytochrome c fold. Structural studies of cyts c and c 2 with exogenous ligands bound (1, 2, 5) show that part of the linker sequence (termed the "hinge" by Dumortier et al. (3)) is rotated to create a slight opening or loosening of the heme binding cavity. The initial and final states are generally referred to as closed and open. However, there is no direct evidence that ligand binding is preceded by a spontaneous conformation change that closely resembles the open state seen in ligand-bound structures or that the heme-methionine linkage is actually broken in any intermediate state. Indeed, the mechanism of ligand entry and access to the heme is still unknown.Here we report on the kinetics of binding of imidazole and N-methylimidazole to cytochrome c 1 in isolated cyt bc 1 complex from Rhodobacter sphaeroides. Cytochrome c 1 is an integral component of the bc 1 complex, playing the role of electron carrier between the iro...

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Section: Journal Of Biological Chemistry 22527supporting

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Binding of Imidazole to the Heme of Cytochrome c1 and Inhibition of the bc1 Complex from Rhodobacter sphaeroides

Kokhan

Shinkarev

Wraight

2010

Journal of Biological Chemistry

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“…The reorganization free energy calculated here is low (Ϫ17.8 kcal͞mol) and is reproduced with a dielectric continuum model where the heme vicinity has a dielectric constant of only 1.1, consistent with earlier work (32,34,37,58). The calculated redox potential relative to a small microperoxidase-8 reference system is in good agreement with experiment (37,59). …”

supporting

confidence: 74%

Gaussian fluctuations and linear response in an electron transfer protein

Simonson

2002

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

115

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In response to charge separation or transfer, polar liquids respond in a simple linear fashion. A similar linear response for proteins might be expected from the central limit theorem and is postulated in widely used theories of protein electrostatics, including the Marcus electron transfer theory and dielectric continuum theories. Although these theories are supported by a variety of experimental data, the exact validity of a linear protein dielectric response has been difficult to determine. Molecular dynamics simulations are presented that establish a linear dielectric response of both protein and surrounding solvent over the course of a biologically relevant electron transfer reaction: oxido-reduction of yeast cytochrome c in solution. Using an umbrella-sampling free energy approach with long simulations, an accurate treatment of long-range electrostatics and both classical and quantum models of the heme, good agreement is obtained with experiment for the redox potential relative to a heme-octapeptide complex. We obtain a reorganization free energy that is only half that for heme-octapeptide and is reproduced with a dielectric continuum model where the heme vicinity has a dielectric constant of only 1.1. This value implies that the contribution of protein reorganization to the electron transfer free energy barrier is reduced almost to the theoretical limit (a dielectric of one), and that the fluctuations of the electrostatic potential on the heme have a simple harmonic form, in accord with Marcus theory, even though the fluctuations of many individual protein groups (especially at the protein surface) are anharmonic. Chemical events in proteins often involve charge separation or transfer: enzyme reactions, photoexcitation of bound chromophores, proton binding and release, and electron transfer (1, 2). In response to such an event, the protein and solvent undergo dielectric relaxation, or reorganization, in the form of electronic polarization and displacement of atomic groups. Thus, enzyme reaction rates and driving forces are sensitive to the dielectric properties of the active site (3). An important goal in biophysics is to find models that can describe the dielectric properties of proteins (3-7). In the case of small molecules in aqueous solution, simple behavior is observed: the reorganization of the solvent is approximately a linear function of the solute charge rearrangement (8)(9)(10)(11)(12). This is consistent with simple models, like the dielectric continuum model (4, 13), or a model where the solvent fluctuations are assumed to be gaussian (14-16).Proteins are much more complex. They are heterogeneous polymers, and fluctuations around their folded structure are governed by an anharmonic, rugged energy surface (17, 18). The average polarity and flexibility of a folded protein are much lower than those of water, so the dielectric properties vary strongly across the protein-solvent interface. Recent experimental studies have used spectroscopic probes (19-23) whose optical absorption and emission are s...

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“…The low-spin character of the harm iron indicates it has two strongfield axial ligands. Furthermore, the weak band at 729 nm in the oxidized cellobiose oxidase spectrum indicates that the harm has a methionine axial ligand ( [13] and the references therein, [18]). This band has been assigned either to a charge-transfer transition from the methionine axial ligand into the Fe(III) d-orbital hole or to a porphyrin to Fe(Ill) charge transfer (see [13] for review, [19]).…”

Section: Optical Absorption Spectramentioning

confidence: 99%