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Yuan B, Long S, Wang H, Luo Q, Zeng K, Gao S, Lin Y. Surfactant-regulated acetylpyrene assemblies as fluorescent probes for identifying heme proteins in an aqueous solution. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2022.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Król S, Fedotovskaya O, Högbom M, Ädelroth P, Brzezinski P. Electron and proton transfer in the M. smegmatis III 2IV 2 supercomplex. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148585. [PMID: 35753381 DOI: 10.1016/j.bbabio.2022.148585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/25/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The M. smegmatis respiratory III2IV2 supercomplex consists of a complex III (CIII) dimer flanked on each side by a complex IV (CIV) monomer, electronically connected by a di-heme cyt. cc subunit of CIII. The supercomplex displays a quinol oxidation‑oxygen reduction activity of ~90 e-/s. In the current work we have investigated the kinetics of electron and proton transfer upon reaction of the reduced supercomplex with molecular oxygen. The data show that, as with canonical CIV, oxidation of reduced CIV at pH 7 occurs in three resolved components with time constants ~30 μs, 100 μs and 4 ms, associated with the formation of the so-called peroxy (P), ferryl (F) and oxidized (O) intermediates, respectively. Electron transfer from cyt. cc to the primary electron acceptor of CIV, CuA, displays a time constant of ≤100 μs, while re-reduction of cyt. cc by heme b occurs with a time constant of ~4 ms. In contrast to canonical CIV, neither the P → F nor the F → O reactions are pH dependent, but the P → F reaction displays a H/D kinetic isotope effect of ~3. Proton uptake through the D pathway in CIV displays a single time constant of ~4 ms, i.e. a factor of ~40 slower than with canonical CIV. The slowed proton uptake kinetics and absence of pH dependence are attributed to binding of a loop from the QcrB subunit of CIII at the D proton pathway of CIV. Hence, the data suggest that function of CIV is modulated by way of supramolecular interactions with CIII.
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Affiliation(s)
- Sylwia Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Olga Fedotovskaya
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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Fedotovskaya O, Albertsson I, Nordlund G, Hong S, Gennis RB, Brzezinski P, Ädelroth P. Identification of a cytochrome bc 1-aa 3 supercomplex in Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148433. [PMID: 33932366 DOI: 10.1016/j.bbabio.2021.148433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Respiration is carried out by a series of membrane-bound complexes in the inner mitochondrial membrane or in the cytoplasmic membrane of bacteria. Increasing evidence shows that these complexes organize into larger supercomplexes. In this work, we identified a supercomplex composed of cytochrome (cyt.) bc1 and aa3-type cyt. c oxidase in Rhodobacter sphaeroides. We purified the supercomplex using a His-tag on either of these complexes. The results from activity assays, native and denaturing PAGE, size exclusion chromatography, electron microscopy, optical absorption spectroscopy and kinetic studies on the purified samples support the formation and coupled quinol oxidation:O2 reduction activity of the cyt. bc1-aa3 supercomplex. The potential role of the membrane-anchored cyt. cy as a component in supercomplexes was also investigated.
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Affiliation(s)
- Olga Fedotovskaya
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ingrid Albertsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gustav Nordlund
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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Kokhan O, Marzolf DR. Detection and quantification of transition metal leaching in metal affinity chromatography with hydroxynaphthol blue. Anal Biochem 2019; 582:113347. [PMID: 31251926 DOI: 10.1016/j.ab.2019.113347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022]
Abstract
The widespread use of immobilized metal-affinity chromatography (IMAC) for fast and efficient purification of recombinant proteins has brought potentially toxic transition elements into common laboratory usage. However, there are few studies on the leaching of metal from the affinity resin, such as nickel-nitrilotriacetic acid (Ni-NTA), with possible deleterious impact on the biological activity. This is of particular importance when reducing or chelating eluants stronger than imidazole are used. We present a detailed study of hydroxynaphthol blue (HNB) as an indicator of several divalent metal cations, but with emphasis on Ni2+, clarifying and correcting many errors and ambiguities in the older literature on this dye compound. The assay is simple and sensitive and many metals, notably Ni2+, Zn2+, Cu2+, Pb2+, Fe2+, Co2+, and Al3+, can be readily detected and quantified at concentrations down to 15-50 nM (1-5 ppb) at neutral pH and in most commonly used buffers using spectroscopic equipment available in typical biochemistry research labs. Using this method, we show that significant amounts of Ni2+ (up to 20 mM) are co-purified with a target protein (cytochrome bc1 complex) when histidine is used to elute from Ni-NTA resin.
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Affiliation(s)
- Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, Harrisonburg, VA, 22807, USA.
| | - Daniel R Marzolf
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, Harrisonburg, VA, 22807, USA
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Schäfer J, Dawitz H, Ott M, Ädelroth P, Brzezinski P. Regulation of cytochrome c oxidase activity by modulation of the catalytic site. Sci Rep 2018; 8:11397. [PMID: 30061583 PMCID: PMC6065377 DOI: 10.1038/s41598-018-29567-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/11/2018] [Indexed: 01/24/2023] Open
Abstract
The respiratory supercomplex factor 1 (Rcf 1) in Saccharomyces cerevisiae binds to intact cytochrome c oxidase (CytcO) and has also been suggested to be an assembly factor of the enzyme. Here, we isolated CytcO from rcf1Δ mitochondria using affinity chromatography and investigated reduction, inter-heme electron transfer and ligand binding to heme a3. The data show that removal of Rcf1 yields two CytcO sub-populations. One of these sub-populations exhibits the same functional behavior as CytcO isolated from the wild-type strain, which indicates that intact CytcO is assembled also without Rcf1. In the other sub-population, which was shown previously to display decreased activity and accelerated ligand-binding kinetics, the midpoint potential of the catalytic site was lowered. The lower midpoint potential allowed us to selectively reduce one of the two sub-populations of the rcf1Δ CytcO, which made it possible to investigate the functional behavior of the two CytcO forms separately. We speculate that these functional alterations reflect a mechanism that regulates O2 binding and trapping in CytcO, thereby altering energy conservation by the enzyme.
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Affiliation(s)
- Jacob Schäfer
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Hannah Dawitz
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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Erman JE, Chinchilla D, Studer J, Vitello LB. Binding of imidazole, 1-methylimidazole and 4-nitroimidazole to yeast cytochrome c peroxidase (CcP) and the distal histidine mutant, CcP(H52L). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:869-81. [PMID: 25907133 DOI: 10.1016/j.bbapap.2015.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 04/05/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
Abstract
Imidazole, 1-methylimidazole and 4-nitroimidazole bind to yeast cytochrome c peroxidase (yCcP) with apparent equilibrium dissociation constants (KD(app)) of 3.3±0.4, 0.85±0.11, and ~0.2M, respectively, at pH7. This is the weakest imidazole binding to a heme protein reported to date and it is about 120 times weaker than imidazole binding to metmyoglobin. Spectroscopic changes associated with imidazole and 1-methylimidazole binding to yCcP suggest partial ionization of bound imidazole to imidazolate. The pKa for ionization of bound imidazole is estimated to be 7.4±0.2, about 7 units lower than that of free imidazole and about 3 units lower than imidazole bound to metmyoglobin. Equilibrium binding of imidazole to CcP(H52L) is biphasic with low- and high-affinity phases having KD(app) values of 9.5±4.5 and 0.13±0.04M, respectively. CcP(H52L) binding of 1-methylimidazole is monophasic with an affinity similar to those of yCcP and rCcP. Binding of 1-methylimidazole to rCcP is associated with two kinetic phases, the initial binding complete within 10s, followed by a process that is consistent with 1-methylimidazole binding to a cavity created by movement of Trp-191 from the interior of the protein to the surface. Both the equilibrium binding and kinetics of 1-methylimidazole binding to yCcP are pH dependent. yCcP has a four-fold increase in 1-methylimidazole binding affinity on decreasing the pH from 7.5 to 4.0, an observation that is unique among the many studies on binding of imidazole and imidazole derivatives to heme proteins.
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Affiliation(s)
- James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Diana Chinchilla
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Jason Studer
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Lidia B Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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Lyu F, Zhang Y, Zare RN, Ge J, Liu Z. One-pot synthesis of protein-embedded metal-organic frameworks with enhanced biological activities. NANO LETTERS 2014; 14:5761-5. [PMID: 25211437 DOI: 10.1021/nl5026419] [Citation(s) in RCA: 586] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Protein molecules were directly embedded in metal-organic frameworks (MOFs) by a coprecipitation method. The protein molecules majorly embedded on the surface region of MOFs display high biological activities. As a demonstration of the power of such materials, the resulting Cyt c embedded in ZIF-8 showed a 10-fold increase in peroxidase activity compared to free Cyt c in solution and thus gave convenient, fast, and highly sensitive detection of trace amounts of explosive organic peroxides in solution.
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Affiliation(s)
- Fengjiao Lyu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
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Chinchilla D, Kilheeney H, Vitello LB, Erman JE. Kinetic and equilibrium studies of acrylonitrile binding to cytochrome c peroxidase and oxidation of acrylonitrile by cytochrome c peroxidase compound I. Biochem Biophys Res Commun 2013; 443:200-4. [PMID: 24291498 DOI: 10.1016/j.bbrc.2013.11.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/21/2013] [Indexed: 11/15/2022]
Abstract
Ferric heme proteins bind weakly basic ligands and the binding affinity is often pH dependent due to protonation of the ligand as well as the protein. In an effort to find a small, neutral ligand without significant acid/base properties to probe ligand binding reactions in ferric heme proteins we were led to consider the organonitriles. Although organonitriles are known to bind to transition metals, we have been unable to find any prior studies of nitrile binding to heme proteins. In this communication we report on the equilibrium and kinetic properties of acrylonitrile binding to cytochrome c peroxidase (CcP) as well as the oxidation of acrylonitrile by CcP compound I. Acrylonitrile binding to CcP is independent of pH between pH 4 and 8. The association and dissociation rate constants are 0.32±0.16 M(-1) s(-1) and 0.34±0.15 s(-1), respectively, and the independently measured equilibrium dissociation constant for the complex is 1.1±0.2 M. We have demonstrated for the first time that acrylonitrile can bind to a ferric heme protein. The binding mechanism appears to be a simple, one-step association of the ligand with the heme iron. We have also demonstrated that CcP can catalyze the oxidation of acrylonitrile, most likely to 2-cyanoethylene oxide in a "peroxygenase"-type reaction, with rates that are similar to rat liver microsomal cytochrome P450-catalyzed oxidation of acrylonitrile in the monooxygenase reaction. CcP compound I oxidizes acrylonitrile with a maximum turnover number of 0.61 min(-1) at pH 6.0.
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Affiliation(s)
- Diana Chinchilla
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Heather Kilheeney
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - Lidia B Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
| | - James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
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Kyndt JA, Fitch JC, Berry RE, Stewart MC, Whitley K, Meyer TE, Walker FA, Cusanovich MA. Tyrosine triad at the interface between the Rieske iron-sulfur protein, cytochrome c1 and cytochrome c2 in the bc1 complex of Rhodobacter capsulatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:811-8. [PMID: 22306765 DOI: 10.1016/j.bbabio.2012.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 01/20/2012] [Accepted: 01/20/2012] [Indexed: 11/25/2022]
Abstract
A triad of tyrosine residues (Y152-154) in the cytochrome c(1) subunit (C1) of the Rhodobacter capsulatus cytochrome bc(1) complex (BC1) is ideally positioned to interact with cytochrome c(2) (C2). Mutational analysis of these three tyrosines showed that, of the three, Y154 is the most important, since its mutation to alanine resulted in significantly reduced levels, destabilization, and inactivation of BC1. A second-site revertant of this mutant that regained photosynthetic capacity was found to have acquired two further mutations-A181T and A200V. The Y152Q mutation did not change the spectral or electrochemical properties of C1, and showed wild-type enzymatic C2 reduction rates, indicating that this mutation did not introduce major structural changes in C1 nor affect overall activity. Mutations Y153Q and Y153A, on the other hand, clearly affect the redox properties of C1 (e.g. by lowering the midpoint potential as much as 117 mV in Y153Q) and the activity by 90% and 50%, respectively. A more conservative Y153F mutant on the other hand, behaves similarly to wild-type. This underscores the importance of an aromatic residue at position Y153, presumably to maintain close packing with P184, which modeling indicates is likely to stabilize the sixth heme ligand conformation.
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Affiliation(s)
- John A Kyndt
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
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Castellani M, Havens J, Kleinschroth T, Millett F, Durham B, Malatesta F, Ludwig B. The acidic domain of cytochrome c₁ in paracoccus denitrificans, analogous to the acidic subunits in eukaryotic bc₁ complexes, is not involved in the electron transfer reaction to its native substrate cytochrome c(552). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1383-9. [PMID: 21856278 DOI: 10.1016/j.bbabio.2011.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 11/19/2022]
Abstract
The cytochrome bc(1) complex is a key component in several respiratory pathways. One of the characteristics of the eukaryotic complex is the presence of a small acidic subunit, which is thought to guide the interaction of the complex with its electron acceptor and facilitate electron transfer. Paracoccus denitrificans represents the only example of a prokaryotic organism in which a highly acidic domain is covalently fused to the cytochrome c(1) subunit. In this work, a deletion variant lacking this acidic domain has been produced and purified by affinity chromatography. The complex is fully intact as shown by its X-ray structure, and is a dimer (Kleinschroth et al., subm.) compared to the tetrameric (dimer-of-dimer) state of the wild-type. The variant complex is studied by steady-state kinetics and flash photolysis, showing wild type turnover and a virtually identical interaction with its substrate cytochrome c(552).
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Affiliation(s)
- Michela Castellani
- Institute of Biochemistry, Molecular Genetics, Goethe University, D-60438 Frankfurt am Main and Cluster of Excellence "Macromolecular Complexes" (CEF-MC), D-60438 Frankfurt am Main, Germany
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Kokhan O, Shinkarev VP, Wraight CA. Binding of imidazole to the heme of cytochrome c1 and inhibition of the bc1 complex from Rhodobacter sphaeroides: II. Kinetics and mechanism of binding. J Biol Chem 2010; 285:22522-31. [PMID: 20448037 PMCID: PMC2903381 DOI: 10.1074/jbc.m110.128082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 04/30/2010] [Indexed: 11/06/2022] Open
Abstract
The kinetics of imidazole (Im) and N-methylimidazole (MeIm) binding to oxidized cytochrome (cyt) c(1) of detergent-solubilized 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 approximately 1 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 rate-limiting 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.
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Affiliation(s)
| | | | - Colin A. Wraight
- From the Center for Biophysics and Computational Biology and
- the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
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