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Erman JE, Vitello LB, Pearl NM, Jacobson T, Francis M, Alberts E, Kou A, Bujarska K. Binding of Yeast Cytochrome c to Forty-Four Charge-Reversal Mutants of Yeast Cytochrome c Peroxidase: Isothermal Titration Calorimetry. Biochemistry 2015. [PMID: 26212209 DOI: 10.1021/acs.biochem.5b00686] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously, we constructed, expressed, and purified 46 charge-reversal mutants of yeast cytochrome c peroxidase (CcP) and determined their electronic absorption spectra, their reaction with H2O2, and their steady-state catalytic properties [ Pearl , N. M. et al. (2008) Biochemistry 47 , 2766 - 2775 ]. Forty-four of the mutants involve the conversion of either an aspartate or glutamate residue to a lysine residue, while two are positive-to-negative mutations, R31E and K149D. In this paper, we report on a calorimetric study of the interaction of each charge-reversal mutant (excluding the internal mutants D76K and D235K) with recombinant yeast iso-1 ferricytochrome c(C102T) (yCc) under conditions where only one-to-one yCc/CcP complex formation is observed. Thirteen of the 44 surface-site charge-reversal mutants decrease the binding affinity for yCc by a factor of 2 or more. Eight of the 13 mutations (E32K, D33K, D34K, E35K, E118K, E201K, E290K, E291K) occur within, or on the immediate periphery, of the crystallographically defined yCc binding site [ Pelletier , H. and Kraut , J. (1992) Science 258 , 1748 - 1755 ], three of the mutations (D37K, E98K, E209K) are slightly removed from the crystallographic site, and two of the mutations (D165K, D241K) occur on the "back-side" of CcP. The current study is consistent with a model for yCc binding to CcP in which yCc binds predominantly near the region defined by crystallographic structure of the 1:1 yCc-CcP complex, whether as a stable electron-transfer active complex or as part of a dynamic encounter complex.
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Affiliation(s)
- James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Lidia B Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Naw May Pearl
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Timothy Jacobson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Meka Francis
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Erik Alberts
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Allen Kou
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
| | - Kathy Bujarska
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, United States
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Volkov AN, Nicholls P, Worrall JA. The complex of cytochrome c and cytochrome c peroxidase: The end of the road? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1482-503. [DOI: 10.1016/j.bbabio.2011.07.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/25/2022]
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3
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Pearl NM, Jacobson T, Meyen C, Clementz AG, Ok EY, Choi E, Wilson K, Vitello LB, Erman JE. Effect of single-site charge-reversal mutations on the catalytic properties of yeast cytochrome c peroxidase: evidence for a single, catalytically active, cytochrome c binding domain. Biochemistry 2008; 47:2766-75. [PMID: 18232645 DOI: 10.1021/bi702271r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty-six charge-reversal mutants of yeast cytochrome c peroxidase (CcP) have been constructed in order to determine the effect of localized charge on the catalytic properties of the enzyme. The mutants include the conversion of all 20 glutamate residues and 24 of the 25 aspartate residues in CcP, one at a time, to lysine residues. In addition, two positive-to-negative charge-reversal mutants, R31E and K149D, are included in the study. The mutants have been characterized by absorption spectroscopy and hydrogen peroxide reactivity at pH 6.0 and 7.5 and by steady-state kinetic studies using recombinant yeast iso-1 ferrocytochrome c (C102T) as substrate at pH 7.5. Many of the charge-reversal mutations cause detectable changes in the absorption spectrum of the enzyme reflecting increased amounts of hexacoordinate heme compared to wild-type CcP. The increase in hexacoordinate heme in the mutant enzymes correlates with an increase in H 2O 2-inactive enzyme. The maximum velocity of the mutants decreases with increasing hexacoordination of the heme group. Steady-state velocity studies indicate that 5 of the 46 mutations (R31E, D34K, D37K, E118K, and E290K) cause large increases in the Michaelis constant indicating a reduced affinity for cytochrome c. Four of the mutations occur within the cytochrome c binding site identified in the crystal structure of the 1:1 complex of yeast cytochrome c and CcP [Pelletier, H., and Kraut, J. (1992) Science 258, 1748-1755] while the fifth mutation site lies outside, but near, the crystallographic site. These data support the hypothesis that the CcP has a single, catalytically active cytochrome c binding domain, that observed in the crystal structures of the cytochrome c/CcP complex.
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Affiliation(s)
- Naw May Pearl
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115, USA
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Pearl NM, Jacobson T, Arisa M, Vitello LB, Erman JE. Effect of single-site charge-reversal mutations on the catalytic properties of yeast cytochrome c peroxidase: mutations near the high-affinity cytochrome c binding site. Biochemistry 2007; 46:8263-72. [PMID: 17580971 PMCID: PMC2547122 DOI: 10.1021/bi700623u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fifteen single-site charge-reversal mutations of yeast cytochrome c peroxidase (CcP) have been constructed to determine the effect of localized charge on the catalytic properties of the enzyme. The mutations are located on the front face of CcP, near the cytochrome c binding site identified in the crystallographic structure of the yeast cytochrome c-CcP complex [Pelletier, H., and Kraut, J. (1992) Science 258, 1748-1755]. The mutants are characterized by absorption spectroscopy and hydrogen peroxide reactivity at both pH 6.0 and 7.5 and by steady-state kinetic studies using recombinant yeast iso-1-ferrocytochrome c(C102T) as a substrate at pH 7.5. Some of the charge-reversal mutations cause detectable changes in the absorption spectrum, especially at pH 7.5, reflecting changes in the equilibrium between penta- and hexacoordinate heme species in the enzyme. An increase in the amount of hexacoordinate heme in the mutant enzymes correlates with an increase in the fraction of enzyme that does not react with hydrogen peroxide. Steady-state velocity measurements indicate that five of the 15 mutations cause large increases in the Michaelis constant (R31E, D34K, D37K, E118K, and E290K). These data support the hypothesis that the cytochrome c-CcP complex observed in the crystal is the dominant catalytically active complex in solution.
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Affiliation(s)
- Naw May Pearl
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115
| | - Timothy Jacobson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115
| | - Moraa Arisa
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115
| | - Lidia B. Vitello
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115
| | - James E. Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115
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Kang SA, Hoke KR, Crane BR. Solvent Isotope Effects on Interfacial Protein Electron Transfer in Crystals and Electrode Films. J Am Chem Soc 2006; 128:2346-55. [PMID: 16478190 DOI: 10.1021/ja0557482] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
D(2)O-grown crystals of yeast zinc porphyrin substituted cytochrome c peroxidase (ZnCcP) in complex with yeast iso-1-cytochrome c (yCc) diffract to higher resolution (1.7 A) and pack differently than H(2)O-grown crystals (2.4-3.0 A). Two ZnCcP's bind the same yCc (porphyrin-to-porphyrin separations of 19 and 29 A), with one ZnCcP interacting through the same interface found in the H(2)O crystals. The triplet excited-state of at least one of the two unique ZnCcP's is quenched by electron transfer (ET) to Fe(III)yCc (k(e) = 220 s(-1)). Measurement of thermal recombination ET between Fe(II)yCc and ZnCcP+ in the D(2)O-treated crystals has both slow and fast components that differ by 2 orders of magnitude (k(eb)(1) = 2200 s(-1), k(eb)(2) = 30 s(-1)). Back ET in H(2)O-grown crystals is too fast for observation, but soaking H(2)O-grown crystals in D(2)O for hours generates slower back ET, with kinetics similar to those of the D(2)O-grown crystals (k(eb)(1) = 7000 s(-1), k(eb)(2) = 100 s(-1)). Protein-film voltammetry of yCc adsorbed to mixed alkanethiol monolayers on gold electrodes shows slower ET for D(2)O-grown yCc films than for H(2)O-grown films (k(H) = 800 s(-1); k(D) = 540 s(-1) at 20 degrees C). Soaking H(2)O- or D(2)O-grown films in the counter solvent produces an immediate inverse isotope effect that diminishes over hours until the ET rate reaches that found in the counter solvent. Thus, D(2)O substitution perturbs interactions and ET between yCc and either CcP or electrode films. The effects derive from slow exchanging protons or solvent molecules that in the crystal produce only small structural changes.
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Affiliation(s)
- Seong A Kang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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Zhang C, Liu S, Zhu Q, Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem 2005; 48:2325-35. [PMID: 15801826 DOI: 10.1021/jm049314d] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed a knowledge-based statistical energy function for protein-ligand, protein-protein, and protein-DNA complexes by using 19 atom types and a distance-scale finite ideal-gas reference (DFIRE) state. The correlation coefficients between experimentally measured protein-ligand binding affinities and those predicted by the DFIRE energy function are around 0.63 for one training set and two testing sets. The energy function also makes highly accurate predictions of binding affinities of protein-protein and protein-DNA complexes. Correlation coefficients between theoretical and experimental results are 0.73 for 82 protein-protein (peptide) complexes and 0.83 for 45 protein-DNA complexes, despite the fact that the structures of protein-protein (peptide) and protein-DNA complexes were not used in training the energy function. The results of the DFIRE energy function on protein-ligand complexes are compared to the published results of 12 other scoring functions generated from either physical-based, knowledge-based, or empirical methods. They include AutoDock, X-Score, DrugScore, four scoring functions in Cerius 2 (LigScore, PLP, PMF, and LUDI), four scoring functions in SYBYL (F-Score, G-Score, D-Score, and ChemScore), and BLEEP. While the DFIRE energy function is only moderately successful in ranking native or near native conformations, it yields the strongest correlation between theoretical and experimental binding affinities of the testing sets and between rmsd values and energy scores of docking decoys in a benchmark of 100 protein-ligand complexes. The parameters and the program of the all-atom DFIRE energy function are freely available for academic users at http://theory.med.buffalo.edu.
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Affiliation(s)
- Chi Zhang
- Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, New York 14214, USA
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7
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Giachetti A, La Penna GL, Perico A, Banci L. Modeling the backbone dynamics of reduced and oxidized solvated rat microsomal cytochrome b5. Biophys J 2005; 87:498-512. [PMID: 15240483 PMCID: PMC1304371 DOI: 10.1529/biophysj.103.036657] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this article, a description of the statistics and dynamics of cytochrome b(5) in both reduced and oxidized forms is given. Results of molecular dynamics computer simulations in the explicit solvent have been combined with mode-coupling diffusion models including and neglecting the molecule-solvent correlations. R(1) and R(1 rho) nuclear magnetic relaxation parameters of (15)N in the protein backbone have been calculated and compared with experiments. Slight changes in charge density in the heme upon oxidation produces a cascade of changes in charge distributions from heme propionates up to charged residues approximately 1.5 nm from Fe. These changes in charge distributions modify the molecular surface and the water shell surrounding the protein. The statistical changes upon oxidation can be included in diffusive models that physically explain the upper and lower limits of R(1 rho) relaxation parameters at high off-resonance fields.
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Affiliation(s)
- Andrea Giachetti
- Magnetic Resonance Center, University of Florence, Florence, Italy
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Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 2004; 56:93-101. [PMID: 15162489 DOI: 10.1002/prot.20019] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Extracting knowledge-based statistical potential from known structures of proteins is proved to be a simple, effective method to obtain an approximate free-energy function. However, the different compositions of amino acid residues at the core, the surface, and the binding interface of proteins prohibited the establishment of a unified statistical potential for folding and binding despite the fact that the physical basis of the interaction (water-mediated interaction between amino acids) is the same. Recently, a physical state of ideal gas, rather than a statistically averaged state, has been used as the reference state for extracting the net interaction energy between amino acid residues of monomeric proteins. Here, we find that this monomer-based potential is more accurate than an existing all-atom knowledge-based potential trained with interfacial structures of dimers in distinguishing native complex structures from docking decoys (100% success rate vs. 52% in 21 dimer/trimer decoy sets). It is also more accurate than a recently developed semiphysical empirical free-energy functional enhanced by an orientation-dependent hydrogen-bonding potential in distinguishing native state from Rosetta docking decoys (94% success rate vs. 74% in 31 antibody-antigen and other complexes based on Z score). In addition, the monomer potential achieved a 93% success rate in distinguishing true dimeric interfaces from artificial crystal interfaces. More importantly, without additional parameters, the potential provides an accurate prediction of binding free energy of protein-peptide and protein-protein complexes (a correlation coefficient of 0.87 and a root-mean-square deviation of 1.76 kcal/mol with 69 experimental data points). This work marks a significant step toward a unified knowledge-based potential that quantitatively captures the common physical principle underlying folding and binding. A Web server for academic users, established for the prediction of binding free energy and the energy evaluation of the protein-protein complexes, may be found at http://theory.med.buffalo.edu.
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Affiliation(s)
- Song Liu
- Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA
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9
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Abstract
The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody-antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near-native structure within the top 2000 predictions at the 6 degrees rotational sampling density, with an average of 52 near-native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/~ rong/dock.
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Affiliation(s)
- Rong Chen
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
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10
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Croney JC, Helms MK, Jameson DM, Larsen RW. Conformational dynamics and temperature dependence of photoinduced electron transfer within self-assembled coproporphyrin:cytochrome c complexes. Biophys J 2003; 84:4135-43. [PMID: 12770916 PMCID: PMC1302992 DOI: 10.1016/s0006-3495(03)75138-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2002] [Accepted: 01/28/2003] [Indexed: 10/21/2022] Open
Abstract
The focus of the present study is to better understand the complex factors influencing intermolecular electron transfer (ET) in biological molecules using a model system involving free-base coproporphyrin (COP) complexed with horse heart cytochrome c (Cc). Coproporphyrin exhibits bathochromic shifts in both the Soret and visible absorption bands in the presence of Cc and an absorption difference titration reveals a 1:1 complex with an association constant of 2.63 +/- 0.05 x 10(5) M(-1). At 20 degrees C, analysis of time-resolved fluorescence data reveals two lifetime components consisting of a discrete lifetime at 15.0 ns (free COP) and a Gaussian distribution of lifetimes centered at 2.8 ns (representing (1)COP --> Cc ET). Temperature-dependent, time-resolved fluorescence data demonstrate a shift in singlet lifetime as well as changes in the distribution width (associated with the complex). By fitting these data to semiclassical Marcus theory, the reorganizational energy (lambda) of the singlet state electron transfer was calculated to be 0.89 eV, consistent with values for other porphyrin/Cc intermolecular ET reactions. Using nanosecond transient absorption spectroscopy the temperature dependences of the forward and thermal back ET originating from triplet state were examined ((3)COP --> Cc ET). Fits of the temperature dependence of the rate constants to semiclassical Marcus theory gave lambda of 0.39 eV and 0.11 eV for the forward and back triplet ET, respectively (k(f) = (7.6 +/- 0.3) x 10(6) s(-1), k(b) = (2.4 +/- 0.3) x 10(5) s(-1)). The differing values of lambda for the forward and back triplet ET demonstrate that these ET reactions do not occur within a static complex. Comparing these results with previous studies of the uroporphyrin:Cc and tetrakis (4-carboxyphenyl)porphyrin:Cc complexes suggests that side-chain flexibility gives rise to the conformational distributions in the (1)COP --> Cc ET whereas differences in overall porphyrin charge regulates gating of the back ET reaction (reduced Cc --> COP(+)).
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Affiliation(s)
- John C Croney
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA
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Erman JE, Vitello LB. Yeast cytochrome c peroxidase: mechanistic studies via protein engineering. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:193-220. [PMID: 12044899 DOI: 10.1016/s0167-4838(02)00317-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cytochrome c peroxidase (CcP) is a yeast mitochondrial enzyme that catalyzes the reduction of hydrogen peroxide to water by ferrocytochrome c. It was the first heme enzyme to have its crystallographic structure determined and, as a consequence, has played a pivotal role in developing ideas about structural control of heme protein reactivity. Genetic engineering of the active site of CcP, along with structural, spectroscopic, and kinetic characterization of the mutant proteins has provided considerable insight into the mechanism of hydrogen peroxide activation, oxygen-oxygen bond cleavage, and formation of the higher-oxidation state intermediates in heme enzymes. The catalytic mechanism involves complex formation between cytochrome c and CcP. The cytochrome c/CcP system has been very useful in elucidating the complexities of long-range electron transfer in biological systems, including protein-protein recognition, complex formation, and intracomplex electron transfer processes.
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Affiliation(s)
- James E Erman
- Department of Chemistry and Biochemistry, Northern Illinois University, Normal Rd., DeKalb, IL 60115-2862, USA.
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12
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Barzykin AV, Seki K, Tachiya M. Kinetics of diffusion-assisted reactions in microheterogeneous systems. Adv Colloid Interface Sci 2001; 89-90:47-140. [PMID: 11215811 DOI: 10.1016/s0001-8686(00)00053-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This review is focused on the basic theory of diffusion-assisted reactions in microheterogeneous systems, from porous solids to self-organized colloids and biomolecules. Rich kinetic behaviors observed experimentally are explained in a unified fashion using simple concepts of competing distance and time scales of the reaction and the embedding structure. We mainly consider pseudo-first-order reactions, such as luminescence quenching, described by the Smoluchowski type of equation for the reactant pair distribution function with a sink term defined by the reaction mechanism. Microheterogeneity can affect the microscopic rate constant. It also enters the evolution equation through various spatial constraints leading to complicated boundary conditions and, possibly, to the reduction of dimensionality of the diffusion space. The reaction coordinate and diffusive motion along this coordinate are understood in a general way, depending on the problem at hand. Thus, the evolution operator can describe translational and rotational diffusion of molecules in a usual sense, it can be a discrete random walk operator when dealing with hopping of adsorbates in solids, or it can correspond to conformational fluctuations in proteins. Mathematical formulation is universal but physical consequences can be different. Understanding the principal features of reaction kinetics in microheterogeneous systems enables one to extract important structural and dynamical information about the host environments by analyzing suitably designed experiments, it helps building effective strategies for computer simulations, and ultimately opens possibilities for designing systems with controllable reactivity properties.
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Affiliation(s)
- A V Barzykin
- National Institute of Materials and Chemical Research, Tsukuba, Ibaraki, Japan.
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13
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Croney JC, Helms MK, Jameson DM, Larsen RW. Temperature Dependence of Photoinduced Electron Transfer within Self-Assembled Uroporphyrin−CytochromecComplexes. J Phys Chem B 2000. [DOI: 10.1021/jp991007+] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Gómez-Moreno C, Martínez-Júlvez M, Medina M, Hurley JK, Tollin G. Protein-protein interaction in electron transfer reactions: the ferredoxin/flavodoxin/ferredoxin:NADP+ reductase system from Anabaena. Biochimie 1998; 80:837-46. [PMID: 9893942 DOI: 10.1016/s0300-9084(00)88878-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Electron transfer reactions involving protein-protein interactions require the formation of a transient complex which brings together the two redox centres exchanging electrons. This is the case for the flavoprotein ferredoxin:NADP+ reductase (FNR) from the cyanobacterium Anabaena, an enzyme which interacts with ferredoxin in the photosynthetic pathway to receive the electrons required for NADP+ reduction. The reductase shows a concave cavity in its structure into which small proteins such as ferredoxin can fit. Flavodoxin, an FMN-containing protein that is synthesised in cyanobacteria under iron-deficient conditions, plays the same role as ferredoxin in its interaction with FNR in spite of its different structure, size and redox cofactor. There are a number of negatively charged amino acid residues on the surface of ferredoxin and flavodoxin that play a role in the electron transfer reaction with the reductase. Thus far, in only one case has charge replacement of one of the acidic residues produced an increase in the rate of electron transfer, whereas in several other cases a decrease in the rate is observed. In the most dramatic example, replacement of Glu at position 94 of Anabaena ferredoxin results in virtually the complete loss of ability to transfer electrons. Charge-reversal of positively charged amino acid residues in the reductase also produces strong effects on the rate of electron transfer. Several degrees of impairment have been observed, the most significant involving a positively charged Lys at position 75 which appears to be essential for the stability of the complex between the reductase and ferredoxin. The results presented in this paper provide a clear demonstration of the importance of electrostatic interactions on the stability of the transient complex formed during electron transfer by the proteins presently under study.
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Affiliation(s)
- C Gómez-Moreno
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
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15
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Moore GR, Cox MC, Crowe D, Osborne MJ, Rosell FI, Bujons J, Barker PD, Mauk MR, Mauk AG. N epsilon,N epsilon-dimethyl-lysine cytochrome c as an NMR probe for lysine involvement in protein-protein complex formation. Biochem J 1998; 332 ( Pt 2):439-49. [PMID: 9601073 PMCID: PMC1219499 DOI: 10.1042/bj3320439] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reductively dimethylated derivatives of horse and yeast iso-1-ferricytochromes c have been prepared and characterized for use as NMR probes of the complexes formed by cytochrome c with bovine liver cytochrome b5 and yeast cytochrome c peroxidase. The electrostatic properties and structures of the derivatized cytochromes are not significantly perturbed by the modifications; neither are the electrostatics of protein-protein complex formation or rates of interprotein electron transfer. Two-dimensional 1H-13C NMR spectroscopy of the complexes formed by the derivatized cytochromes with cytochrome b5 and cytochrome c peroxidase has been used to investigate the number and identity of lysine residues of cytochrome c that are involved in interprotein interactions of cytochrome c. The NMR data are incompatible with simple static models proposed previously for the complexes formed by these proteins, but are consistent with the presence of multiple, interconverting complexes of comparable stability, consistent with studies employing Brownian dynamics to model the complexes. The NMR characteristics of the Nepsilon,Nepsilon-dimethyl-lysine groups, their chemical shift dispersion, oxidation state and temperature dependences and the possibility of chemical exchange phenomena are discussed with relevance to the utility of Nepsilon, Nepsilon-dimethyl-lysine's being a generally useful derivative for characterizing protein-protein complexes.
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Affiliation(s)
- G R Moore
- School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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16
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Hake R, Corin A, McLendon G. Extragenic Compensation in Complex Formation: Restoration of Binding of a Charge Reversal Mutant of Cytochrome c Peroxidase (D217K) by a Compensatory Charge Reversal in Cytochrome c (K77D). J Am Chem Soc 1997. [DOI: 10.1021/ja970260p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard Hake
- Miami Valley Laboratories, Proctor and Gamble Cincinnati, Ohio 45253-8707 Scriptgen Pharmaceuticals, Incorporated 200 Boston Avenue, Medford, Massachusetts 02155 Department of Chemistry, Princeton University Princeton, New Jersey 08544
| | - Alan Corin
- Miami Valley Laboratories, Proctor and Gamble Cincinnati, Ohio 45253-8707 Scriptgen Pharmaceuticals, Incorporated 200 Boston Avenue, Medford, Massachusetts 02155 Department of Chemistry, Princeton University Princeton, New Jersey 08544
| | - George McLendon
- Miami Valley Laboratories, Proctor and Gamble Cincinnati, Ohio 45253-8707 Scriptgen Pharmaceuticals, Incorporated 200 Boston Avenue, Medford, Massachusetts 02155 Department of Chemistry, Princeton University Princeton, New Jersey 08544
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17
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Larsen RW, Omdal DH, Jasuja R, Niu SL, Jameson DM. Conformational Modulation of Electron Transfer within Electrostatic Porphyrin: Cytochrome c Complexes. J Phys Chem B 1997. [DOI: 10.1021/jp9640235] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Randy W. Larsen
- Departments of Chemistry and Biochemistry and Biophysics, University of Hawaii at Manoa, 2545 The Mall, Honolulu, Hawaii 96822
| | - Dawn H. Omdal
- Departments of Chemistry and Biochemistry and Biophysics, University of Hawaii at Manoa, 2545 The Mall, Honolulu, Hawaii 96822
| | - Ravi Jasuja
- Departments of Chemistry and Biochemistry and Biophysics, University of Hawaii at Manoa, 2545 The Mall, Honolulu, Hawaii 96822
| | - Shui Lin Niu
- Departments of Chemistry and Biochemistry and Biophysics, University of Hawaii at Manoa, 2545 The Mall, Honolulu, Hawaii 96822
| | - David M. Jameson
- Departments of Chemistry and Biochemistry and Biophysics, University of Hawaii at Manoa, 2545 The Mall, Honolulu, Hawaii 96822
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18
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Zhou JS, Tran ST, McLendon G, Hoffman BM. Photoinduced Electron Transfer between CytochromecPeroxidase (D37K) and Zn-Substituted Cytochromec: Probing the Two-Domain Binding and Reactivity of the Peroxidase. J Am Chem Soc 1997. [DOI: 10.1021/ja962399q] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Nocek JM, Zhou JS, De Forest S, Priyadarshy S, Beratan DN, Onuchic JN, Hoffman BM. Theory and Practice of Electron Transfer within Proteinminus signProtein Complexes: Application to the Multidomain Binding of Cytochrome c by Cytochrome c Peroxidase. Chem Rev 1996; 96:2459-2490. [PMID: 11848833 DOI: 10.1021/cr9500444] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judith M. Nocek
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and Department of Physics, University of California at San Diego, LaJolla, California 92093-0319
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20
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The cytochrome C peroxidase oxidation of ferrocytochrome C. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1057-8943(96)80006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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21
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Matthis AL, Vitello LB, Erman JE. Oxidation of yeast iso-1 ferrocytochrome c by yeast cytochrome c peroxidase compounds I and II. Dependence upon ionic strength. Biochemistry 1995; 34:9991-9. [PMID: 7632698 DOI: 10.1021/bi00031a022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The reduction of cytochrome c peroxidase compound I by excess yeast iso-1 ferrocytochrome c is biphasic. Two pseudo-first-order rate constants can be measured by stopped-flow techniques. The fastest rate process is the reduction of cytochrome c peroxidase compound I to compound II, and the slower process is the reduction of II to the native enzyme. The yeast iso-1 ferrocytochrome c concentration dependence of the reduction of cytochrome c peroxidase compound I to compound II is consistent with a mechanism involving two binding sites for cytochrome c on cytochrome c peroxidase. Electron transfer from cytochrome c bound at the high-affinity binding site to the Fe(IV) site in cytochrome c peroxidase compound I is dependent upon ionic strength, increasing from 15 +/- 6 to 2000 +/- 100 s-1 over the ionic strength range 0.01-0.20 M. The reduction rate of the Fe(IV) site in the 2:1 yeast iso-1 ferrocytochrome c/cytochrome c peroxidase compound I complex is essentially independent of ionic strength with a value of 3800 +/- 300 s-1. The Fe(IV) site in cytochrome c peroxidase compound I is preferentially reduced by yeast ferrocytochrome c between 0.01 and 0.20 M ionic strength while the Trp-191 radical is preferentially reduced above 0.30 M ionic strength. The association rate constant for the binding of yeast iso-1 ferrocytochrome c to cytochrome c peroxidase compound I can be evaluated and varies from a remarkable 1 x 10(10) M-1 s-1 at 0.01 M ionic strength to 1.2 x 10(5) M-1 s-1 at 1.0 M ionic strength. Between 0.01 and 0.20 M ionic strength, the reduction of cytochrome c peroxidase compound II to the native enzyme is anomalous. The reaction is independent of the cytochrome c concentration and directly proportional to the initial cytochrome c peroxidase compound I concentration.
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Affiliation(s)
- A L Matthis
- Department of Chemistry, Northern Illinois University, DeKalb 60115, USA
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22
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Matthis AL, Erman JE. Cytochrome c peroxidase-catalyzed oxidation of yeast iso-1 ferrocytochrome c by hydrogen peroxide. Ionic strength dependence of the steady-state parameters. Biochemistry 1995; 34:9985-90. [PMID: 7632697 DOI: 10.1021/bi00031a021] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The cytochrome c peroxidase-catalyzed oxidation of yeast iso-1 ferrocytochrome c by hydrogen peroxide can be understood on the basis of a mechanism involving two cytochrome c-binding sites on cytochrome c peroxidase. Values of the equilibrium dissociation constants for both the high- and low-affinity binding sites determined from the steady-state kinetic measurements agree well with published values obtained by vastly different techniques, providing strong support for the two-binding site mechanism. Maximum enzyme turnover via oxidation of cytochrome c bound at the high-affinity site increases from 2 to 860 s-1 as the ionic strength is increased from 0.010 to 0.20 M. Oxidation of yeast iso-1 ferrocytochrome c is faster in the 2:1 complexes of cytochrome c peroxidase compounds I and II in comparison to the 1:1 complexes. The oxidation rates in the 2:1 complex are macroscopic rate constants equal to the sum of the oxidation rates via both the high- and low-affinity sites. The maximum enzyme turnover via the 2:1 complex increases from 1100 to 2700 s-1 over the ionic strength range 0.010-0.070 M.
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Affiliation(s)
- A L Matthis
- Department of Chemistry, Northern Illinois University, DeKalb 60115, USA
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23
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Kresheck GC, Vitello LB, Erman JE. Calorimetric studies on the interaction of horse ferricytochrome c and yeast cytochrome c peroxidase. Biochemistry 1995; 34:8398-405. [PMID: 7599130 DOI: 10.1021/bi00026a022] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding of horse ferricytochrome c to yeast cytochrome c peroxidase at pH 6.0 in 8.7 mM phosphate buffer (0.0100 M ionic strength) is characterized by a small, unfavorable enthalpy change (+1.91 +/- 0.16 kcal mol-1) and a large, positive entropy change (+37 +/- 1 eu). The free energy of binding depends strongly upon ionic strength, increasing from -9.01 to -4.51 kcal mol-1 between 0.0100 and 0.200 M ionic strength. The increase in free energy is due solely to the change in entropy over this ionic strength range, with the entropy change decreasing from 37 +/- 1 to 22 +/- 3 eu between 0.0100 and 0.200 M ionic strength. The observed enthalpy change remains constant over the same ionic strength range. At 0.0100 M ionic strength, complex formation is accompanied by the release of 0.54 +/- 0.11 proton, causing a variation in the observed enthalpy of reaction depending upon the buffer. After accounting for proton binding to the buffer, the corrected values for the enthalpy and entropy of binding are +2.84 +/- 0.26 kcal mol-1 and +21 +/- 3 eu, respectively. At 0.05 M ionic strength, the observed change in heat capacity, delta Cp, for the reaction between horse ferricytochrome c and cytochrome c peroxidase is essentially zero, 1.6 +/- 9.6 cal mol-1 K-1. The corrected delta Cp for binding is -28 +/- 10 cal mol-1 K-1 after accounting for proton binding to the buffer. No evidence for formation of a 2:1 horse ferricytochrome c/cytochrome c peroxidase complex was obtained in this study.
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Affiliation(s)
- G C Kresheck
- Department of Chemistry, Northern Illinois University, DeKalb 60115, USA
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24
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Wang ZX. An exact mathematical expression for describing competitive binding of two different ligands to a protein molecule. FEBS Lett 1995; 360:111-4. [PMID: 7875313 DOI: 10.1016/0014-5793(95)00062-e] [Citation(s) in RCA: 284] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The dissociation constant for the binding of a spectroscopically invisible or non-radioactive ligand to its protein receptor can be determined in a competition experiment by using a structural analog that contains a reporter group. Many plotting and numerical analysis methods have been developed to calculate the binding constant of unlabeled ligand from the displacement experiments. However, a common problem with these plotting methods is that the equation transformations inevitably result in non-standard error distribution, and thus simple linear regression can not be used to extract correct values for the parameters. In the case of the numerical analysis methods, one would be faced with the possible existence of multiple solutions. In this paper, the exact mathematical expression for describing competitive binding of two different ligands to a protein molecule is presented in terms of the total concentrations of species in the system. Thus, using a commercially available non-linear regression program, all unknown parameters for describing this system can be determined by fitting the experimental data to the algebraically explicit equation without any data transformations. The distribution curves of all the species in the system can also be constructed with this equation. It is particularly useful for the cases in which the concentrations of all the species in the system are comparable to each other.
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Affiliation(s)
- Z X Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, China
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25
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Abstract
A considerable part of important biological processes is governed by the noncovalent association of peptides and proteins. Various types of intermolecular forces may be involved in the formation of these molecular assemblies. This review gives a brief account of the physicochemical bases of interactive forces, with special emphasis on their impact on various peptide-protein interactions; summarizes the newest biochemical and biophysical methods for the study of such interactions; and discusses the role of various hydrophilic and hydrophobic forces in peptide-protein interactions in various fields of life sciences, such as immunology, enzymology, receptor binding, and toxicology.
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Affiliation(s)
- T Cserháti
- Central Research Institute for Chemistry, Hungarian Academy of Sciences, Budapest
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26
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English AM, Tsaprailis G. Catalytic Structure–Function Relationships in Heme Peroxidases. ADVANCES IN INORGANIC CHEMISTRY 1995. [DOI: 10.1016/s0898-8838(08)60116-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Zhou HX. Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics. Biophys J 1993; 64:1711-26. [PMID: 8396447 PMCID: PMC1262506 DOI: 10.1016/s0006-3495(93)81543-1] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A unified model is presented for protein-protein association processes that are under the influences of electrostatic interaction and diffusion (e.g., protein oligomerization, enzyme catalysis, electron and energy transfer). The proteins are modeled as spheres that bear point charges and undergo translational and rotational Brownian motion. Before association can occur the two spheres have to be aligned properly to form a reaction complex via diffusion. The reaction complex can either go on to form the product or it can dissociate into the separate reactants through diffusion. The electrostatic interaction, like diffusion, influences every step except the one that brings the reaction complex into the product. The interaction potential is obtained by extending the Kirkwood-Tanford protein model (Tanford, C., and J. G. Kirkwood. 1957. J. Am. Chem. Soc. 79:5333-5339) to two charge-embedded spheres and solving the consequent equations under a particular basis set. The time-dependent association rate coefficient is then obtained through Brownian dynamics simulations according an algorithm developed earlier (Zhou, H.-X. 1990. J. Phys. Chem. 94:8794-8800). This method is applied to a model system of the cytochrome c and cytochrome c peroxidase association process and the results confirm the experimental dependence of the association rate constant on the solution ionic strength. An important conclusion drawn from this study is that when the product is formed by very specific alignment of the reactants, as is often the case, the effect of the interaction potential is simply to scale the association rate constant by a Boltzmann factor. This explains why mutations in the interface of the reaction complex have strong influences on the association rate constant whereas those away from the interface have minimal effects. It comes about because the former mutations change the interaction potential of the reaction complex significantly and the latter ones do not.
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Affiliation(s)
- H X Zhou
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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28
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Corin AF, Hake RA, McLendon G, Hazzard JT, Tollin G. Effects of surface amino acid replacements in cytochrome c peroxidase on intracomplex electron transfer from cytochrome c. Biochemistry 1993; 32:2756-62. [PMID: 8384478 DOI: 10.1021/bi00062a004] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Transient absorption techniques were used to measure the intracomplex electron transfer rates between four recombinant yeast cytochrome c peroxidases and iso-1 cytochrome c (cytc). The binding affinities and catalytic activities with cytc were previously examined [Corin et al. (1991) Biochemistry 30, 11585]. The four include a wild-type peroxidase (ECcP) and three others, each of which has one surface aspartic acid converted to lysine at position 37, 79, or 217. These sites have been suggested to be within or proximal to the recognition site for cytc. These mutants conduct electron transfer with cytc but differ with respect to the ionic strength profiles of their limiting rate constants. At pH and mu = 114 mM, ECcP and D217K show similar limiting rate constants for electron transfer with cytc, k(lim), of ca. 2000 s-1. In the same peroxidase concentration range, the D37K mutant exhibits a k(obs) of ca. 100 s-1. Instability of the compound I form of D79K prevented a complete study of the intracomplex kinetics of this mutant by this technique. At pH 6 and low ionic strength (8 mM), D37K exhibits a dramatic increase in k(obs) to ca. 800 s-1 while the other two recombinants show a marked decrease to values < 150 s-1. D37K displays much lower affinity for cytc than do the other peroxidases at higher ionic strengths [Hake et al. (1992) J. Am. Chem. Soc. 114, 5442], thus preventing adequate complexation necessary for efficient electron transfer. Variations in binding affinity do not explain the more subtle ionic strength kinetic profile observed for D217K.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A F Corin
- NSF Center for Photoinduced Charge Transfer, University of Rochester, New York 14627
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29
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Pelletier H, Kraut J. Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Science 1992; 258:1748-55. [PMID: 1334573 DOI: 10.1126/science.1334573] [Citation(s) in RCA: 576] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The crystal structure of a 1:1 complex between yeast cytochrome c peroxidase and yeast iso-1-cytochrome c was determined at 2.3 A resolution. This structure reveals a possible electron transfer pathway unlike any previously proposed for this extensively studied redox pair. The shortest straight line between the two hemes closely follows the peroxidase backbone chain of residues Ala194, Ala193, Gly192, and finally Trp191, the indole ring of which is perpendicular to, and in van der Waals contact with, the peroxidase heme. The crystal structure at 2.8 A of a complex between yeast cytochrome c peroxidase and horse heart cytochrome c was also determined. Although crystals of the two complexes (one with cytochrome c from yeast and the other with cytochrome c from horse) grew under very different conditions and belong to different space groups, the two complex structures are closely similar, suggesting that cytochrome c interacts with its redox partners in a highly specific manner.
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Affiliation(s)
- H Pelletier
- Department of Chemistry, University of California, San Diego, La Jolla 92093-0317
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30
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Kuzmic P, Moss ML, Kofron JL, Rich DH. Fluorescence displacement method for the determination of receptor-ligand binding constants. Anal Biochem 1992; 205:65-9. [PMID: 1332537 DOI: 10.1016/0003-2697(92)90579-v] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The equilibrium constant for the binding of a spectroscopically invisible ligand to its protein receptor can be determined in a competition experiment, by using a structural analog that contains a reporter group (fluorophor). A novel mathematical treatment of the multiple equilibria allows the analysis to be performed under tight-binding conditions. The equilibrium equation for mixtures of two mutually competitive tight-binding ligands can be expressed in a recursive form, a form in which the dependent variable appears on both sides and the solution is found iteratively. The algorithm is also applicable to the special case of weak binding, where the concentration of the bound ligand can be neglected in the mass balance. The fluorescence displacement method is demonstrated on the determination cyclophilin binding to cyclosporin A (CsA), in competition with its fluorescent derivative, [D-Lys(Dns)]8-CsA.
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Affiliation(s)
- P Kuzmic
- School of Pharmacy, University of Wisconsin-Madison 53706
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