Literature DB >> 14727167

On the role of the axial ligand in heme proteins: a theoretical study.

Patrik Rydberg1, Emma Sigfridsson, Ulf Ryde.   

Abstract

We present a systematic investigation of how the axial ligand in heme proteins influences the geometry, electronic structure, and spin states of the active site, and the energies of the reaction cycles. Using the density functional B3LYP method and medium-sized basis sets, we have compared models with His, His+Asp, Cys, Tyr, and Tyr+Arg as found in myoglobin and hemoglobin, peroxidases, cytochrome P450, and heme catalases, respectively. We have studied 12 reactants and intermediates of the reaction cycles of these enzymes, including complexes with H(2)O, OH(-), O(2-), CH(3)OH, O(2), H(2)O(2), and HO(2)(-) in various formal oxidation states of the iron ion (II to V). The results show that His gives ~0.6 V higher reduction potentials than the other ligands. In particular, it is harder to reduce and protonate the O(2) complex with His than with the other ligands, in accordance with the O(2) carrier function of globins and the oxidative chemistry of the other proteins. For most properties, the trend Cys<Tyr<Tyr+Arg<His+Asp<His is found, reflecting the donor capacity of the various ligands. Thus, it is easier to reduce compound I with a His+Asp ligand than with a Cys ligand, in accordance with the one-electron chemistry of peroxidases and the hydroxylation reactions of cytochromes P450. However, the Tyr complexes have an unusually low affinity for all neutral ligands, giving them a slightly enhanced driving force in the oxidation of H(2)O(2) by compound I.

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Year:  2004        PMID: 14727167     DOI: 10.1007/s00775-003-0515-y

Source DB:  PubMed          Journal:  J Biol Inorg Chem        ISSN: 0949-8257            Impact factor:   3.358


  64 in total

1.  Role of the heme active site and protein environment in structure, spectra, and function of the cytochrome p450s.

Authors:  G H Loew; D L Harris
Journal:  Chem Rev       Date:  2000-02-09       Impact factor: 60.622

2.  Peroxidase activity in prostaglandin endoperoxide H synthase-1 occurs with a neutral histidine proximal heme ligand.

Authors:  S A Seibold; J F Cerda; A M Mulichak; I Song; R M Garavito; T Arakawa; W L Smith; G T Babcock
Journal:  Biochemistry       Date:  2000-06-06       Impact factor: 3.162

Review 3.  Heme enzyme crystal structures.

Authors:  T L Poulos
Journal:  Adv Inorg Biochem       Date:  1988

4.  Roles of the proximal heme thiolate ligand in cytochrome p450(cam).

Authors:  K Auclair; P Moënne-Loccoz; P R Ortiz de Montellano
Journal:  J Am Chem Soc       Date:  2001-05-30       Impact factor: 15.419

5.  Engineering cytochrome c peroxidase into cytochrome P450: a proximal effect on heme-thiolate ligation.

Authors:  J A Sigman; A E Pond; J H Dawson; Y Lu
Journal:  Biochemistry       Date:  1999-08-24       Impact factor: 3.162

6.  A nuclear Overhauser effect study of the heme crevice in the resting state and compound I of horseradish peroxidase: evidence for cation radical delocalization to the proximal histidine.

Authors:  V Thanabal; G N La Mar; J S de Ropp
Journal:  Biochemistry       Date:  1988-07-26       Impact factor: 3.162

7.  The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations.

Authors:  Jan C Schöneboom; Hai Lin; Nathalie Reuter; Walter Thiel; Shimrit Cohen; François Ogliaro; Sason Shaik
Journal:  J Am Chem Soc       Date:  2002-07-10       Impact factor: 15.419

8.  Role of the proximal ligand in peroxidase catalysis. Crystallographic, kinetic, and spectral studies of cytochrome c peroxidase proximal ligand mutants.

Authors:  K Choudhury; M Sundaramoorthy; A Hickman; T Yonetani; E Woehl; M F Dunn; T L Poulos
Journal:  J Biol Chem       Date:  1994-08-12       Impact factor: 5.157

9.  Comparison of the chemical properties of iron and cobalt porphyrins and corrins.

Authors:  Kasper P Jensen; Ulf Ryde
Journal:  Chembiochem       Date:  2003-05-09       Impact factor: 3.164

10.  The proximal ligand variant His93Tyr of horse heart myoglobin.

Authors:  D P Hildebrand; D L Burk; R Maurus; J C Ferrer; G D Brayer; A G Mauk
Journal:  Biochemistry       Date:  1995-02-14       Impact factor: 3.162

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  31 in total

Review 1.  Spectroscopic studies of the cytochrome P450 reaction mechanisms.

Authors:  Piotr J Mak; Ilia G Denisov
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-06-28       Impact factor: 3.036

2.  How are hydrogen bonds modified by metal binding?

Authors:  Charlotte Husberg; Ulf Ryde
Journal:  J Biol Inorg Chem       Date:  2013-03-31       Impact factor: 3.358

3.  The intrinsic axial ligand effect on propene oxidation by horseradish peroxidase versus cytochrome P450 enzymes.

Authors:  Devesh Kumar; Sam P de Visser; Pankaz K Sharma; Etienne Derat; Sason Shaik
Journal:  J Biol Inorg Chem       Date:  2005-02-19       Impact factor: 3.358

4.  Histidine-Lysine Axial Ligand Switching in a Hemoglobin: A Role for Heme Propionates.

Authors:  Dillon B Nye; Matthew R Preimesberger; Ananya Majumdar; Juliette T J Lecomte
Journal:  Biochemistry       Date:  2018-01-10       Impact factor: 3.162

5.  Fe L-edge X-ray absorption spectroscopy of low-spin heme relative to non-heme Fe complexes: delocalization of Fe d-electrons into the porphyrin ligand.

Authors:  Rosalie K Hocking; Erik C Wasinger; Yi-Long Yan; Frank M F Degroot; F Ann Walker; Keith O Hodgson; Britt Hedman; Edward I Solomon
Journal:  J Am Chem Soc       Date:  2007-01-10       Impact factor: 15.419

6.  Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study.

Authors:  Dmytro Bykov; Frank Neese
Journal:  J Biol Inorg Chem       Date:  2010-12-02       Impact factor: 3.358

Review 7.  Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins.

Authors:  Xiongyi Huang; John T Groves
Journal:  Chem Rev       Date:  2017-12-29       Impact factor: 60.622

8.  The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.

Authors:  Kristina Nilsson; Hans-Petter Hersleth; Thomas H Rod; K Kristoffer Andersson; Ulf Ryde
Journal:  Biophys J       Date:  2004-08-31       Impact factor: 4.033

9.  Noninnocent effect of axial ligand on the heme degradation process: a theoretical approach to hydrolysis pathway of verdoheme to biliverdin.

Authors:  Parisa R Jamaat; Nasser Safari; Mina Ghiasi; S Shahab-al-din Naghavi; Mansour Zahedi
Journal:  J Biol Inorg Chem       Date:  2007-10-23       Impact factor: 3.358

10.  Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin.

Authors:  Justin E Elenewski; John C Hackett
Journal:  J Comput Chem       Date:  2013-05-14       Impact factor: 3.376

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