1
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Sun MZ, Lyu LS, Zheng QC. How does multiple substrate binding lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan? A theoretical study. Phys Chem Chem Phys 2023; 25:5164-5173. [PMID: 36723118 DOI: 10.1039/d2cp05634h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CYP2D6 is one of the most important metalloenzymes involved in the biodegradation of many drug molecules in the human body. It has been found that multiple substrate binding can lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan (DM), but the corresponding theoretical mechanism is rarely reported. Therefore, we chose DM as the probe and performed molecular dynamics simulations and quantum mechanical calculations on CYP2D6-DM systems to investigate the mechanism of how the multiple substrate binding leads to the substrate inhibition of CYP2D6 metabolizing substrates. According to our results, three gate residues (Arg221, Val374, and Phe483) for the catalytic pocket are determined. We also found that the multiple substrate binding can lead to substrate inhibition by reducing the stability of CYP2D6 binding DM and increasing the reactive activation energy of the rate-determining step. Our findings would help to understand the substrate inhibition of CYP2D6 metabolizing the DM and enrich the knowledge of the drug-drug interactions for the cytochrome P450 superfamily.
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Affiliation(s)
- Min-Zhang Sun
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Ling-Shan Lyu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qing-Chuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130023, China. .,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
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2
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Tian G, Hao G, Chen X, Liu Y. Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC. Inorg Chem 2021; 60:13539-13549. [PMID: 34382397 DOI: 10.1021/acs.inorgchem.1c01864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.
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Affiliation(s)
- Ge Tian
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China.,School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Gangping Hao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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3
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Mukherjee S, Nayek A, Bhunia S, Dey SG, Dey A. A Single Iron Porphyrin Shows pH Dependent Switch between "Push" and "Pull" Effects in Electrochemical Oxygen Reduction. Inorg Chem 2020; 59:14564-14576. [PMID: 32970430 DOI: 10.1021/acs.inorgchem.0c02408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The "push-pull" effects associated with heme enzymes manifest themselves through highly evolved distal amino acid environments and axial ligands to the heme. These conserved residues enhance their reactivities by orders of magnitude relative to small molecules that mimic the primary coordination. An instance of a mononuclear iron porphyrin with covalently attached pendent phenanthroline groups is reported which exhibit reactivity indicating a pH dependent "push" to "pull" transition in the same molecule. The pendant phenanthroline residues provide proton transfer pathways into the iron site, ensuring selective 4e-/4H+ reduction of O2 to water. The protonation of these residues at lower pH mimics the pull effect of peroxidases, and a coordination of an axial hydroxide ligand at high pH emulates the push effect of P450 monooxygenases. Both effects enhance the rate of O2 reduction by orders of magnitude over its value at neutral pH while maintaining exclusive selectivity for 4e-/4H+ oxygen reduction reaction.
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Affiliation(s)
- Sudipta Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sarmistha Bhunia
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
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4
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Chaturvedi SS, Ramanan R, Waheed SO, Ainsley J, Evison M, Ames JM, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Conformational Dynamics Underlies Different Functions of Human KDM7 Histone Demethylases. Chemistry 2019; 25:5422-5426. [PMID: 30817054 DOI: 10.1002/chem.201900492] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/26/2019] [Indexed: 11/11/2022]
Abstract
The human KDM7 subfamily histone H3 Nϵ-methyl lysine demethylases PHF8 (KDM7B) and KIAA1718 (KDM7A) have different substrate selectivities and are linked to genetic diseases and cancer. We describe experimentally based computational studies revealing that flexibility of the region linking the PHD finger and JmjC domains in PHF8 and KIAA1718 regulates interdomain interactions, the nature of correlated motions, and ultimately H3 binding and demethylation site selectivity. F279S an X-linked mental retardation mutation in PHF8 is involved in correlated motions with the iron ligands and second sphere residues. The calculations reveal key roles of a flexible protein environment in productive formation of enzyme-substrate complexes and suggest targeting the flexible KDM7 linker region is of interest from a medicinal chemistry perspective.
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Affiliation(s)
- Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Jon Ainsley
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
| | - Martin Evison
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
| | - Jennifer M Ames
- Centre for Research in Biosciences, University of West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | | | - Tatyana G Karabencheva-Christova
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 BST, UK
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5
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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6
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Mak PJ, Denisov IG. Spectroscopic studies of the cytochrome P450 reaction mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:178-204. [PMID: 28668640 PMCID: PMC5709052 DOI: 10.1016/j.bbapap.2017.06.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Saint Louis University, St. Louis, MO, United States.
| | - Ilia G Denisov
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States.
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7
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Shaik S, Mandal D, Ramanan R. Oriented electric fields as future smart reagents in chemistry. Nat Chem 2016; 8:1091-1098. [DOI: 10.1038/nchem.2651] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022]
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8
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Salvadori A, Del Frate G, Pagliai M, Mancini G, Barone V. Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2016; 116:1731-1746. [PMID: 27867214 PMCID: PMC5101850 DOI: 10.1002/qua.25207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 05/31/2023]
Abstract
The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.
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Affiliation(s)
- Andrea Salvadori
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | | | - Marco Pagliai
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
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9
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Davydov R, Im S, Shanmugam M, Gunderson WA, Pearl NM, Hoffman BM, Waskell L. Role of the Proximal Cysteine Hydrogen Bonding Interaction in Cytochrome P450 2B4 Studied by Cryoreduction, Electron Paramagnetic Resonance, and Electron-Nuclear Double Resonance Spectroscopy. Biochemistry 2016; 55:869-83. [PMID: 26750753 DOI: 10.1021/acs.biochem.5b00744] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crystallographic studies have shown that the F429H mutation of cytochrome P450 2B4 introduces an H-bond between His429 and the proximal thiolate ligand, Cys436, without altering the protein fold but sharply decreases the enzymatic activity and stabilizes the oxyferrous P450 2B4 complex. To characterize the influence of this hydrogen bond on the states of the catalytic cycle, we have used radiolytic cryoreduction combined with electron paramagnetic resonance (EPR) and (electron-nuclear double resonance (ENDOR) spectroscopy to study and compare their characteristics for wild-type (WT) P450 2B4 and the F429H mutant. (i) The addition of an H-bond to the axial Cys436 thiolate significantly changes the EPR signals of both low-spin and high-spin heme-iron(III) and the hyperfine couplings of the heme-pyrrole (14)N but has relatively little effect on the (1)H ENDOR spectra of the water ligand in the six-coordinate low-spin ferriheme state. These changes indicate that the H-bond introduced between His and the proximal cysteine decreases the extent of S → Fe electron donation and weakens the Fe(III)-S bond. (ii) The added H-bond changes the primary product of cryoreduction of the Fe(II) enzyme, which is trapped in the conformation of the parent Fe(II) state. In the wild-type enzyme, the added electron localizes on the porphyrin, generating an S = (3)/2 state with the anion radical exchange-coupled to the Fe(II). In the mutant, it localizes on the iron, generating an S = (1)/2 Fe(I) state. (iii) The additional H-bond has little effect on g values and (1)H-(14)N hyperfine couplings of the cryogenerated, ferric hydroperoxo intermediate but noticeably slows its decay during cryoannealing. (iv) In both the WT and the mutant enzyme, this decay shows a significant solvent kinetic isotope effect, indicating that the decay reflects a proton-assisted conversion to Compound I (Cpd I). (v) We confirm that Cpd I formed during the annealing of the cryogenerated hydroperoxy intermediate and that it is the active hydroxylating species in both WT P450 2B4 and the F429H mutant. (vi) Our data also indicate that the added H-bond of the mutation diminishes the reactivity of Cpd I.
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Affiliation(s)
- Roman Davydov
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
| | - Muralidharan Shanmugam
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - William A Gunderson
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Naw May Pearl
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, and VA Medical Center , 2215 Fuller Road, Ann Arbor, Michigan 48105, United States
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10
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Mittra K, Sengupta K, Singha A, Bandyopadhyay S, Chatterjee S, Rana A, Samanta S, Dey A. Second sphere control of spin state: Differential tuning of axial ligand bonds in ferric porphyrin complexes by hydrogen bonding. J Inorg Biochem 2016; 155:82-91. [DOI: 10.1016/j.jinorgbio.2015.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/02/2015] [Accepted: 11/10/2015] [Indexed: 11/16/2022]
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11
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Mancini G, Zazza C. F429 Regulation of Tunnels in Cytochrome P450 2B4: A Top Down Study of Multiple Molecular Dynamics Simulations. PLoS One 2015; 10:e0137075. [PMID: 26415031 PMCID: PMC4587367 DOI: 10.1371/journal.pone.0137075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/12/2015] [Indexed: 01/22/2023] Open
Abstract
The root causes of the outcomes of the single-site mutation in enzymes remain by and large not well understood. This is the case of the F429H mutant of the cytochrome P450 (CYP) 2B4 enzyme where the substitution, on the proximal surface of the active site, of a conserved phenylalanine 429 residue with histidine seems to hamper the formation of the active species, Compound I (porphyrin cation radical-Fe(IV) = O, Cpd I) from the ferric hydroperoxo (Fe(III)OOH-, Cpd 0) precursor. Here we report a study based on extensive molecular dynamic (MD) simulations of 4 CYP-2B4 point mutations compared to the WT enzyme, having the goal of better clarifying the importance of the proximal Phe429 residue on CYP 2B4 catalytic properties. To consolidate the huge amount of data coming from five simulations and extract the most distinct structural features of the five species studied we made an extensive use of cluster analysis. The results show that all studied single polymorphisms of F429, with different side chain properties: i) drastically alter the reservoir of conformations accessible by the protein, perturbing global dynamics ii) expose the thiolate group of residue Cys436 to the solvent, altering the electronic properties of Cpd0 and iii) affect the various ingress and egress channels connecting the distal sites with the bulk environment, altering the reversibility of these channels. In particular, it was observed that the wild type enzyme exhibits unique structural features as compared to all mutant species in terms of weak interactions (hydrogen bonds) that generate a completely different dynamical behavior of the complete system. Albeit not conclusive, the current computational investigation sheds some light on the subtle and critical effects that proximal single-site mutations can exert on the functional mechanisms of human microsomal CYPs which should go rather far beyond local structure characterization.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126, Pisa, Italy, and Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127, Pisa, Italy
- * E-mail:
| | - Costantino Zazza
- Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185, Roma, Italy
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12
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Smith AT, Pazicni S, Marvin KA, Stevens DJ, Paulsen KM, Burstyn JN. Functional divergence of heme-thiolate proteins: a classification based on spectroscopic attributes. Chem Rev 2015; 115:2532-58. [PMID: 25763468 DOI: 10.1021/cr500056m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T Smith
- †Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208, United States
| | - Samuel Pazicni
- ‡Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, United States
| | - Katherine A Marvin
- §Department of Chemistry, Hendrix College, 1600 Washington Avenue, Conway, Arkansas 72032, United States
| | - Daniel J Stevens
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Katherine M Paulsen
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Judith N Burstyn
- ∥Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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13
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Wang B, Usharani D, Li C, Shaik S. Theory uncovers an unusual mechanism of DNA repair of a lesioned adenine by AlkB enzymes. J Am Chem Soc 2014; 136:13895-901. [PMID: 25203306 DOI: 10.1021/ja507934g] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA-base lesions cause cancer and propagate into the genome. We use in-protein QM/MM calculations to study the repair of etheno-bridged adenine (εA) by the iron(IV)-oxo species of AlkB enzymes. Recent experimental investigations, using mass-spectrometry and in crystallo isolation, suggested that εA was repaired by formation of an epoxide (εA-ep) that further transforms to a glycol (εA-gl), ending finally in adenine and glyoxal. Theory reproduces the experimentally observed barrier for the rate-determining step and its pH dependence. However, as we show, the mass-spectrometrically identified species are side-byproducts unassociated with the repair mechanism. The repair is mediated by a zwitterionic species, of the same molecular mass as the epoxide, which transforms to an intermediate that matches the in crystallo trapped species in structure and mass, but is NOT the assumed εA-gl iron-glycol complex. Verifiable/falsifiable predictions, regarding the key protein residues, follow. The paper underscores the indispensable role of theory by providing atomistic descriptions of this vital mechanism, and guiding further experimental investigations.
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Affiliation(s)
- Binju Wang
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, Hebrew University of Jerusalem , 91904 Jerusalem, Israel
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14
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Yang Y, Zhang H, Usharani D, Bu W, Im S, Tarasev M, Rwere F, Pearl NM, Meagher J, Sun C, Stuckey J, Shaik S, Waskell L. Structural and functional characterization of a cytochrome P450 2B4 F429H mutant with an axial thiolate-histidine hydrogen bond. Biochemistry 2014; 53:5080-91. [PMID: 25029089 PMCID: PMC4131899 DOI: 10.1021/bi5003794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 07/15/2014] [Indexed: 02/02/2023]
Abstract
The structural basis of the regulation of microsomal cytochrome P450 (P450) activity was investigated by mutating the highly conserved heme binding motif residue, Phe429, on the proximal side of cytochrome P450 2B4 to a histidine. Spectroscopic, pre-steady-state and steady-state kinetic, thermodynamic, theoretical, and structural studies of the mutant demonstrate that formation of an H-bond between His429 and the unbonded electron pair of the Cys436 axial thiolate significantly alters the properties of the enzyme. The mutant lost >90% of its activity; its redox potential was increased by 87 mV, and the half-life of the oxyferrous mutant was increased ∼37-fold. Single-crystal electronic absorption and resonance Raman spectroscopy demonstrated that the mutant was reduced by a small dose of X-ray photons. The structure revealed that the δN atom of His429 forms an H-bond with the axial Cys436 thiolate whereas the εN atom forms an H-bond with the solvent and the side chain of Gln357. The amide of Gly438 forms the only other H-bond to the tetrahedral thiolate. Theoretical quantification of the histidine-thiolate interaction demonstrates a significant electron withdrawing effect on the heme iron. Comparisons of structures of class I-IV P450s demonstrate that either a phenylalanine or tryptophan is often found at the location corresponding to Phe429. Depending on the structure of the distal pocket heme, the residue at this location may or may not regulate the thermodynamic properties of the P450. Regardless, this residue appears to protect the thiolate from solvent, oxidation, protonations, and other deleterious reactions.
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Affiliation(s)
- Yuting Yang
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Haoming Zhang
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Dandamudi Usharani
- Institute
of Chemistry and Lise Meitner-Minerva Center for Computational Quantum
Chemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Weishu Bu
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Sangchoul Im
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Michael Tarasev
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Freeborn Rwere
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Naw May Pearl
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Jennifer Meagher
- Life
Science Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Cuthbert Sun
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Jeanne Stuckey
- Life
Science Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Sason Shaik
- Institute
of Chemistry and Lise Meitner-Minerva Center for Computational Quantum
Chemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lucy Waskell
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
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15
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Stranava M, Martínková M, Stiborová M, Man P, Kitanishi K, Muchová L, Vítek L, Martínek V, Shimizu T. Introduction of water into the heme distal side by Leu65 mutations of an oxygen sensor, YddV, generates verdoheme and carbon monoxide, exerting the heme oxygenase reaction. J Inorg Biochem 2014; 140:29-38. [PMID: 25046385 DOI: 10.1016/j.jinorgbio.2014.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/21/2014] [Accepted: 06/16/2014] [Indexed: 12/26/2022]
Abstract
The globin-coupled oxygen sensor, YddV, is a heme-based oxygen sensor diguanylate cyclase. Oxygen binding to the heme Fe(II) complex in the N-terminal sensor domain of this enzyme substantially enhances its diguanylate cyclase activity which is conducted in the C-terminal functional domain. Leu65 is located on the heme distal side and is important for keeping the stability of the heme Fe(II)-O2 complex by preventing the entry of the water molecule to the heme complex. In the present study, it was found that (i) Escherichia coli-overexpressed and purified L65N mutant of the isolated heme-bound domain of YddV (YddV-heme) contained the verdoheme iron complex and other modified heme complexes as determined by optical absorption spectroscopy and mass spectrometry; (ii) CO was generated in the reconstituted system composed of heme-bound L65N and NADPH:cytochrome P450 reductase as confirmed by gas chromatography; (iii) CO generation of heme-bound L65N in the reconstituted system was inhibited by superoxide dismutase and catalase. In a concordance with the result, the reactive oxygen species increased the CO generation; (iv) the E. coli cells overexpressing the L65N protein of YddV-heme also formed significant amounts of CO compared to the cells overexpressing the wild type protein; (v) generation of verdoheme and CO was also observed for other mutants at Leu65 as well, but to a lesser extent. Since Leu65 mutations are assumed to introduce the water molecule into the heme distal side of YddV-heme, it is suggested that the water molecule would significantly contribute to facilitating heme oxygenase reactions for the Leu65 mutants.
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Affiliation(s)
- Martin Stranava
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Markéta Martínková
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic.
| | - Marie Stiborová
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Petr Man
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic; Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Videnska 1083, Prague 4, Czech Republic
| | - Kenichi Kitanishi
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Lucie Muchová
- Institute of Medical Biochemistry and Laboratory Diagnostics, 1(st) Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Libor Vítek
- Institute of Medical Biochemistry and Laboratory Diagnostics, 1(st) Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Václav Martínek
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
| | - Toru Shimizu
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova (Albertov) 2030/8, Prague 2, 128 43, Czech Republic
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16
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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17
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Metz S, Kästner J, Sokol AA, Keal TW, Sherwood P. C
hem
S
hell—a modular software package for
QM
/
MM
simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1163] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Metz
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Johannes Kästner
- Institute of Theoretical ChemistryUniversity of StuttgartStuttgartGermany
| | | | - Thomas W. Keal
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
| | - Paul Sherwood
- Scientific Computing DepartmentSTFC Daresbury LaboratoryDaresburyWarringtonUK
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18
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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19
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Li C, Shaik S. How Do Perfluorinated Alkanoic Acids Elicit Cytochrome P450 to Catalyze Methane Hydroxylation? An MD and QM/MM Study. RSC Adv 2013; 3:2995-3005. [PMID: 23682310 DOI: 10.1039/c2ra22294a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent experimental studies show that usage of perfluoro decanoic acid (PFDA), as a dummy substrate, can elicit P450BM3 to perform hydroxylation of small alkanes, such as methane (ref. 17) and propane (ref. 17 and ref. 18). To comprehend the mechanism whereby PFDA operates to potentiate P450BM3 to catalyze the hydroxylation of small alkanes, we used molecular dynamics (MD) and hybrid quantum mechanical / molecular mechanical (QM/MM) calculations. The MD results show that without the PFDA, methane escapes the active site, while the presence of PFDA can potentially induce a productive Cpd I-Methane juxtaposition for rapid oxidation. Nevertheless, when only a single methane molecule is present near the PFDA, it still escapes the pocket within less than a nanosecond. However, when three methane molecules are present in the pocket, they alternate quasi-periodically such that at all times (within 10 ns), a molecule of methane is always present in the proximity of Cpd I in a reactive conformation. Our results further demonstrate that the PFDA does not exert any electrostatic catalysis, whether the PFDA is in the protonated or deprotonated forms. Taken together, we conclude that methane hydroxylation requires, in addition to PFDA, a high partial pressure of methane that will cause a high methane concentration in the active site. Further study of ethane and propane hydroxylations demonstrates that higher alkane concentration is helpful for all the three small alkanes. Thus for the smallest alkane, methane, at least three molecules are necessary whereas for the larger ethane, two molecules are needed to force one ethane to be closer to Cpd I. Finally, for propane a second molecule is helpful but not absolutely necessary; for this molecule the PFDA may well be sufficient to keep propane close to Cpd I for efficient oxidation. We therefore propose that high alkane pressure should assist small alkane hydroxylation by P450 in a manner inversely proportional to the size of the alkanes.
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Affiliation(s)
- Chunsen Li
- Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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20
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Das PK, Chatterjee S, Samanta S, Dey A. EPR, resonance Raman, and DFT calculations on thiolate- and imidazole-bound iron(III) porphyrin complexes: role of the axial ligand in tuning the electronic structure. Inorg Chem 2012; 51:10704-14. [PMID: 23013308 DOI: 10.1021/ic3016035] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Iron(III) porphyrin complexes bearing covalently attached imidazole and thiolate axial ligands are investigated using resonance Raman, electron paramagnetic resonance, and cyclic voltammetry. The thiolate ligand stabilizes a low-spin ground state in solvent-bound six-coordinate species, weakens the Fe-N(pyr) bonds, and shifts the Fe(III/II) potential more negative by ~500 mV relative to an imidazole-bound species. Density functional theory calculations reproduce the experimental observation and indicate that the covalent charge donation from thiolate to iron reduces the Z(eff) on the iron. This increases the Fe(3d) orbital energies, which changes the bonding interaction present in these complexes significantly. In particular, the increase of the Fe(3d) energies activates an iron-to-porphyrin π*-back-bonding interaction not present in the imidazole-bound complex.
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Affiliation(s)
- Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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21
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Mak PJ, Yang Y, Im S, Waskell LA, Kincaid JR. Experimental Documentation of the Structural Consequences of Hydrogen-Bonding Interactions to the Proximal Cysteine of a Cytochrome P450. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205912] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Mak PJ, Yang Y, Im S, Waskell LA, Kincaid JR. Experimental documentation of the structural consequences of hydrogen-bonding interactions to the proximal cysteine of a cytochrome P450. Angew Chem Int Ed Engl 2012; 51:10403-7. [PMID: 22968976 DOI: 10.1002/anie.201205912] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Piotr J Mak
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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23
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Smith AT, Su Y, Stevens DJ, Majtan T, Kraus JP, Burstyn JN. Effect of the disease-causing R266K mutation on the heme and PLP environments of human cystathionine β-synthase. Biochemistry 2012; 51:6360-70. [PMID: 22738154 DOI: 10.1021/bi300421z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cystathionine β-synthase (CBS) is an essential pyridoxal 5'-phosphate (PLP)-dependent enzyme of the transsulfuration pathway that condenses serine with homocysteine to form cystathionine; intriguingly, human CBS also contains a heme b cofactor of unknown function. Herein we describe the enzymatic and spectroscopic properties of a disease-associated R266K hCBS variant, which has an altered hydrogen-bonding environment. The R266K hCBS contains a low-spin, six-coordinate Fe(III) heme bearing a His/Cys ligation motif, like that of WT hCBS; however, there is a geometric distortion that exists at the R266K heme. Using rR spectroscopy, we show that the Fe(III)-Cys(thiolate) bond is longer and weaker in R266K, as evidenced by an 8 cm(-1) downshift in the ν(Fe-S) resonance. Presence of this longer and weaker Fe(III)-Cys(thiolate) bond is correlated with alteration of the fluorescence spectrum of the active PLP ketoenamine tautomer. Activity data demonstrate that, relative to WT, the R266K variant is more impaired in the alternative cysteine-synthesis reaction than in the canonical cystathionine-synthesis reaction. This diminished cysteine synthesis activity and a greater sensitivity to exogenous PLP correlate with the change in PLP environment. Fe-S(Cys) bond weakening causes a nearly 300-fold increase in the rate of ligand switching upon reduction of the R266K heme. Combined, these data demonstrate cross talk between the heme and PLP active sites, consistent with previous proposals, revealing that alteration of the Arg(266)-Cys(52) interaction affects PLP-dependent activity and dramatically destabilizes the ferrous thiolate-ligated heme complex, underscoring the importance of this hydrogen-bonding residue pair.
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Affiliation(s)
- Aaron T Smith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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24
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Liao RZ, Thiel W. Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study. J Phys Chem B 2012; 116:9396-408. [DOI: 10.1021/jp305510c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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25
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Kamachi T, Nishimi T, Yoshizawa K. A new understanding on how heme metabolism occurs in heme oxygenase: water-assisted oxo mechanism. Dalton Trans 2012; 41:11642-50. [PMID: 22825429 DOI: 10.1039/c2dt30777d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Heme metabolism by heme oxygenase (HO) is investigated with quantum mechanical/molecular mechanical (QM/MM) calculations. A mechanism assisted by water is proposed: (1) an iron-oxo species and a water molecule are generated by the heterolytic cleavage of the O-O bond of an iron-hydroperoxo species in a similar way to P450-mediated reactions, (2) a hydrogen atom abstraction by the iron-oxo species from the generated water molecule and the C-O bond formation between the water molecule and the α-meso carbon take place simultaneously. The water molecule is hydrogen-bonded to the oxo ligand and to the water cluster in the active site of HO. The water cluster can control the position of the generated water molecule to ensure the regioselective oxidation of heme at the α-meso position, at the same time, can facilitate the oxidation by stabilizing a positive charge on the water molecule in the transition state. A key difference between HO and P450 is observed in the structure of the active site; Thr252 in P450 blocks the access of the water molecule to the α-meso position, and can thus suppress the undesired heme oxidation for P450.
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Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan
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26
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Kwiecień RA, Le Questel JY, Lebreton J, Delaforge M, André F, Pihan E, Roussel A, Fournial A, Paneth P, Robins RJ. Cytochrome P450-Catalyzed Degradation of Nicotine: Fundamental Parameters Determining Hydroxylation by Cytochrome P450 2A6 at the 5′-Carbon or the N-Methyl Carbon. J Phys Chem B 2012; 116:7827-40. [DOI: 10.1021/jp304276v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Renata A. Kwiecień
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Jean-Yves Le Questel
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Jacques Lebreton
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Marcel Delaforge
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - François André
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Emilie Pihan
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Anaïs Roussel
- Laboratoire Stress Oxydant et Détoxication, CNRS UMR8221, iBiTec-S/SB2SM, CEA Saclay, 91191 Saclay, France
| | - Anaïs Fournial
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
| | - Piotr Paneth
- Laboratory for Isotope Effects
Studies, Faculty of Chemistry, Institute
of Applied Radiation Chemistry, University of Technology Lodz, Zeromskiego 116, 90-924 Łodź, Poland
| | - Richard J. Robins
- Laboratory
for the Study of Biosynthesis by Isotopic Spectroscopy, Interdisciplinary
Chemistry: Synthesis, Analysis and Modeling (CEISAM), UMR6230, University of Nantes-CNRS, 2 rue de la Houssinière,
BP 92208, F-44322 Nantes 3, France
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27
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Isobe H, Yamaguchi K, Okumura M, Shimada J. Role of Perferryl–Oxo Oxidant in Alkane Hydroxylation Catalyzed by Cytochrome P450: A Hybrid Density Functional Study. J Phys Chem B 2012; 116:4713-30. [DOI: 10.1021/jp211184y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroshi Isobe
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Kizashi Yamaguchi
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate
School of Science, Osaka University, Toyonaka,
Osaka 560-0043, Japan
| | - Jiro Shimada
- Green
Innovation Research Laboratories, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki
305-8501, Japan
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