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Ri YK, Kim SA, Kye YH, Jong YC, Kang MS, Yu CJ. First-principles study of molecular hydrogen binding to heme in competition with O 2, NO and CO. RSC Adv 2024; 14:16629-16638. [PMID: 38784410 PMCID: PMC11110138 DOI: 10.1039/d4ra02091j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Molecular hydrogen shows antioxidant activity and distinct efficacy towards vascular diseases, but the understanding of this is not yet satisfactory at the atomic level. In this work, we study the binding properties of H2 to the heme group in relation with other diatomic molecules (DMs), including O2, NO and CO, and their displacement reactions, using first-principles calculations. We carry out molecular modeling of the heme group, using iron-porphyrin with the imidazole ligand, i.e., FePIm, and smaller models of Fe(CnHn+2N2)2NH3 with n = 3 and 1, and of molecular complexes of heme-DM and -H. Through analysis of optimized geometries and energetics, it is found that the order of binding strength of DMs or H to the Fe of heme is NO > O2 > CO > H > H2 for FePIm-based systems, while it is H > O2 > NO > CO > H2 for model-based systems. We calculate the activation energies for displacement reactions of H2 and H by other DMs, revealing that the H2 displacements occur spontaneously while the H displacements require a large amount of energy. Finally, our calculations corroborate that the rate constants increase with increasing temperature according to the Arrhenius relation.
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Affiliation(s)
- Yun-Kyong Ri
- Chair of Computational Materials Design, Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Song-Ae Kim
- Institute of Molecular Biology, Faculty of Life Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Yun-Hyok Kye
- Chair of Computational Materials Design, Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Yu-Chol Jong
- Chair of Chemical Process, Faculty of Chemistry, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Myong-Su Kang
- Institute of Molecular Biology, Faculty of Life Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
| | - Chol-Jun Yu
- Chair of Computational Materials Design, Faculty of Materials Science, Kim Il Sung University PO Box 76 Pyongyang Democratic People's Republic of Korea
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2
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Singla K, M P SK, Bhattacharjya A, Saxena R, Choudhary N, Goyal B. Bilirubin in wound healing: A double-edged sword. Cell Biochem Funct 2023; 41:953-958. [PMID: 37653690 DOI: 10.1002/cbf.3849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/27/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The impact of bilirubin levels on wound healing remains a topic of controversy. The present study is a literature review that examines the impact of increased levels of bilirubin in the bloodstream on the process of wound healing. The physiological pathways and their interrelationships, as well as the relevant research publications, were comprehensively addressed in our discussion. The present study undertook a comprehensive review of the extant literature pertaining to the impact of bilirubin concentration on the process of wound healing, with particular emphasis on its association with reactive oxygen species. This scholarly article provides an overview of several studies that elucidate the mechanisms and correlation between bilirubin and the process of wound healing. The impact of bilirubin on wound healing has been observed, and it appears to function as a modulator. This review demonstrates that there exists a spectrum of bilirubin concentrations that can function as precise regulators, although this range falls under pathological hyperbilirubinemia. Further research is required to determine the precise boundary of this range. Within a certain range, bilirubin serves as a positive regulator in the process of wound healing. Beyond this range, it has the potential to function as a negative regulator.
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Affiliation(s)
- Kshitij Singla
- All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Sarath Krishnan M P
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | | | - Rahul Saxena
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Nitin Choudhary
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Bela Goyal
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
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3
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Liu S, Xia S, Yue D, Sun H, Hirao H. The Bonding Nature of Fe–CO Complexes in Heme Proteins. Inorg Chem 2022; 61:17494-17504. [DOI: 10.1021/acs.inorgchem.2c02387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shuyang Liu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Songyan Xia
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Dongxiao Yue
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Haoran Sun
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
| | - Hajime Hirao
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong518172, P. R. China
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4
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Rozza AM, Papp M, McFarlane NR, Harvey JN, Oláh J. The Mechanism of Biochemical NO‐Sensing: Insights from Computational Chemistry. Chemistry 2022; 28:e202200930. [PMID: 35670519 PMCID: PMC9542423 DOI: 10.1002/chem.202200930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/22/2022]
Abstract
The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO‐receptor in humans is soluble guanylyl cyclase (sGC) – a histidine‐ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO‐signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high‐level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H‐NOX protein from Shewanella oneidensis (So H‐NOX) homologous to the NO‐binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six‐coordinate intermediate heme‐NO complex, followed by relatively facile His decoordination yielding a five‐coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.
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Affiliation(s)
- Ahmed M. Rozza
- Department of Inorganic and Analytical Chemistry Budapest University of Technology and Economics 1111 Budapest Műegyetem rakpart 3. Hungary
- Department of Biotechnology Faculty of Agriculture Al-Azhar University Cairo 11651 Egypt
| | - Marcell Papp
- Department of Inorganic and Analytical Chemistry Budapest University of Technology and Economics 1111 Budapest Műegyetem rakpart 3. Hungary
| | - Neil R. McFarlane
- Department of Chemistry KU Leuven 3001 Leuven Celestijnenlaan 200 f- box 2404 Belgium
| | - Jeremy N. Harvey
- Department of Chemistry KU Leuven 3001 Leuven Celestijnenlaan 200 f- box 2404 Belgium
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry Budapest University of Technology and Economics 1111 Budapest Műegyetem rakpart 3. Hungary
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5
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Fateminasab F, de la Lande A, Omidyan R. Insights into the effect of distal histidine and water hydrogen bonding on NO ligation to ferrous and ferric heme: a DFT study. RSC Adv 2022; 12:4703-4713. [PMID: 35425484 PMCID: PMC8981399 DOI: 10.1039/d1ra08398h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/30/2022] [Indexed: 11/29/2022] Open
Abstract
The effect of distal histidine on ligation of NO to ferrous and ferric-heme, has been investigated with the high-level density functional theoretical (DFT) method. It has been predicted that the distal histidine significantly stabilizes the interaction of NO ferrous-heme (by −2.70 kcal mol−1). Also, water hydrogen bonding is quite effective in strengthening the Fe–NO bond in ferrous heme. In contrast in ferric heme, due to the large distance between the H2O and O(NO) and lack of hydrogen bonding, the distal histidine exhibits only a slight effect on the binding of NO to the ferric analogue. Concerning the bond nature of FeII–NO and FeIII–NO in heme, a QTAIM analysis predicts a partially covalent and ionic bond nature in both systems. The effect of distal histidine on ligation of NO to ferrous and ferric-heme, has been investigated with the high-level density functional theoretical (DFT) method.![]()
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Affiliation(s)
- Fatemeh Fateminasab
- Department of Chemistry, University of Isfahan 81746-73441 Isfahan Iran +98 31 3668 9732
| | - Aurelien de la Lande
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000 91405 Orsay France
| | - Reza Omidyan
- Department of Chemistry, University of Isfahan 81746-73441 Isfahan Iran +98 31 3668 9732
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6
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Fateminasab F, Aarabi M, de la Lande A, Omidyan R. Theoretical insights on the effect of environments on binding of CO to the Heme :Ferrous and Ferric systems. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Specht P, Oßberger M, Klüfers P, Schindler S. Kinetic studies on the reaction of NO with iron(ii) complexes using low temperature stopped-flow techniques. Dalton Trans 2020; 49:9480-9486. [PMID: 32608457 DOI: 10.1039/d0dt01764g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Low temperature stopped-flow techniques were used to investigate the reaction of three different iron(ii) complexes with nitrogen monoxide. The kinetic studies allowed calculation of the activation parameters from the corresponding Eyring plots for all three systems. The reaction of iron(ii) chloride with NO leading to the formation of MNIC (mononitrosyl-iron-complex) and DNIC (dinitrosyl-iron-complex) led to activation parameters of ΔH‡ = 55.4 ± 0.4 kJ mol-1 and ΔS‡ = 13 ± 2 J K-1 mol-1 for MNIC and ΔH‡ = 32 ± 6 kJ mol-1 and ΔS‡ = -193 ± 21 J K-1 mol-1 for DNIC. Formation of MNIC turned out to be much faster in comparison with DNIC. In contrast, activation parameters for the formation of monoculear [Fe(bztpen)(NO)](OTf)2 (bztpen = N-benzyl-N,N',N'-tris(2-pyridylmethyl)-ethylenediamine) ΔH‡ = 17.8 ± 0.8 kJ mol-1 and ΔS‡ = -181 ± 3 J K-1 mol-1 supported an associative mechanism. Interestingly, [Fe(bztpen)(CH3CN)](OTf)2 does not react with dioxygen at all. Furthermore, activation parameters of ΔH‡ = 37.7 ± 0.7 kJ mol-1 and ΔS‡ = -66 ± 3 J K-1 mol-1 were obtained for the reaction of NO with the dinuclear iron(ii) H-HPTB complex (H-HPTB = N,N,N',N'-tetrakis(2-benzimidazolylmethyl)-2-hydroxy-1,3-diaminopropane), [Fe2(H-HPTB)(Cl)3]. The kinetic data allowed postulation of the mechanisms for all of these reactions.
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Affiliation(s)
- Pascal Specht
- Institut für Anorganische und Analytische Chemie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany.
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8
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Zhang S, Liu Y. Mechanical Insights into the Enzymatic Cleavage of Double C-C Bond in Poly( cis-1,4-isoprene) by the Latex Clearing Protein. Inorg Chem 2020; 59:9627-9637. [PMID: 32644783 DOI: 10.1021/acs.inorgchem.0c00726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The b-type cytochrome LcpK30 is a latex clearing protein (Lcp), which acts as an endotype dioxygenase to catalyze the extracellular cleavage of the chemically inert aliphatic polymer poly(cis-1,4-isoprene), producing oligo-isoprenoids with different terminal carbonyl groups (aldehyde and ketone, -CH2-CHO and -CH2-COCH3). On the basis of the fact that the muteins of E148A, E148Q, and E148H have substantially reduced reactivity, and the E148-initiated reaction mechanism has been previously proposed, in which a cyclic dioxetane intermediate or an epoxide intermediate may be involved, however, open questions still remain. In this paper, on the basis of the crystal structure of LcpK30, the enzyme-substrate reactant model was constructed, and the cleavage mechanism of the central double bond of poly(cis-1,4-isoprene) was elucidated by performing quantum mechanics/molecular mechanics calculations. Our calculation results revealed that the oxidative cleavage reaction is triggered by the addition of the heme-bound dioxygen to the double bond of the polymer, and E148 does not act as the catalytic base to extract the allylic proton to assist the reaction as previously suggested. Of the two considered pathways, the pathway that involves the dioxetane intermediate was calculated to be more favorable. During the catalysis, the distal oxygen first adds to the double bond of the substrate to form a radical intermediate, and then the Fe-O1 (proximal oxygen) bond cleaves to generate the dioxetane intermediate, which can easily collapse affording the final ketone and aldehyde products. In general, the cleavage mechanism of double C-C bond catalyzed by LcpK30 is similar to those of indoleamine 2,3-dioxygenase, tryptophan 2,3-dioxygenase, and the nonheme stilbene cleavage oxygenase NOV1 that all depend on the iron-bound dioxygen to initiate the cleavage reaction.
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Affiliation(s)
- Shiqing Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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9
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Li R, Dai X, Feng Z, Li Y, Zhao M, Liu J, Li H, Chen Y, Ma Y, Tang Y. Effect of toxic ligands on O 2 binding to heme and their toxicity mechanism. Phys Chem Chem Phys 2019; 21:14957-14963. [PMID: 31236551 DOI: 10.1039/c9cp02583a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme, as the cofactor and active site of Hb, enables Hb to carry out the necessary function required for O2 management for life, that is, reversible O2 binding for transport. In this paper, the microscopic mechanism of heme-associated poisoning has been elucidated from the perspective of electronic interaction by performing first-principles calculations. The results show that the functional groups (-CHO, -COOH, -NO2, -NH2) and CN exhibit a stronger affinity for heme than O2 and are more likely to occupy the O2 binding site, which results in the loss of the ability of heme to carry O2. Moreover, the addition of functional groups, CO and CN to heme at the side site can cause a pronounced enhancement toward the O2 binding characteristics of heme, which prevents heme from releasing O2 to oxygen-consuming tissues as the blood circulates. The reversible O2 binding function of heme is disrupted by the presence of these toxic ligands in the heme binding pocket, which greatly affects O2 transport in the blood. The inability of tissues to obtain O2 leads to tissue hypoxia, which is the main cause of poisoning. Based on the energy, geometry and electronic properties, the hypoxia mechanism proposed by us coincides well with experiment, and the research has the potential to provide a theoretical reference for the relevant areas of bioscience.
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Affiliation(s)
- Renyi Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Xianqi Dai
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Zhen Feng
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Yi Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Mingyu Zhao
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Jing Liu
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Huiting Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Yang Chen
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Yaqiang Ma
- College of Physics and Materials Science, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Yanan Tang
- Quantum Materials Research Center, College of Physics and Electronic Engineering, Zhengzhou Normal University, Zhengzhou 450044, China.
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10
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Aarabi M, Omidyan R, Soorkia S, Grégoire G, Broquier M, Crestoni ME, de la Lande A, Soep B, Shafizadeh N. The dramatic effect of N-methylimidazole on trans axial ligand binding to ferric heme: experiment and theory. Phys Chem Chem Phys 2019; 21:1750-1760. [PMID: 30623949 DOI: 10.1039/c8cp06210b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The binding energy of CO, O2 and NO to isolated ferric heme, [FeIIIP]+, was studied in the presence and absence of a σ donor (N-methylimidazole and histidine) as the trans axial ligand. This study combines the experimental determination of binding enthalpies by equilibrium measurements in a low temperature ion trap using the van't Hoff equation and high level DFT calculations. It was found that the presence of N-methylimidazole as the axial ligand on the [FeIIIP]+ porphyrin dramatically weakens the [FeIIIP-ligand]+ bond with an up to sevenfold decrease in binding energy owing to the σ donation by N-methylimidazole to the FeIII(3d) orbitals. This trans σ donor effect is characteristic of ligation to iron in hemes in both ferrous and ferric redox forms; however, to date, this has not been observed for ferric heme.
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Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran.
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11
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Li XX, Cho KB, Nam W. A theoretical investigation into the first-row transition metal–O2 adducts. Inorg Chem Front 2019. [DOI: 10.1039/c9qi00407f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Effects of both metal center and ligand ring size on the properties of metal–O2 adducts.
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Affiliation(s)
- Xiao-Xi Li
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 03760
- Korea
| | - Kyung-Bin Cho
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 03760
- Korea
- Department of Chemistry
| | - Wonwoo Nam
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 03760
- Korea
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12
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Kurokawa D, Gueriba JS, Diño WA. Spin-Dependent O 2 Binding to Hemoglobin. ACS OMEGA 2018; 3:9241-9245. [PMID: 31459056 PMCID: PMC6645249 DOI: 10.1021/acsomega.8b00879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/06/2018] [Indexed: 06/09/2023]
Abstract
We report results of our study on the mechanism of spin-dependent O2 binding to hemoglobin, which we represent as FePIm (Fe = iron, P = porphyrin, Im = imidazole). This involves the transition between two states, viz., the oxyhemoglobin state and the deoxyhemoglobin state. The deoxyhemoglobin state pertains to FePIm and a free O2 molecule, while the oxyhemoglobin state pertains to an O2 bound to FePIm. The deoxyhemoglobin and oxyhemoglobin systems have triplet and singlet total magnetizations, respectively. We found that a spin transition from triplet to quintet to singlet mediates the O2 binding process, and this accelerates the reaction. We also found that the position of the Fe atom out of the porphyrin plane is an important indicator of O2 affinity.
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Affiliation(s)
- Daiichi Kurokawa
- Department
of Applied Physics and Center for Atomic and Molecular Technologies, Osaka University, Suita, Osaka 565-0871, Japan
| | - Jessiel Siaron Gueriba
- Department
of Applied Physics and Center for Atomic and Molecular Technologies, Osaka University, Suita, Osaka 565-0871, Japan
- Department
of Physics, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines
| | - Wilson Agerico Diño
- Department
of Applied Physics and Center for Atomic and Molecular Technologies, Osaka University, Suita, Osaka 565-0871, Japan
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13
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Savagatrup S, Schroeder V, He X, Lin S, He M, Yassine O, Salama KN, Zhang XX, Swager TM. Bio-Inspired Carbon Monoxide Sensors with Voltage-Activated Sensitivity. Angew Chem Int Ed Engl 2017; 56:14066-14070. [PMID: 28952172 PMCID: PMC5658252 DOI: 10.1002/anie.201707491] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/16/2017] [Indexed: 11/08/2022]
Abstract
Carbon monoxide (CO) outcompetes oxygen when binding to the iron center of hemeproteins, leading to a reduction in blood oxygen level and acute poisoning. Harvesting the strong specific interaction between CO and the iron porphyrin provides a highly selective and customizable sensor. We report the development of chemiresistive sensors with voltage-activated sensitivity for the detection of CO comprising iron porphyrin and functionalized single-walled carbon nanotubes (F-SWCNTs). Modulation of the gate voltage offers a predicted extra dimension for sensing. Specifically, the sensors show a significant increase in sensitivity toward CO when negative gate voltage is applied. The dosimetric sensors are selective to ppm levels of CO and functional in air. UV/Vis spectroscopy, differential pulse voltammetry, and density functional theory reveal that the in situ reduction of FeIII to FeII enhances the interaction between the F-SWCNTs and CO. Our results illustrate a new mode of sensors wherein redox active recognition units are voltage-activated to give enhanced and highly specific responses.
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Affiliation(s)
- Suchol Savagatrup
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Vera Schroeder
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Xin He
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Sibo Lin
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Maggie He
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
| | - Omar Yassine
- Sensors Lab, Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Khaled N Salama
- Sensors Lab, Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Xi-Xiang Zhang
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Timothy M Swager
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
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14
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Savagatrup S, Schroeder V, He X, Lin S, He M, Yassine O, Salama KN, Zhang X, Swager TM. Bio‐Inspired Carbon Monoxide Sensors with Voltage‐Activated Sensitivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Suchol Savagatrup
- Department of Chemistry and Institute for Soldier Nanotechnologies Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Vera Schroeder
- Department of Chemistry and Institute for Soldier Nanotechnologies Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Xin He
- Physical Science and Engineering Division King Abdullah University of Science and Technology, KAUST Thuwal 23955-6900 Saudi Arabia
| | - Sibo Lin
- Department of Chemistry and Institute for Soldier Nanotechnologies Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Maggie He
- Department of Chemistry and Institute for Soldier Nanotechnologies Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Omar Yassine
- Sensors Lab, Computer, Electrical and Mathematical Science and Engineering Division King Abdullah University of Science and Technology, KAUST Thuwal 23955-6900 Saudi Arabia
| | - Khaled N. Salama
- Sensors Lab, Computer, Electrical and Mathematical Science and Engineering Division King Abdullah University of Science and Technology, KAUST Thuwal 23955-6900 Saudi Arabia
| | - Xi‐Xiang Zhang
- Physical Science and Engineering Division King Abdullah University of Science and Technology, KAUST Thuwal 23955-6900 Saudi Arabia
| | - Timothy M. Swager
- Department of Chemistry and Institute for Soldier Nanotechnologies Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
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15
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Poiana F, von Ballmoos C, Gonska N, Blomberg MRA, Ädelroth P, Brzezinski P. Splitting of the O-O bond at the heme-copper catalytic site of respiratory oxidases. SCIENCE ADVANCES 2017; 3:e1700279. [PMID: 28630929 PMCID: PMC5473675 DOI: 10.1126/sciadv.1700279] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/20/2017] [Indexed: 05/30/2023]
Abstract
Heme-copper oxidases catalyze the four-electron reduction of O2 to H2O at a catalytic site that is composed of a heme group, a copper ion (CuB), and a tyrosine residue. Results from earlier experimental studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (PR ; Fe4+=O2-, CuB2+-OH-). We show that with the Thermus thermophilus ba3 oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the PR ferryl (τ ≅110 μs), which indicates that O2 is reduced before the splitting of the O-O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe3+-O--O-(H+)], which is formed before the PR ferryl. The rates of heme b oxidation and PR ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O2 reduction by heme-copper oxidases.
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Affiliation(s)
- Federica Poiana
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | - Nathalie Gonska
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Margareta R. A. Blomberg
- Department of Organic Chemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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16
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de Matos Mourão Neto I, Silva ALP, Tanaka AA, de Jesus Gomes Varela J. Density functional theory study of interactions between carbon monoxide and iron tetraaza macrocyclic complexes, FeTXTAA (X = −Cl, −OH, −OCH3, −NH2, and –NO2). J Mol Model 2017; 23:64. [DOI: 10.1007/s00894-017-3250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 01/23/2017] [Indexed: 10/20/2022]
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17
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Nicolaides A, Soulimane T, Varotsis C. Nanosecond ligand migration and functional protein relaxation in ba3 oxidoreductase: Structures of the B0, B1 and B2 intermediate states. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1534-1540. [PMID: 27207588 DOI: 10.1016/j.bbabio.2016.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/13/2016] [Accepted: 05/15/2016] [Indexed: 11/28/2022]
Abstract
Nanosecond time-resolved step-scan FTIR spectroscopy (nTRS (2) -FTIR) has been applied to literally probe the active site of the carbon monoxide (CO)-bound thermophilic ba3 heme-copper oxidoreductase as it executes its function. The nTRS (2) - snapshots of the photolysed heme a3 Fe-CO/CuB species captured a "transition state" whose side chains prevent the photolysed CO to enter the docking cavity. There are three sets of ba3 photoproduct bands of docked CO with different orientation exhibiting different kinetics. The trajectories of the "docked" CO at 2122, 2129 and 2137cm(-1) is referred to in the literature as B2, B1 and B0 intermediate states, respectively. The present data provided direct evidence for the role of water in controlling ligand orientation in an intracavity protein environment.
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Affiliation(s)
- Antonis Nicolaides
- Cyprus University of Technology, Department of Environmental Science and Technology, P.O. Box 50329, 3603 Lemesos, Cyprus
| | - Tewfik Soulimane
- Chemical and Environmental Science Department, University of Limerick, Limerick, Ireland; Materials & Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Constantinos Varotsis
- Cyprus University of Technology, Department of Environmental Science and Technology, P.O. Box 50329, 3603 Lemesos, Cyprus.
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18
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Magierowska K, Magierowski M, Surmiak M, Adamski J, Mazur-Bialy AI, Pajdo R, Sliwowski Z, Kwiecien S, Brzozowski T. The Protective Role of Carbon Monoxide (CO) Produced by Heme Oxygenases and Derived from the CO-Releasing Molecule CORM-2 in the Pathogenesis of Stress-Induced Gastric Lesions: Evidence for Non-Involvement of Nitric Oxide (NO). Int J Mol Sci 2016; 17:442. [PMID: 27023525 PMCID: PMC4848898 DOI: 10.3390/ijms17040442] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 02/08/2023] Open
Abstract
Carbon monoxide (CO) produced by heme oxygenase (HO)-1 and HO-2 or released from the CO-donor, tricarbonyldichlororuthenium (II) dimer (CORM-2) causes vasodilation, with unknown efficacy against stress-induced gastric lesions. We studied whether pretreatment with CORM-2 (0.1-10 mg/kg oral gavage (i.g.)), RuCl₃ (1 mg/kg i.g.), zinc protoporphyrin IX (ZnPP) (10 mg/kg intraperitoneally (i.p.)), hemin (1-10 mg/kg i.g.) and CORM-2 (1 mg/kg i.g.) combined with N(G)-nitro-l-arginine (l-NNA, 20 mg/kg i.p.), 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one (ODQ, 10 mg/kg i.p.), indomethacin (5 mg/kg i.p.), SC-560 (5 mg/kg i.g.), and celecoxib (10 mg/kg i.g.) affects gastric lesions following 3.5 h of water immersion and restraint stress (WRS). Gastric blood flow (GBF), the number of gastric lesions and gastric CO and nitric oxide (NO) contents, blood carboxyhemoglobin (COHb) level and the gastric expression of HO-1, HO-2, hypoxia inducible factor 1α (HIF-1α), tumor necrosis factor α (TNF-α), cyclooxygenase (COX)-2 and inducible NO synthase (iNOS) were determined. CORM-2 (1 mg/kg i.g.) and hemin (10 mg/kg i.g.) significantly decreased WRS lesions while increasing GBF, however, RuCl₃ was ineffective. The impact of CORM-2 was reversed by ZnPP, ODQ, indomethacin, SC-560 and celecoxib, but not by l-NNA. CORM-2 decreased NO and increased HO-1 expression and CO and COHb content, downregulated HIF-1α, as well as WRS-elevated COX-2 and iNOS mRNAs. Gastroprotection by CORM-2 and HO depends upon CO's hyperemic and anti-inflammatory properties, but is independent of NO.
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Affiliation(s)
- Katarzyna Magierowska
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Marcin Magierowski
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Marcin Surmiak
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
- Division of Molecular Biology and Clinical Genetics, Department of Medicine, Jagiellonian University Medical College, 31-006 Cracow, Poland.
| | - Juliusz Adamski
- Department of Forensic Toxicology, Institute of Forensic Research, 31-033 Cracow, Poland.
| | - Agnieszka Irena Mazur-Bialy
- Department of Ergonomics and Exercise Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Robert Pajdo
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Zbigniew Sliwowski
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Slawomir Kwiecien
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Tomasz Brzozowski
- Department of Physiology, Jagiellonian University Medical College, 31-531 Cracow, Poland.
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19
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Todde G, Hovmöller S, Laaksonen A. Influence of mutations at the proximal histidine position on the Fe-O2 bond in hemoglobin from density functional theory. J Chem Phys 2016; 144:095101. [PMID: 26957180 DOI: 10.1063/1.4942614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Four mutated hemoglobin (Hb) variants and wild type hemoglobin as a reference have been investigated using density functional theory methods focusing on oxygen binding. Dispersion-corrected B3LYP functional is used and found to provide reliable oxygen binding energies. It also correctly reproduces the spin distribution of both bound and free heme groups as well as provides correct geometries at their close vicinity. Mutations in hemoglobin are not only an intrigued biological problem and it is also highly important to understand their effects from a clinical point of view. This study clearly shows how even small structural differences close to the heme group can have a significant effect in reducing the oxygen binding of mutated hemoglobins and consequently affecting the health condition of the patient suffering from the mutations. All of the studied mutated Hb variants did exhibit much weaker binding of molecular oxygen compared to the wild type of hemoglobin.
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Affiliation(s)
- Guido Todde
- Division of Physical Chemistry, Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, S 106 91 Stockholm, Sweden
| | - Sven Hovmöller
- Division of Structural Chemistry, Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, S 106 91 Stockholm, Sweden
| | - Aatto Laaksonen
- Division of Physical Chemistry, Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, S 106 91 Stockholm, Sweden
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20
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Xu H, Zhang Y, Chen L, Li Y, Li C, Liu L, Ogura T, Kitagawa T, Li Z. Entry of water into the distal heme pocket of soluble guanylate cyclase β1 H-NOX domain alters the ligated CO structure: a resonance Raman and in silico simulation study. RSC Adv 2016. [DOI: 10.1039/c6ra06515e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Water accessing into the heme pocket and alters the structures of CO–sGC (heme), exhibiting two different vFe–CO stretching modes.
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Affiliation(s)
- Haoran Xu
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Yuebin Zhang
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Lei Chen
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Yan Li
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
| | - Chen Li
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Li Liu
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
| | - Takashi Ogura
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Teizo Kitagawa
- Picobiology Institute
- Graduate School of Life Science
- University of Hyogo
- RSC-UH Leading Program Center
- Hyogo 679-5148
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- School of Life Sciences
- Jilin University
- Changchun 130012
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21
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Cortopassi WA, Simion R, Honsby CE, França TCC, Paton RS. Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment. Chemistry 2015; 21:18983-92. [PMID: 26577067 DOI: 10.1002/chem.201502983] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 12/17/2022]
Abstract
JMJD2A catalyses the demethylation of di- and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O2 , using a combination of quantum and classical simulations. O2 binding to this histone demethylase is computed to occur preferentially as an end-on superoxo radical bound to a high-spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O2 binding. Charge separation in the superoxo-intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition.
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Affiliation(s)
- Wilian A Cortopassi
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk.,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Robert Simion
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk.,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Charles E Honsby
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk.,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Tanos C C França
- Department of Chemical Engineering, Military Institute of Engineering, 80 Praça General Tibúrcio, Urca, 22290 270, Rio de Janeiro (Brazil).,Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove (Czech Republic)
| | - Robert S Paton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk. .,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK).
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22
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Radoń M. Role of Spin States in Nitric Oxide Binding to Cobalt(II) and Manganese(II) Porphyrins. Is Tighter Binding Always Stronger? Inorg Chem 2015; 54:5634-45. [PMID: 26000802 DOI: 10.1021/ic503109a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Binding of nitric oxide (NO) to metalloporphyrins and heme groups is important in biochemistry while challenging to describe accurately by density functional theory (DFT) calculations. Here, the structural and thermochemical aspect of NO binding to Co(II) and Mn(II) porphyrins is investigated by DFT and DFT-D (dispersion-corrected) calculations, supported by reliable coupled-cluster methodology (CCSD(T)), and critically correlated with the experimental data. It is argued that whereas the bonding of NO to Co(II) porphyrin is a simple radical recombination, the bonding of NO to Mn(II) porphyrin is accompanied by a crossing of spin states. For this reason, the spin-state conversion energy contributes to the Mn-NO bond energy, and the paradigmatic correlation between bond length and bond energy is violated for the considered nitrosyl complexes: the Mn-NO bond is (structurally) shorter by ∼0.2 Å, albeit (energetically) weaker by a few kcal/mol, compared with the Co-NO bond. Moreover, none of the many tested DFT methods can reproduce the Co-NO and Mn-NO bond energies simultaneously, except for calculations with B3LYP*-D3, TPSSh-D3, and M06-D3 methods supplemented with the proposed spin-state energy correction (to compensate for an error on the calculated spin-state conversion energy). The results of this study are important to appreciate the role of spin-state changes in ligand binding properties of heme-related models. They also highlight the need for accurate calculations for correct interpretation of experimental data, including the qualitative structure-energy relationship.
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Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland
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23
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Shafizadeh N, Ha-Thi MH, Poisson L, Soep B, Maillard P. Observation in the gas phase of the ligation of 1-methylimidazole to hemoprotein mimics. J Chem Phys 2014; 141:174310. [PMID: 25381517 DOI: 10.1063/1.4900638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hemoprotein mimics, cobalt picket fence porphyrins have been prepared in the gas phase as neutral molecules for the first time. Their ligation properties have been studied with 1-methylimidazole and compared with those of other cobalt porphyrins, tetraphenyl porphyrin, and cobalt protoporphyrin IX chloride, in view of studying the sterical properties of the ligation. It is shown that the cobalt picket fence porphyrin can only accept one 1-methylimidazole ligand in contrast to less sterically crowded porphyrins like cobalt tetraphenylporphyrin that present two accessible ligation sites. The femtosecond dynamics of these ligated systems have been studied after excitation at 400 nm, in comparison with the unligated ones. The observed transients are formed in much shorter times, 30 fs for the ligated species, as compared to free species (100 fs), supporting the porphyrin to metal charge transfer nature of these transients. The similar decays of the ligated transients <1 ps reveal the absence of photodissociation of the cobalt-1-methylimidazole bond at this step of evolution.
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Affiliation(s)
- Niloufar Shafizadeh
- Institut des Sciences Moléculaires d'Orsay UMR8214, CNRS Université de Paris-Sud, Bat 210, 91405 Orsay, Cedex, France
| | - Minh-Huong Ha-Thi
- Institut des Sciences Moléculaires d'Orsay UMR8214, CNRS Université de Paris-Sud, Bat 210, 91405 Orsay, Cedex, France
| | - Lionel Poisson
- Laboratoire Francis Perrin CEA/DSM/IRAMIS/LIDyL - CNRS URA 2453, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Benoît Soep
- Laboratoire Francis Perrin CEA/DSM/IRAMIS/LIDyL - CNRS URA 2453, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Philippe Maillard
- Institut Curie, Section de Recherches, Bât 110-112, Centre Universitaire, F-91405 Orsay, France
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24
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Radoń M. Spin-State Energetics of Heme-Related Models from DFT and Coupled Cluster Calculations. J Chem Theory Comput 2014; 10:2306-21. [DOI: 10.1021/ct500103h] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University in Kraków, ul. Ingardena 3, 30-060 Kraków, Poland
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25
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Quantum chemical DFT study of the interaction between molecular oxygen and FeN4 complexes, and effect of the macrocyclic ligand. J Mol Model 2014; 20:2131. [DOI: 10.1007/s00894-014-2131-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 12/27/2013] [Indexed: 10/25/2022]
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26
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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27
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Silva ALP, de Almeida LF, Marques ALB, Varela JDJG, Tanaka AA, da Silva ABF. CO bonding in FeN4 complexes and the effect of the macrocycle ligand: A DFT study. Polyhedron 2014. [DOI: 10.1016/j.poly.2013.08.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Liao MS, Huang MJ, Watts JD. Binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins. A theoretical study. J Phys Chem B 2013; 117:10103-14. [PMID: 23926882 PMCID: PMC3810174 DOI: 10.1021/jp403998u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The binding of O2 and NO to heme in heme-nitric oxide/oxygen-binding (H-NOX) proteins has been investigated with DFT as well as dispersion-corrected DFT methods. The local protein environment was accounted for by including the six nearest surrounding residues in the studied systems. Attention was also paid to the effects of the protein environment, particularly the distal Tyr140, on the proximal iron-histidine (Fe-His) binding. The Heme-AB (AB = O2, NO) and Fe-His binding energies in iron porphyrin FeP(His)(AB), myoglobin Mb(AB), H-NOX(AB), and Tyr140 → Phe mutated H-NOX[Y140F(AB)] were determined for comparison. The calculated stabilization of bound O2 is even higher in H-NOX than that in a myoglobin (Mb), consistent with the observation that the H-NOX domain of T. tengcongensis has a very high affinity for its oxygen molecule. Among the two different X-ray crystal structures for the Tt H-NOX protein, the calculated results for both AB = O2 and NO appear to support the crystal structure with the PDB code 1XBN , where the Trp9 and Asn74 residues do not form a hydrogen-bonding network with Tyr140. A hydrogen bond interaction from the polar residue does not have obvious effects on the Fe-His binding strength, but a dispersion contribution to Ebind(Fe-His) may be significant, depending on the crystal structure used. We speculate that the Fe-His binding strength in the deoxy form of a native protein could be an important factor in determining whether the bond of His to Fe is broken or maintained upon binding of NO to Fe.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - Ming-Ju Huang
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - John D. Watts
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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29
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Liao MS, Huang MJ, Watts JD. Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies. J Mol Model 2013; 19:3307-23. [PMID: 23661270 PMCID: PMC3726265 DOI: 10.1007/s00894-013-1864-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
Abstract
The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - Ming-Ju Huang
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
| | - John D. Watts
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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30
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Karpuschkin T, Kappes MM, Hampe O. Fixierung von O2und CO an Metallporphyrin-Anionen in der Gasphase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Karpuschkin T, Kappes MM, Hampe O. Binding of O2and CO to Metal Porphyrin Anions in the Gas Phase. Angew Chem Int Ed Engl 2013; 52:10374-7. [DOI: 10.1002/anie.201303200] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 11/06/2022]
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32
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Soldatova AV, Ibrahim M, Spiro TG. Electronic structure and ligand vibrations in FeNO, CoNO, and FeOO porphyrin adducts. Inorg Chem 2013; 52:7478-86. [PMID: 23763617 PMCID: PMC3766410 DOI: 10.1021/ic400364x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gaseous ligands, CO, NO, and O2 interact with the Fe ion in heme proteins largely via backbonding of Fe electrons to the π* orbitals of the XO (X = C, N, O) ligands. In these FeXO adducts, the Fe-X stretching frequency varies inversely with the X-O stretching frequency, since increased backbonding strengthens the Fe-X bond while weakening the X-O bond. Inverse frequency correlations have been observed for all three ligands, despite differing electronic and geometric structures, and despite variable composition of the "FeX" vibrational mode, in which Fe-X stretching and Fe-X-O coordinates are mixed for bent FeXO adducts. We report experimental data for 5-coordinate Co(II)(NO) porphyrin adducts (isoelectronic with Fe(II)(OO) adducts), and the results of density functional theory (DFT) modeling for 5-coordinate Fe(II)(NO), Co(II)(NO), and Fe(II)(OO) adducts. Inverse ν(MX)/ν(XO) correlations are obtained computationally, using model porphyrins with graded electron-donating and -withdrawing substituents to modulate the backbonding. Computed slopes agree satisfactorily with experiment, provided nonhybrid functionals are used, which avoid overemphasizing high-spin states. The BP86 functional gives correct ground states, a closed-shell singlet for Co(II)(NO) and an open-shell singlet for the isoelectronic Fe(II)(OO), as corroborated by structural data for Co(II)(NO), and the ν(MX)/ν(XO) slope agreement with experiment for both adducts. However, for Fe(II)(OO) adducts, the computed inverse ν(MX)/ν(XO) correlation applies only to porphyrins with electron-donating and withdrawing substituents of moderate strength. For substituents more donating than -CH3, a direct correlation is obtained, the Fe-O and O-O bonds weakening in concert. This effect is ascribed to the dominance of σ bonding via the in-plane dxz(+dz(2))-π* orbital, when electron-donating substituents raise the d orbital energies sufficiently to render backbonding (dyz-π*) unimportant.
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Affiliation(s)
- Alexandra V. Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
| | | | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195
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33
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Kepp KP, Dasmeh P. Effect of Distal Interactions on O2 Binding to Heme. J Phys Chem B 2013; 117:3755-70. [DOI: 10.1021/jp400260u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Pouria Dasmeh
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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34
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Liu YF, Yu JG, Siegbahn PEM, Blomberg MRA. Theoretical Study of the Oxidation of Phenolates by the [Cu2O2(N,N′-di-tert-butylethylenediamine)2]2+Complex. Chemistry 2013; 19:1942-54. [DOI: 10.1002/chem.201203052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Indexed: 01/06/2023]
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35
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Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study. J Inorg Biochem 2012; 118:28-38. [PMID: 23123336 DOI: 10.1016/j.jinorgbio.2012.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 09/05/2012] [Accepted: 09/07/2012] [Indexed: 11/21/2022]
Abstract
DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX. The natural tendency of the heme is to be planar. The strong structural distortion in H-NOX is mainly brought about by the intermolecular interactions between the whole heme molecule (heme ring plus its peripheral substituents) and the surrounding residues, among which the polar residues (Tyr140, Pro115, Mse98) play major roles in distorting the heme structure. The two peripheral propionate substituents that are oriented on the same side of the heme plane can also make the molecule distort, but the distortion caused by this factor is not significant. In Mb, the surrounding residues considered are all nonpolar and do not cause a structural distortion. The different structural features of the heme macrocycle in the different proteins (H-NOX and Mb) are reproduced by the calculations. The dispersion correction is necessary, since it improves the calculated structures. The effects of the distortion on the binding affinity of the axial ligand to the heme were also examined.
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36
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Ali ME, Sanyal B, Oppeneer PM. Electronic structure, spin-states, and spin-crossover reaction of heme-related Fe-porphyrins: a theoretical perspective. J Phys Chem B 2012; 116:5849-59. [PMID: 22512398 DOI: 10.1021/jp3021563] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).
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Affiliation(s)
- Md Ehesan Ali
- Centre for Theoretical Chemistry, Ruhr-Universität, D-44780 Bochum, Germany.
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37
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Siletsky SA, Konstantinov AA. Cytochrome c oxidase: Charge translocation coupled to single-electron partial steps of the catalytic cycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:476-88. [DOI: 10.1016/j.bbabio.2011.08.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 11/28/2022]
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38
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Sundararajan M, Neese F. Detailed QM/MM study of the Electron Paramagnetic Resonance Parameters of Nitrosyl Myoglobin. J Chem Theory Comput 2012; 8:563-74. [DOI: 10.1021/ct200401q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mahesh Sundararajan
- Max-Planck Institutfür Bioanorganische Chemie, Stiftstrasse 32-34, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck Institutfür Bioanorganische Chemie, Stiftstrasse 32-34, D-45470 Mülheim an der Ruhr, Germany
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39
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Cytochrome c
oxidase: Intermediates of the catalytic cycle and their energy-coupled interconversion. FEBS Lett 2011; 586:630-9. [DOI: 10.1016/j.febslet.2011.08.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 11/20/2022]
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40
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Liao MS, Huang MJ, Watts JD. FeP(Im)-AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). Mol Phys 2011; 109:2035-2048. [PMID: 22228914 PMCID: PMC3251830 DOI: 10.1080/00268976.2011.609141] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (E(bond)) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O(2)). The results indicate that an accurate prediction of E(bond) for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield E(bond) values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O(2), respectively, which are in reasonable agreement with experimental data (0.78 - 0.85 eV for CO, 0.99 eV for NO, and 0.44 - 0.53 eV for O(2)). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, Mississippi 39217
| | - Ming-Ju Huang
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, Mississippi 39217
| | - John D. Watts
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, Mississippi 39217
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41
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Lanucara F, Chiavarino B, Crestoni ME, Scuderi D, Sinha RK, Maı̂tre P, Fornarini S. Naked Five-Coordinate FeIII(NO) Porphyrin Complexes: Vibrational and Reactivity Features. Inorg Chem 2011; 50:4445-52. [DOI: 10.1021/ic200073v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Francesco Lanucara
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
| | - Debora Scuderi
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Rajeev K. Sinha
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Philippe Maı̂tre
- Laboratoire de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris Sud, Bâtiment 350, 91405 Orsay Cedex, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, P.le A. Moro 5, I-00185, Roma, Italy
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42
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Lessons on O2 and NO bonding to heme from ab initio multireference/multiconfiguration and DFT calculations. J Biol Inorg Chem 2011; 16:841-55. [DOI: 10.1007/s00775-011-0763-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 02/03/2011] [Indexed: 12/29/2022]
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43
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Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb(3). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:813-8. [PMID: 21315685 DOI: 10.1016/j.bbabio.2011.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 11/21/2022]
Abstract
The proton-pumping cbb(3)-type cytochrome c oxidases catalyze cell respiration in many pathogenic bacteria. For reasons not yet understood, the apparent dioxygen (O(2)) affinity in these enzymes is very high relative to other members of the heme-copper oxidase (HCO) superfamily. Based on density functional theory (DFT) calculations on intermediates of the oxygen scission reaction in active-site models of cbb(3)- and aa(3)-type oxidases, we find that a transient peroxy intermediate (I(P), Fe[III]-OOH(-)) is ~6kcal/mol more stable in the former case, resulting in more efficient kinetic trapping of dioxygen and hence in a higher apparent oxygen affinity. The major molecular basis for this stabilization is a glutamate residue, polarizing the proximal histidine ligand of heme b(3) in the active site.
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44
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Radoul M, Bykov D, Rinaldo S, Cutruzzolà F, Neese F, Goldfarb D. Dynamic hydrogen-bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase. J Am Chem Soc 2011; 133:3043-55. [PMID: 21309511 DOI: 10.1021/ja109688w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
cd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme cofactor, found only in this class of enzymes, where the substrate, nitrite, binds and is converted to NO. For a long time, it was believed that NO must be released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of ferrous-nitroso complex, which was considered as a dead-end product. However, recently an enhanced rate of NO dissociation from the ferrous form, not observed in standard b-type hemes, has been reported and attributed to the unique d(1)-heme structure (Rinaldo, S.; Arcovito, A.; Brunori, M.; Cutruzzolà, F. J. Biol. Chem. 2007, 282, 14761-14767). Here, we report on a detailed study of the spatial and electronic structure of the ferrous d(1)-heme NO complex from Pseudomonas aeruginosa cd(1) NIR and two mutants Y10F and H369A/H327A in solution, searching for the unique properties that are responsible for the relatively fast release. There are three residues at the "distal" side of the heme (Tyr(10), His(327), and His(369)), and in this work we focus on the identification and characterization of possible H-bonds they can form with the NO, thereby affecting the stability of the complex. For this purpose, we have used high field pulse electron-nuclear double resonance (ENDOR) combined with density functional theory (DFT) calculations. The DFT calculations were essential for assigning and interpreting the ENDOR spectra in terms of geometric structure. We have shown that the NO in the nitrosyl d(1)-heme complex of cd(1) NIR forms H-bonds with Tyr(10) and His(369), whereas the second conserved histidine, His(327), appears to be less involved in NO H-bonding. This is in contrast to the crystal structure that shows that Tyr(10) is removed from the NO. We have also observed a larger solvent accessibility to the distal pocket in the mutants as compared to the wild-type. Moreover, it was shown that the H-bonding network within the active site is dynamic and that a change in the protonation state of one of the residues does affect the strength and position of the H-bonds formed by the others. In the Y10F mutant, His(369) is closer to the NO, whereas mutation of both distal histidines displaces Tyr(10), removing its H-bond. The implications of the H-bonding network found in terms of the complex stability and catalysis are discussed.
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Affiliation(s)
- Marina Radoul
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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45
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Kaila VRI, Oksanen E, Goldman A, Bloch DA, Verkhovsky MI, Sundholm D, Wikström M. A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:769-78. [PMID: 21211513 DOI: 10.1016/j.bbabio.2010.12.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 12/20/2010] [Accepted: 12/26/2010] [Indexed: 01/12/2023]
Abstract
Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallographic studies ((Aoyama et al. Proc. Natl. Acad. Sci. USA 106 (2009) 2165-2169) and (Koepke et al. Biochim. Biophys. Acta 1787 (2009) 635-645)), suggested that a peroxide dianion might be bound to the active site of oxidized CcO. We have investigated this hypothesis by combining quantum chemical calculations with a re-refinement of the X-ray crystallographic data and optical spectroscopic measurements. Our data suggest that dianionic peroxide, superoxide, and dioxygen all form a similar superoxide species when inserted into a fully oxidized ferric/cupric binuclear site (BNC). We argue that stable peroxides are unlikely to be confined within the oxidized BNC since that would be expected to lead to bond splitting and formation of the catalytic P intermediate. Somewhat surprisingly, we find that binding of dioxygen to the oxidized binuclear site is weakly exergonic, and hence, the observed structure might have resulted from dioxygen itself or from superoxide generated from O(2) by the X-ray beam. We show that the presence of O(2) is consistent with the X-ray data. We also discuss how other structures, such as a mixture of the aqueous species (H(2)O+OH(-) and H(2)O) and chloride fit the experimental data.
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Affiliation(s)
- Ville R I Kaila
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland.
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46
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Liao MS, Huang MJ, Watts JD. Iron porphyrins with different imidazole ligands. A theoretical comparative study. J Phys Chem A 2010; 114:9554-69. [PMID: 20712371 PMCID: PMC2964071 DOI: 10.1021/jp1052216] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A theoretical comparative study of a series of five- and six-coordinate iron porphyrins, FeP(L) and FeP(L)(O(2)), has been carried out using DFT methods, where P = porphine and L = imidazole (Im), 1-methylimidazole (1-MeIm), 2-methylimidazole (2-MeIm), 1,2-dimethylimidazole (1,2-Me(2)Im), 4-ethylimidazole (4-EtIm), or histidine (His). Two ligated "picket-fence" iron porphyrins, FeTpivPP(2-MeIm) and FeTpivPP(2-MeIm)(O(2)), were also included in the study for comparison. A number of density functionals were employed in the computations to obtain reliable results. The performance of functionals and basis set effects were investigated in detail on FeP, FeP(Im), and FeP(Im)(O(2)), for which certain experimental information is available and there are some previous calculations in the literature for comparison. Many subtle distinctions in the effects of the different imidazole ligands on the structures and energetics of the deoxy- and oxy iron porphyrins are revealed. While FeP(2-MeIm) is identified to be high spin (S = 2), the ground state of FeP(1-MeIm) may be an admixture of a high-spin (S = 2) and an intermediate-spin (S = 1) state. The ground state of FeP(L)(O(2)) may be different with different L. A weaker Fe-L bond more likely leads to an open-shell singlet ground state for the oxy complex. The 2-methyl group in 2-MeIm, which increases steric contact between the ligand and the porphyrinato skeleton, weakens the Fe-O(2) bond, and thus iron porphyrins with 2-MeIm mimic T-state (low affinity) hemoglobin. The calculated FeP(2-MeIm)-O(2) bonding energy is comparable to the FeTpivPP(2-MeIm)-O(2) one, in agreement with the fact that the picket-fence iron porphyrin binds O(2) with affinity similar to that of myoglobin but different from the result obtained by the CPMD scheme. Im and 4-EtIm closely resemble His, the biologically axial base, and so future computations on hemoprotein models can be simplified safely by using Im.
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Affiliation(s)
- Meng-Sheng Liao
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, Mississippi 39217
| | - Ming-Ju Huang
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, Mississippi 39217
| | - John D. Watts
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, Mississippi 39217
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47
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Chung LW, Li X, Sugimoto H, Shiro Y, Morokuma K. ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants. J Am Chem Soc 2010; 132:11993-2005. [DOI: 10.1021/ja103530v] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
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48
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Liu H, Xu Z, Wang N, Yu C, Gao N, Zhao J, Li N. Theoretical investigation on the chemical sensing of metalloporphyrin-based molecular junction. J Chem Phys 2010; 132:244702. [DOI: 10.1063/1.3456542] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Lin X, Zhao W, Wang X. Characterization of conformational changes and noncovalent complexes of myoglobin by electrospray ionization mass spectrometry, circular dichroism and fluorescence spectroscopy. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:618-626. [PMID: 20527030 DOI: 10.1002/jms.1747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was employed to monitor the heme release and the conformational changes of myoglobin (Mb) under different solvent conditions, and to observe ligand bindings of Mb. ESI-MS, complemented by circular dichroism and fluorescence spectroscopy, was used to study the mechanism of acid- and organic solvent-induced denaturation by probing the changes in the secondary and the tertiary structure of Mb. The results obtained show that complete disruption of the heme-protein interactions occurs when Mb is subjected to one of the following solution conditions: pH 3.2-3.6, or solution containing 20-30% acetonitrile or 40-50% methanol. Outside these ranges, Mb is present entirely in its native state (binding with a heme group) or as apomyoglobin (i.e. without the heme). Spectroscopic data demonstrate that the denaturation mechanism of Mb induced by acid may be significantly different from that by the organic solvent. Low pH reduces helices in Mb, whereas certain organic content level in solution results in the loss of the tertiary structure. ESI-MS conditions were established to observe the H(2)O- and CO-bound Mb complexes, respectively. H(2)O binding to metmyoglobin (17,585 Da), where the heme iron is in the ferric oxidation state, is observed in ESI-MS. CO binding to Mb (17,595 Da), on the other hand, can be only observed after the heme iron is reduced to the ferrous form. Therefore, ESI-MS combined with spectroscopic techniques provides a useful means for probing the formation of ligand-binding complexes and characterizing protein conformational changes.
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Affiliation(s)
- Xin Lin
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, China
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50
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Radoul M, Sundararajan M, Potapov A, Riplinger C, Neese F, Goldfarb D. Revisiting the nitrosyl complex of myoglobin by high-field pulse EPR spectroscopy and quantum mechanical calculations. Phys Chem Chem Phys 2010; 12:7276-89. [PMID: 20490401 DOI: 10.1039/c000652a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of NO to reduced myoglobin in solution results in the formation of two paramagnetic nitrosyl myoglobin (MbNO) complexes: one with a rhombic g-factor and the other with an axial one, referred to as the R- and A-forms. In spite of past extensive studies of MbNO by crystallography, spectroscopy and quantum chemical calculations it is still not clear what factors determine the appearance of the two forms. In this work we applied a combination of state of the art quantum chemical calculations and high field pulsed EPR spectroscopy (W-band, 3.4 T/95 GHz) to further characterize the two forms. Specifically, we have used (1)H and (2)H electron-nuclear double resonance (ENDOR) spectroscopy to identify and characterize the H-bond to the NO, and hyperfine sub-level correlation (HYSCORE) spectroscopy to determine the hyperfine and quadrupole interactions of the Fe(ii) coordinated (14)N of the proximal histidine (14)N(His93). The calculations employed quantum mechanics (QM), particularly density functional theory (DFT) methods in combination with molecular mechanics (MM) force-field to model the protein environment. Through QM/MM calculations of the EPR parameters we have explored their dependence on several geometrical factors of the Fe-NO bond and found those that reproduce the best experimental results. The spread of the W-band EPR spectrum of MbNO due to the g-anisotropy is large and there is a significant part of the spectrum where the R-form is the sole contributor. This allowed us to resolve some new characteristics of the R-form: (i) a NO-H hydrogen bond has been detected and characterized and through QM/MM calculations has been unambiguously assigned to (epsilon2)H(His64). (ii) The complete hyperfine and quadrupole interactions of (14)N(His93) have been determined and correlated with structural parameters again using QM/MM calculations. The agreement between the experimental results and calculations varied between excellent and good, depending on the EPR parameter in question. As for the more elusive A-form, the results only suggest that it does have a (14)N(His93) ligand with a hyperfine comparable to that of the R-form and it has less hydrogen bonding interaction with His(64). The calculations also established the orientation of the principal g-values, finding that they are closely related to the orientation of the NO bond. This information is essential for deriving structural information from the experimental orientation selective HYSCORE and ENDOR data.
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Affiliation(s)
- Marina Radoul
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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