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Palermo JC, Carllinni Colombo M, Semelak JA, Scocozza MF, Boubeta FM, Murgida DH, Estrin DA, Bari SE. Autocatalytic Mechanism in the Anaerobic Reduction of Metmyoglobin by Sulfide Species. Inorg Chem 2023; 62:11304-11317. [PMID: 37439562 DOI: 10.1021/acs.inorgchem.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The mechanism of the metal centered reduction of metmyoglobin (MbFeIII) by sulfide species (H2S/HS-) under an argon atmosphere has been studied by a combination of spectroscopic, kinetic, and computational methods. Asymmetric S-shaped time-traces for the formation of MbFeII at varying ratios of excess sulfide were observed at pH 5.3 < pH < 8.0 and 25 °C, suggesting an autocatalytic reaction mechanism. An increased rate at more alkaline pHs points to HS- as relevant reactive species for the reduction. The formation of the sulfanyl radical (HS•) in the slow initial phase was assessed using the spin-trap phenyl N-tert-butyl nitrone. This radical initiates the formation of S-S reactive species as disulfanuidyl/ disulfanudi-idyl radical anions and disulfide (HSSH•-/HSS•2- and HSS-, respectively). The autocatalysis has been ascribed to HSS-, formed after HSSH•-/HSS•2- disproportionation, which behaves as a fast reductant toward the intermediate complex MbFeIII(HS-). We propose a reaction mechanism for the sulfide-mediated reduction of metmyoglobin where only ferric heme iron initiates the oxidation of sulfide species. Beside the chemical interest, this insight into the MbFeIII/sulfide reaction under an argon atmosphere is relevant for the interpretation of biochemical aspects of ectopic myoglobins found on hypoxic tissues toward reactive sulfur species.
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Affiliation(s)
- Juan Cruz Palermo
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Melisa Carllinni Colombo
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Jonathan A Semelak
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Magalí F Scocozza
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Fernando M Boubeta
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Daniel H Murgida
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Darío A Estrin
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Sara E Bari
- Instituto de Química Física de Los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
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Sewell KE, Gola GF, Pignataro MF, Herrera MG, Noguera ME, Olmos J, Ramírez JA, Capece L, Aran M, Santos J. Direct Cysteine Desulfurase Activity Determination by NMR and the Study of the Functional Role of Key Structural Elements of Human NFS1. ACS Chem Biol 2023; 18:1534-1547. [PMID: 37410592 DOI: 10.1021/acschembio.3c00147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The mitochondrial cysteine desulfurase NFS1 is an essential PLP-dependent enzyme involved in iron-sulfur cluster assembly. The enzyme catalyzes the desulfurization of the l-Cys substrate, producing a persulfide and l-Ala as products. In this study, we set the measurement of the product l-Ala by NMR in vitro by means of 1H NMR spectra acquisition. This methodology provided us with the possibility of monitoring the reaction in both fixed-time and real-time experiments, with high sensitivity and accuracy. By studying I452A, W454A, Q456A, and H457A NFS1 variants, we found that the C-terminal stretch (CTS) of the enzyme is critical for function. Specifically, mutation of the extremely conserved position W454 resulted in highly decreased activity. Additionally, we worked on two singular variants: "GGG" and C158A. In the former, the catalytic Cys-loop was altered by including two Gly residues to increase the flexibility of this loop. This variant had significantly impaired activity, indicating that the Cys-loop motions are fine-tuned in the wild-type enzyme. In turn, for C158A, we found an unanticipated increase in l-Cys desulfurase activity. Furthermore, we carried out molecular dynamics simulations of the supercomplex dedicated to iron-sulfur cluster biosynthesis, which includes NFS1, ACP, ISD11, ISCU2, and FXN subunits. We identified CTS as a key element that established interactions with ISCU2 and FXN concurrently; we found specific interactions that are established when FXN is present, reinforcing the idea that FXN not only forms part of the iron-sulfur cluster assembly site but also modulates the internal motions of ISCU2.
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Affiliation(s)
- Karl E Sewell
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - Gabriel F Gola
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET─Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - María Florencia Pignataro
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - María Georgina Herrera
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - Martín E Noguera
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Junín 956, Buenos Aires 1113AAD, Argentina
| | - Justo Olmos
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
| | - Javier A Ramírez
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET─Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), Universidad de Buenos Aires. Buenos Aires C1428EGA, Argentina
| | - Martín Aran
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Javier Santos
- Laboratorio de Genómica e Ingeniería de Sistemas Biológicos. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Autónoma de Buenos Aires C1428EGA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Rivadavia 1917, Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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Clemente CM, Capece L, Martí MA. Best Practices on QM/MM Simulations of Biological Systems. J Chem Inf Model 2023; 63:2609-2627. [PMID: 37100031 DOI: 10.1021/acs.jcim.2c01522] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
During the second half of the 20th century, following structural biology hallmark works on DNA and proteins, biochemists shifted their questions from "what does this molecule look like?" to "how does this process work?". Prompted by the theoretical and practical developments in computational chemistry, this led to the emergence of biomolecular simulations and, along with the 2013 Nobel Prize in Chemistry, to the development of hybrid QM/MM methods. QM/MM methods are necessary whenever the problem we want to address involves chemical reactivity and/or a change in the system's electronic structure, with archetypal examples being the studies of an enzyme's reaction mechanism and a metalloprotein's active site. In the last decades QM/MM methods have seen an increasing adoption driven by their incorporation in widely used biomolecular simulation software. However, properly setting up a QM/MM simulation is not an easy task, and several issues need to be properly addressed to obtain meaningful results. In the present work, we describe both the theoretical concepts and practical issues that need to be considered when performing QM/MM simulations. We start with a brief historical perspective on the development of these methods and describe when and why QM/MM methods are mandatory. Then we show how to properly select and analyze the performance of the QM level of theory, the QM system size, and the position and type of the boundaries. We show the relevance of performing prior QM model system (or QM cluster) calculations in a vacuum and how to use the corresponding results to adequately calibrate those derived from QM/MM. We also discuss how to prepare the starting structure and how to select an adequate simulation strategy, including those based on geometry optimizations as well as free energy methods. In particular, we focus on the determination of free energy profiles using multiple steered molecular dynamics (MSMD) combined with Jarzynski's equation. Finally, we describe the results for two illustrative and complementary examples: the reaction performed by chorismate mutase and the study of ligand binding to hemoglobins. Overall, we provide many practical recommendations (or shortcuts) together with important conceptualizations that we hope will encourage more and more researchers to incorporate QM/MM studies into their research projects.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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Yamada T, Morita Y, Takada R, Funamoto M, Okamoto W, Kohno M, Komatsu T. Zinc Substituted Myoglobin-Albumin Fusion Protein: A Photosensitizer for Cancer Therapy. Chemistry 2023; 29:e202203952. [PMID: 36689636 DOI: 10.1002/chem.202203952] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 01/25/2023]
Abstract
Myoglobin combined with human serum albumin (Mb-HSA) can be produced using yeast Pichia pastoris as a host strain, with secretion into the culture medium. This Mb-HSA fusion protein possesses identical O2 binding affinity to that of naked Mb. The Mb unit is reconstituted with a zinc(II) protoporphyrin IX, yielding (zinc substituted Mb)-HSA, ZnMb-HSA. The photophysical property and singlet O2 generation ability of ZnMb-HSA are equivalent to those of ZnMb. In vitro cell experiments revealed that ZnMb-HSA acts as a superior photosensitizer for photodynamic cancer therapy. It is noteworthy that ZnMb-HSA shows long circulation lifetime in vivo.
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Affiliation(s)
- Taiga Yamada
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Yoshitsugu Morita
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Ryoya Takada
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Mizuki Funamoto
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Wataru Okamoto
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Mitsutomo Kohno
- Department of General Thoracic Surgery, Saitama Medical Center, Saitama Medical University, 1981 Kamoda, Kawagoe-shi, Saitama, 350-8550, Japan
| | - Teruyuki Komatsu
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
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5
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Espeche LD, Sewell KE, Castro IH, Capece L, Pignataro MF, Dain L, Santos J. Conformational stability, dynamics and function of human frataxin: Tryptophan side chain interplay. Arch Biochem Biophys 2022; 715:109086. [PMID: 34801473 DOI: 10.1016/j.abb.2021.109086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 11/02/2022]
Abstract
In humans, the loss of frataxin results in Friedreich's Ataxia, a neurodegenerative disease, in which a deficit in the iron-sulfur cluster assembly is observed. In this work, we analyzed three frataxin variants in which one tryptophan was replaced by a glycine: W155G, W168G and W173G. As expected, given its localization in the assembly site, W155G was not able to activate the desulfurase activity of the supercomplex for iron-sulfur cluster assembly. In turn, W168G, which was significantly more unstable than W155G, was fully active. W173G, which was highly unstable as W168G, showed a significantly decreased activity, only slightly higher than W155G. As W168G and W173G were highly sensitive to proteolysis, we investigated the protein motions by molecular dynamic simulations. We observed that W173G may display altered motions at the Trp155 site. Furthermore, we revealed a H-bond network in which Trp155 takes part, involving residues Gln148, Asn151, Gln153 and Arg165. We suggest that this motion modulation that specifically alters the population of different Trp155 rotamers can be directly transferred to the assembly site, altering the dynamics of the ISCU His137 key residue. This hypothesis was also contrasted by means of molecular dynamic simulations of frataxin in the context of the complete supercomplex. We propose that the supercomplex requires very definite motions of Trp155 to consolidate the assembly site.
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Affiliation(s)
- Lucía D Espeche
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla" A.N.L.I.S., Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina
| | - Karl Ellioth Sewell
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Ignacio H Castro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina.
| | - María Florencia Pignataro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Liliana Dain
- Departamento de Diagnóstico Genético, Centro Nacional de Genética Médica "Dr. Eduardo E. Castilla" A.N.L.I.S., Av. Las Heras 2670, C1425ASQ, C.A.B.A, Argentina; Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina.
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Patterson DC, Liu Y, Das S, Yennawar NH, Armache JP, Kincaid JR, Weinert EE. Heme-Edge Residues Modulate Signal Transduction within a Bifunctional Homo-Dimeric Sensor Protein. Biochemistry 2021; 60:3801-3812. [PMID: 34843212 DOI: 10.1021/acs.biochem.1c00581] [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
Bifunctional enzymes, which contain two domains with opposing enzymatic activities, are widely distributed in bacteria, but the regulatory mechanism(s) that prevent futile cycling are still poorly understood. The recently described bifunctional enzyme, DcpG, exhibits unusual heme properties and is surprisingly able to differentially regulate its two cyclic dimeric guanosine monophosphate (c-di-GMP) metabolic domains in response to heme gaseous ligands. Mutagenesis of heme-edge residues was used to probe the heme pocket and resulted in decreased O2 dissociation kinetics, identifying roles for these residues in modulating DcpG gas sensing. In addition, the resonance Raman spectra of the DcpG wild type and heme-edge mutants revealed that the mutations alter the heme electrostatic environment, vinyl group conformations, and spin state population. Using small-angle X-ray scattering and negative stain electron microscopy, the heme-edge mutations were demonstrated to cause changes to the protein conformation, which resulted in altered signaling transduction and enzyme kinetics. These findings provide insights into molecular interactions that regulate DcpG gas sensing as well as mechanisms that have evolved to control multidomain bacterial signaling proteins.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Sayan Das
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Emily E Weinert
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Julió Plana L, Martinez Grundman JE, Estrin DA, Lecomte JTJ, Capece L. Distal lysine (de)coordination in the algal hemoglobin THB1: A combined computer simulation and experimental study. J Inorg Biochem 2021; 220:111455. [PMID: 33882423 DOI: 10.1016/j.jinorgbio.2021.111455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/26/2022]
Abstract
THB1 is a monomeric truncated hemoglobin from the green alga Chlamydomonas reinhardtii. In the absence of exogenous ligands and at neutral pH, the heme group of THB1 is coordinated by two protein residues, Lys53 and His77. THB1 is thought to function as a nitric oxide dioxygenase, and the distal binding of O2 requires the cleavage of the Fe-Lys53 bond accompanied by protonation and expulsion of the lysine from the heme cavity into the solvent. Nuclear magnetic resonance spectroscopy and crystallographic data have provided dynamic and structural insights of the process, but the details of the mechanism have not been fully elucidated. We applied a combination of computer simulations and site-directed mutagenesis experiments to shed light on this issue. Molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics restrained optimizations were performed to explore the nature of the transition between the decoordinated and lysine-bound states of the ferrous heme in THB1. Lys49 and Arg52, which form ionic interactions with the heme propionates in the X-ray structure of lysine-bound THB1, were observed to assist in maintaining Lys53 inside the protein cavity and play a key role in the transition. Lys49Ala, Arg52Ala and Lys49Ala/Arg52Ala THB1 variants were prepared, and the consequences of the replacements on the Lys (de)coordination equilibrium were characterized experimentally for comparison with computational prediction. The results reinforced the dynamic role of protein-propionate interactions and strongly suggested that cleavage of the Fe-Lys53 bond and ensuing conformational rearrangement is facilitated by protonation of the amino group inside the distal cavity.
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Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jaime E Martinez Grundman
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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8
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Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions. J Inorg Biochem 2021; 219:111437. [PMID: 33892380 DOI: 10.1016/j.jinorgbio.2021.111437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 12/25/2022]
Abstract
THB1 is a monomeric truncated hemoglobin (TrHb) found in the cytoplasm of the green alga Chlamydomonas reinhardtii. The canonical heme coordination scheme in hemoglobins is a proximal histidine ligand and an open distal site. In THB1, the latter site is occupied by Lys53, which is likely to facilitate Fe(II)/Fe(III) redox cycling but hinders dioxygen binding, two features inherent to the NO dioxygenase activity of the protein. TrHb surveys show that a lysine at a position aligning with Lys53 is an insufficient determinant of coordination, and in this study, we sought to identify factors controlling lysine affinity for the heme iron. We solved the "Lys-off" X-ray structure of THB1, represented by the cyanide adduct of the Fe(III) protein, and hypothesized that interactions that differ between the known "Lys-on" structure and the Lys-off structure participate in the control of Lys53 affinity for the heme iron. We applied an experimental approach (site-directed mutagenesis, heme modification, pH titrations in the Fe(III) and Fe(II) states) and a computational approach (MD simulations in the Fe(II) state) to assess the role of heme propionate-protein interactions, distal helix capping, and the composition of the distal pocket. All THB1 modifications resulted in a weakening of lysine affinity and affected the coupling between Lys53 proton binding and heme redox potential. The results supported the importance of specific heme peripheral interactions for the pH stability of iron coordination and the ability of the protein to undergo redox reactions.
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9
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Maglio O, Chino M, Vicari C, Pavone V, Louro RO, Lombardi A. Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts. Chem Commun (Camb) 2021; 57:990-993. [PMID: 33399143 DOI: 10.1039/d0cc06676a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fe-Mimochrome VI*a is a synthetic peroxidase and peroxygenase, featuring two different peptides that are covalently-linked to deuteroheme. To perform a systematic structure/function correlation, we purposely shortened the distance between the distal peptide and the heme, allowing for the separation and characterization of two regioisomers. They differ in both His axial-ligand orientation, as determined by paramagnetic NMR shifts, and activity. These findings highlight that synthetic metalloenzymes may provide an efficient tool for disentangling the role of axial ligand orientation over peroxidase activity.
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Affiliation(s)
- Ornella Maglio
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy. and IBB-CNR, Via Mezzocannone 16, Naples, 80134, Italy
| | - Marco Chino
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Claudia Vicari
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Vincenzo Pavone
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Ricardo O Louro
- ITQB-UNL, Av. da Republica (EAN), Oeiras 2780-157, Portugal.
| | - Angela Lombardi
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
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10
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Benchoam D, Cuevasanta E, Julió Plana L, Capece L, Banerjee R, Alvarez B. Heme-Thiolate Perturbation in Cystathionine β-Synthase by Mercury Compounds. ACS OMEGA 2021; 6:2192-2205. [PMID: 33521459 PMCID: PMC7841933 DOI: 10.1021/acsomega.0c05475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/22/2020] [Indexed: 05/11/2023]
Abstract
Cystathionine β-synthase (CBS) is an enzyme involved in sulfur metabolism that catalyzes the pyridoxal phosphate-dependent condensation of homocysteine with serine or cysteine to form cystathionine and water or hydrogen sulfide (H2S), respectively. CBS possesses a b-type heme coordinated by histidine and cysteine. Fe(III)-CBS is inert toward exogenous ligands, while Fe(II)-CBS is reactive. Both Fe(III)- and Fe(II)-CBS are sensitive to mercury compounds. In this study, we describe the kinetics of the reactions with mercuric chloride (HgCl2) and p-chloromercuribenzoic acid. These reactions were multiphasic and resulted in five-coordinate CBS lacking thiolate ligation, with six-coordinate species as intermediates. Computational QM/MM studies supported the feasibility of formation of species in which the thiolate is proximal to both the iron ion and the mercury compound. The reactions of Fe(II)-CBS were faster than those of Fe(III)-CBS. The observed rate constants of the first phase increased hyperbolically with concentration of the mercury compounds, with limiting values of 0.3-0.4 s-1 for Fe(III)-CBS and 40 ± 4 s-1 for Fe(II)-CBS. The data were interpreted in terms of alternative models of conformational selection or induced fit. Exposure of Fe(III)-CBS to HgCl2 led to heme release and activity loss. Our study reveals the complexity of the interactions between mercury compounds and CBS.
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Affiliation(s)
- Dayana Benchoam
- Laboratorio
de Enzimología, Instituto de Química Biológica,
Facultad de Ciencias, Universidad de la
República, Montevideo, 11400 Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, 11800 Uruguay
| | - Ernesto Cuevasanta
- Laboratorio
de Enzimología, Instituto de Química Biológica,
Facultad de Ciencias, Universidad de la
República, Montevideo, 11400 Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, 11800 Uruguay
- Unidad
de Bioquímica Analítica, Centro de Investigaciones Nucleares,
Facultad de Ciencias, Universidad de la
República, Montevideo, 11400 Uruguay
| | - Laia Julió Plana
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/Instituto de Química
Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA Buenos
Aires, Argentina
| | - Luciana Capece
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/Instituto de Química
Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA Buenos
Aires, Argentina
| | - Ruma Banerjee
- Department
of Biological Chemistry, University of Michigan
Medical School, Ann Arbor, Michigan 48109, United States
| | - Beatriz Alvarez
- Laboratorio
de Enzimología, Instituto de Química Biológica,
Facultad de Ciencias, Universidad de la
República, Montevideo, 11400 Uruguay
- Centro
de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo, 11800 Uruguay
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11
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Castro IH, Bringas M, Doni D, Noguera ME, Capece L, Aran M, Blaustein M, Costantini P, Santos J. Relationship between activity and stability: Design and characterization of stable variants of human frataxin. Arch Biochem Biophys 2020; 691:108491. [PMID: 32707090 DOI: 10.1016/j.abb.2020.108491] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 11/16/2022]
Abstract
The relationships between conformational dynamics, stability and protein function are not obvious. Frataxin (FXN) is an essential protein that forms part of a supercomplex dedicated to the iron-sulfur (Fe-S) cluster assembly within the mitochondrial matrix. In humans, the loss of FXN expression or a decrease in its functionality results in Friedreich's Ataxia, a cardio-neurodegenerative disease. Recently, the way in which FXN interacts with the rest of the subunits of the supercomplex was uncovered. This opens a window to explore relationships between structural dynamics and function. In this study, we prepared a set of FXN variants spanning a broad range of conformational stabilities. Variants S160I, S160M and A204R were more stable than the wild-type and showed similar biological activity. Additionally, we prepared SILCAR, a variant that combines S160I, L203C and A204R mutations. SILCAR was 2.4 kcal mol-1 more stable and equally active. Some of the variants were significantly more resistant to proteolysis than the wild-type FXN. SILCAR showed the highest resistance, suggesting a more rigid structure. It was corroborated by means of molecular dynamics simulations. Relaxation dispersion NMR experiments comparing SILCAR and wild-type variants suggested similar internal motions in the microsecond to millisecond timescale. Instead, variant S157I showed higher denaturation resistance but a significant lower function, similarly to that observed for the FRDA variant N146K. We concluded that the contribution of particular side chains to the conformational stability of FXN might be highly subordinated to their impact on both the protein function and the stability of the functional supercomplex.
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Affiliation(s)
- Ignacio Hugo Castro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), C1428EGA, Buenos Aires, Argentina
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Martin Ezequiel Noguera
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Instituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), C1428EGA, Buenos Aires, Argentina
| | - Martín Aran
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Matías Blaustein
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB(3)). Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina.
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12
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Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions. J Biol Inorg Chem 2020; 25:267-283. [PMID: 32048044 PMCID: PMC7082302 DOI: 10.1007/s00775-020-01759-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022]
Abstract
Hemoglobins (Hbs) utilize heme b as a cofactor and are found in all kingdoms of life. The current knowledge reveals an enormous variability of Hb primary sequences, resulting in topological, biochemical and physiological individuality. As Hbs appear to modulate their reactivities through specific combinations of structural features, predicting the characteristics of a given Hb is still hardly possible. The unicellular green alga Chlamydomonas reinhardtii contains 12 genes encoding diverse Hbs of the truncated lineage, several of which possess extended N- or C-termini of unknown function. Studies on some of the Chlamydomonas Hbs revealed yet unpredictable structural and biochemical variations, which, along with a different expression of their genes, suggest diverse physiological roles. Chlamydomonas thus represents a promising system to analyze the diversification of Hb structure, biochemistry and physiology. Here, we report the crystal structure, resolved to 1.75 Å, of the heme-binding domain of cyanomet THB11 (Cre16.g662750), one of the pentacoordinate algal Hbs, which offer a free Fe-coordination site in the reduced state. The overall fold of THB11 is conserved, but individual features such as a kink in helix E, a tilted heme plane and a clustering of methionine residues at a putative tunnel exit appear to be unique. Both N- and C-termini promote the formation of oligomer mixtures, and the absence of the C terminus results in reduced nitrite reduction rates. This work widens the structural and biochemical knowledge on the 2/2Hb family and suggests that the N- and C-terminal extensions of the Chlamydomonas 2/2Hbs modulate their reactivity by intermolecular interactions.
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13
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Herrera MG, Noguera ME, Sewell KE, Agudelo Suárez WA, Capece L, Klinke S, Santos J. Structure of the Human ACP-ISD11 Heterodimer. Biochemistry 2019; 58:4596-4609. [PMID: 31664822 DOI: 10.1021/acs.biochem.9b00539] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the mammalian mitochondrial protein complex for iron-sulfur cluster assembly has been the focus of important studies. This is partly because of its high degree of relevance in cell metabolism and because mutations of the involved proteins are the cause of several human diseases. Cysteine desulfurase NFS1 is the key enzyme of the complex. At present, it is well-known that the active form of NFS1 is stabilized by the small protein ISD11. In this work, the structure of the human mitochondrial ACP-ISD11 heterodimer was determined at 2.0 Å resolution. ACP-ISD11 forms a cooperative unit stabilized by several ionic interactions, hydrogen bonds, and apolar interactions. The 4'-phosphopantetheine-acyl chain, which is covalently bound to ACP, interacts with several residues of ISD11, modulating together with ACP the foldability of ISD11. Recombinant human ACP-ISD11 was able to interact with the NFS1 desulfurase, thus yielding an active enzyme, and the NFS1/ACP-ISD11 core complex was activated by frataxin and ISCU proteins. Internal motions of ACP-ISD11 were studied by molecular dynamics simulations, showing the persistence of the interactions between both protein chains. The conformation of the dimer is similar to that found in the context of the (NFS1/ACP-ISD11)2 supercomplex core, which contains the Escherichia coli ACP instead of the human variant. This fact suggests a sequential mechanism for supercomplex consolidation, in which the ACP-ISD11 complex may fold independently and, after that, the NFS1 dimer would be stabilized.
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Affiliation(s)
- María Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina.,Instituto de Química y Fisicoquímica Biológicas , Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET , Junín 956 , C1113AAD Buenos Aires , Argentina
| | - Karl Ellioth Sewell
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
| | - William Armando Agudelo Suárez
- Fundación Instituto de Inmunología de Colombia (FIDIC) , Av. 50 No. 26-20 , Bogotá D.C. , Colombia.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET) , C1428EGA Buenos Aires , Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET) , C1428EGA Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM , Av. Patricias Argentinas 435 , C1405BWE Buenos Aires , Argentina
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160-Ciudad Universitaria , C1428EGA Buenos Aires , Argentina
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14
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Julió Plana L, Nadra AD, Estrin DA, Luque FJ, Capece L. Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. J Chem Inf Model 2018; 59:441-452. [PMID: 30516994 DOI: 10.1021/acs.jcim.8b00840] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins are sensitive to temperature, and abrupt changes in the normal temperature conditions can have a profound impact on both structure and function, leading to protein unfolding. However, the adaptation of certain organisms to extreme conditions raises questions about the structural features that permit the structure and function of proteins to be preserved under these adverse conditions. To gain insight into the molecular basis of protein thermostability in the globin family, we have examined three representative examples: human neuroglobin, horse heart myoglobin, and Drosophila hemoglobin, which differ in their melting temperatures and coordination states of the heme iron in the absence of external ligands. In order to elucidate the possible mechanisms that govern the thermostability of these proteins, microsecond-scale classical molecular dynamics simulations were performed at different temperatures. Structural fluctuations and essential dynamics were analyzed, indicating that the flexibility of the CD region, which includes the two short C and D helixes and the connecting CD loop, is directly related to the thermostability. We observed that a larger inherent flexibility of the protein produces higher thermostability, probably concentrating the thermal fluctuations observed at high temperature in flexible regions, preventing unfolding. Globally, the results of this work improve our understanding of thermostability in the globin family.
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Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - Alejandro D Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/IQUIBICEN-CONICET , C1428EGA Buenos Aires , Argentina
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences , University of Barcelona , Campus Torribera , 08921 Santa Coloma de Gramenet , Spain.,Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB) , University of Barcelona , 08028 Barcelona , Spain
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
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15
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Yamamoto Y, Araki H, Shinomiya R, Hayasaka K, Nakayama Y, Ochi K, Shibata T, Momotake A, Ohyama T, Hagihara M, Hemmi H. Structures and Catalytic Activities of Complexes between Heme and All Parallel-Stranded Monomeric G-Quadruplex DNAs. Biochemistry 2018; 57:5938-5948. [PMID: 30234971 DOI: 10.1021/acs.biochem.8b00792] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Heme in its ferrous and ferric states [heme(Fe2+) and heme(Fe3+), respectively] binds selectively to the 3'-terminal G-quartet of all parallel-stranded monomeric G-quadruplex DNAs formed from inosine(I)-containing sequences, i.e., d(TAGGGTGGGTTGGGTGIG) DNA(18mer) and d(TAGGGTGGGTTGGGTGIGA) DNA(18mer/A), through a π-π stacking interaction between the porphyrin moiety of the heme and the G-quartet, to form 1:1 complexes [heme-DNA(18mer) and heme-DNA(18mer/A) complexes, respectively]. These complexes exhibited enhanced peroxidase activities, compared with that of heme(Fe3+) alone, and the activity of the heme(Fe3+)-DNA(18mer/A) complex was greater than that of the heme(Fe3+)-DNA(18mer) one, indicating that the 3'-terminal A of the DNA sequence acts as an acid-base catalyst that promotes the catalytic reaction. In the complexes, a water molecule (H2O) at the interface between the heme and G-quartet is coordinated to the heme Fe atom as an axial ligand and possibly acts as an electron-donating ligand that promotes heterolytic peroxide bond cleavage of hydrogen peroxide bound to the heme Fe atom, trans to the H2O, for the generation of an active species. The intermolecular nuclear Overhauser effects observed among heme, DNA, and Fe-bound H2O indicated that the H2O rotates about the H2O-Fe coordination bond with respect to both the heme and DNA in the complex. Thus, the H2O in the complex is unique in terms of not only its electronic properties but also its dynamic ones. These findings provide novel insights into the design of heme-deoxyribozymes and -ribozymes.
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Affiliation(s)
- Yasuhiko Yamamoto
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan.,Tsukuba Research Center for Energy Materials Science (TREMS) , University of Tsukuba , Tsukuba 305-8571 , Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577 , Japan
| | - Haruka Araki
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Ryosuke Shinomiya
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Kosuke Hayasaka
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Yusaku Nakayama
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Kentaro Ochi
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Tomokazu Shibata
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Atsuya Momotake
- Department of Chemistry , University of Tsukuba , Tsukuba 305-8571 , Japan
| | - Takako Ohyama
- NMR Division, RIKEN SPring-8 Center , RIKEN , Suehiro-cho , Tsurumi-ku, Yokohama 230-0045 , Japan
| | - Masaki Hagihara
- Graduate School of Science and Technology , Hirosaki University , Hirosaki 036-8561 , Japan
| | - Hikaru Hemmi
- Food Research Institute , NARO , Tsukuba 305-8642 , Japan
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16
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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17
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Boubeta FM, Bieza SA, Bringas M, Estrin DA, Boechi L, Bari SE. Mechanism of Sulfide Binding by Ferric Hemeproteins. Inorg Chem 2018; 57:7591-7600. [DOI: 10.1021/acs.inorgchem.8b00478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fernando M. Boubeta
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Silvina A. Bieza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Mauro Bringas
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Darío A. Estrin
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | | | - Sara E. Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
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18
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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19
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Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations. Sci Rep 2017; 7:10926. [PMID: 28883619 PMCID: PMC5589765 DOI: 10.1038/s41598-017-11259-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Abstract
Human hemoglobin (Hb) is a benchmark protein of structural biology that shaped our view of allosterism over 60 years ago, with the introduction of the MWC model based on Perutz structures of the oxy(R) and deoxy(T) states and the more recent Tertiary Two-State model that proposed the existence of individual subunit states -“r” and “t”-, whose structure is yet unknown. Cooperative oxygen binding is essential for Hb function, and despite decades of research there are still open questions related to how tertiary and quaternary changes regulate oxygen affinity. In the present work, we have determined the free energy profiles of oxygen migration and for HisE7 gate opening, with QM/MM calculations of the oxygen binding energy in order to address the influence of tertiary differences in the control of oxygen affinity. Our results show that in the α subunit the low to high affinity transition is achieved by a proximal effect that mostly affects oxygen dissociation and is the driving force of the allosteric transition, while in the β subunit the affinity change results from a complex interplay of proximal and distal effects, including an increase in the HE7 gate opening, that as shown by free energy profiles promotes oxygen uptake.
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20
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Boubeta FM, Bari SE, Estrin DA, Boechi L. Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata. J Phys Chem B 2016; 120:9642-53. [DOI: 10.1021/acs.jpcb.6b06686] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fernando M. Boubeta
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Sara E. Bari
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Dario A. Estrin
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo/CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires,
Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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21
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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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22
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Bustamante JP, Radusky L, Boechi L, Estrin DA, ten Have A, Martí MA. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family. PLoS Comput Biol 2016; 12:e1004701. [PMID: 26788940 PMCID: PMC4720485 DOI: 10.1371/journal.pcbi.1004701] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022] Open
Abstract
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends.
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Affiliation(s)
- Juan P. Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leandro Radusky
- Departamento de Química Biológica e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Arjen ten Have
- Instituto de Investigación Biológica, CONICET, Universidad Nacional de Mar del Plata. Buenos Aires, Argentina
| | - Marcelo A. Martí
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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23
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Kruft BI, Magliozzo RS, Jarzęcki AA. Density Functional Theory Insights into the Role of the Methionine–Tyrosine–Tryptophan Adduct Radical in the KatG Catalase Reaction: O2 Release from the Oxyheme Intermediate. J Phys Chem A 2015; 119:6850-66. [DOI: 10.1021/jp511358p] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bonnie I. Kruft
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Richard S. Magliozzo
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
| | - Andrzej A. Jarzęcki
- Department of Chemistry, Brooklyn College, Brooklyn, New York 11210, United States
- The Graduate Center, City University of New York, Brooklyn, New York 10016, United States
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24
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Makino R, Obayashi E, Hori H, Iizuka T, Mashima K, Shiro Y, Ishimura Y. Initial O2 Insertion Step of the Tryptophan Dioxygenase Reaction Proposed by a Heme-Modification Study. Biochemistry 2015; 54:3604-16. [DOI: 10.1021/acs.biochem.5b00048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Makino
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Eiji Obayashi
- Department
of Biochemistry, Shimane University School of Medicine, Izumo, Shimane 693-8501, Japan
| | - Hiroshi Hori
- Center
for Quantum Science and Technology under Extreme Conditions, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tetsutaro Iizuka
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Keisuke Mashima
- Department
of Life Science, College of Science, Rikkyo University, Nishi-ikebukuro
3-34-1, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoshitsugu Shiro
- RIKEN Harima Institute/Spring 8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yuzuru Ishimura
- Department
of Biochemistry, School of Medicine, Keio University, 35 Shinanomachi,
Shinjuku-ku, Tokyo 160-8582, Japan
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25
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Shibata T, Furuichi E, Imai K, Suzuki A, Yamamoto Y. Effects of heme modification on oxygen affinity and cooperativity of human adult hemoglobin. J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424615500200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We substituted strongly electron-withdrawing trifluoromethyl ( CF 3) group(s) as heme side chain(s) of human adult hemoglobin (Hb) to achieve large alterations of the heme electronic structure, in order to elucidate the relationship between the oxygen ( O 2) binding properties of Hb and the electronic properties of heme peripheral side chains. The obtained results were compared with those of similar studies performed on myoglobin (Mb), e.g. (Nishimura R, Matsumoto D, Shibata T, Yanagisawa S, Ogura T, Tai H, Matsuo T, Hirota S, Neya S, Suzuki A, and Yamamoto Y. Inorg. Chem. 2014; 53: 9156–9165). These two proteins shared the common feature of a decrease in O 2 affinity upon the CF 3 substitution(s). Using the P50 value, which is the partial pressure of O 2 required for 50% oxygenation of a protein, and the equilibrium constant ( p K a ) of the "acid-alkaline transition" in the met form of a protein as measures of the O 2 affinity and the electron density of heme Fe atom of the protein, respectively, a linear p K a - log (1/P50) relationship was demonstrated for the Hb and Mb systems. The native Hb, however, deviated from the p K a - log (1/P50) relationship, while the native Mb followed it. These results highlighted the significance of the vinyl side chains of the heme cofactor in the functional control of Hb through tertiary and quaternary structural changes upon the oxygenation of the protein.
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Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Eisuke Furuichi
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Tokyo 184-8584, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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26
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Nie Y, Li L, Wei Z. Recent advancements in Pt and Pt-free catalysts for oxygen reduction reaction. Chem Soc Rev 2015; 44:2168-201. [DOI: 10.1039/c4cs00484a] [Citation(s) in RCA: 1606] [Impact Index Per Article: 178.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Based on the understanding of the ORR catalytic mechanism, advanced Pt-based and Pt-free catalysts have been explored.
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Affiliation(s)
- Yao Nie
- The State Key Laboratory of Power Transmission Equipment & System Security and New Technology
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing
- China
| | - Li Li
- The State Key Laboratory of Power Transmission Equipment & System Security and New Technology
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing
- China
| | - Zidong Wei
- The State Key Laboratory of Power Transmission Equipment & System Security and New Technology
- School of Chemistry and Chemical Engineering
- Chongqing University
- Chongqing
- China
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27
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Jones EM, Monza E, Balakrishnan G, Blouin GC, Mak PJ, Zhu Q, Kincaid JR, Guallar V, Spiro TG. Differential control of heme reactivity in alpha and beta subunits of hemoglobin: a combined Raman spectroscopic and computational study. J Am Chem Soc 2014; 136:10325-39. [PMID: 24991732 PMCID: PMC4353013 DOI: 10.1021/ja503328a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Indexed: 12/05/2022]
Abstract
The use of hybrid hemoglobin (Hb), with mesoheme substituted for protoheme, allows separate monitoring of the α or β hemes along the allosteric pathway. Using resonance Raman (rR) spectroscopy in silica gel, which greatly slows protein motions, we have observed that the Fe-histidine stretching frequency, νFeHis, which is a monitor of heme reactivity, evolves between frequencies characteristic of the R and T states, for both α or β chains, prior to the quaternary R-T and T-R shifts. Computation of νFeHis, using QM/MM and the conformational search program PELE, produced remarkable agreement with experiment. Analysis of the PELE structures showed that the νFeHis shifts resulted from heme distortion and, in the α chain, Fe-His bond tilting. These results support the tertiary two-state model of ligand binding (Henry et al., Biophys. Chem. 2002, 98, 149). Experimentally, the νFeHis evolution is faster for β than for α chains, and pump-probe rR spectroscopy in solution reveals an inflection in the νFeHis time course at 3 μs for β but not for α hemes, an interval previously shown to be the first step in the R-T transition. In the α chain νFeHis dropped sharply at 20 μs, the final step in the R-T transition. The time courses are fully consistent with recent computational mapping of the R-T transition via conjugate peak refinement by Karplus and co-workers (Fischer et al., Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 5608). The effector molecule IHP was found to lower νFeHis selectively for α chains within the R state, and a binding site in the α1α2 cleft is suggested.
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Affiliation(s)
- Eric M. Jones
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Emanuele Monza
- Joint
BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Gurusamy Balakrishnan
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - George C. Blouin
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Piotr J. Mak
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Qianhong Zhu
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - James R. Kincaid
- Department
of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Victor Guallar
- Joint
BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas G. Spiro
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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28
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Nitsche MA, Ferreria M, Mocskos EE, González Lebrero MC. GPU Accelerated Implementation of Density Functional Theory for Hybrid QM/MM Simulations. J Chem Theory Comput 2014; 10:959-67. [DOI: 10.1021/ct400308n] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Matías A. Nitsche
- Departamento
de Computación, FCEN, UBA, Buenos Aires C1428EGA, Argentina
| | - Manuel Ferreria
- Centro de Simulación
Computacional para Aplicaciones Tecnológicas, CSC, CONICET, Buenos Aires C1425FQD, Argentina
| | - Esteban E. Mocskos
- Departamento
de Computación, FCEN, UBA, Buenos Aires C1428EGA, Argentina
- Centro de Simulación
Computacional para Aplicaciones Tecnológicas, CSC, CONICET, Buenos Aires C1425FQD, Argentina
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29
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Sun S, Sono M, Wang C, Du J, Lebioda L, Dawson JH. Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations. Arch Biochem Biophys 2014; 545:108-15. [PMID: 24440609 DOI: 10.1016/j.abb.2014.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 11/28/2022]
Abstract
Sea worm, Amphitrite ornata, has evolved its globin (an O(2) carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O(2) partition constant measurement method in this study, we have examined the effects of these structural factors on the O(2) equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O(2) affinity and increasing catalytic activity along with the increase in the distal His N(ε)-heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O(2) affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O(2) affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O(2) carrier.
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Affiliation(s)
- Shengfang Sun
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Masanori Sono
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.
| | - Chunxue Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Jing Du
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Lukasz Lebioda
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.
| | - John H Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States; School of Medicine, University of South Carolina, United States.
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30
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Sun J, Fang YH, Liu ZP. Electrocatalytic oxygen reduction kinetics on Fe-center of nitrogen-doped graphene. Phys Chem Chem Phys 2014; 16:13733-40. [DOI: 10.1039/c4cp00037d] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OOH dissociation is the key step in electrocatalytic oxygen reduction on Fe–N centers of graphite, as revealed from first principles.
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Affiliation(s)
- Jing Sun
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Key Laboratory of Computational Physical Science (Ministry of Education)
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Ya-Hui Fang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Key Laboratory of Computational Physical Science (Ministry of Education)
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Zhi-Pan Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Key Laboratory of Computational Physical Science (Ministry of Education)
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
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31
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Nishimura R, Shibata T, Ishigami I, Ogura T, Tai H, Nagao S, Matsuo T, Hirota S, Shoji O, Watanabe Y, Imai K, Neya S, Suzuki A, Yamamoto Y. Electronic Control of Discrimination between O2 and CO in Myoglobin Lacking the Distal Histidine Residue. Inorg Chem 2013; 53:1091-9. [DOI: 10.1021/ic402625s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate
School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate
School of Life Science, University of Hyogo, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hulin Tai
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience, Faculty
of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate
School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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32
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Shi R, Li W, Liu G, Tang Y. Catalytic Mechanism of Cytochrome P450 2D6 for 4-Hydroxylation of Aripiprazole: A QM/MM Study. CHINESE J CHEM 2013. [DOI: 10.1002/cjoc.201300427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Weinert EE, Phillips-Piro CM, Marletta MA. Porphyrin π-stacking in a heme protein scaffold tunes gas ligand affinity. J Inorg Biochem 2013; 127:7-12. [PMID: 23831583 DOI: 10.1016/j.jinorgbio.2013.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
The role of π-stacking in controlling redox and ligand binding properties of porphyrins has been of interest for many years. The recent discovery of H-NOX domains has provided a model system to investigate the role of porphyrin π-stacking within a heme protein scaffold. Removal of a phenylalanine-porphyrin π-stack dramatically increased O2, NO, and CO affinities and caused changes in redox potential (~40mV) without any structural changes. These results suggest that small changes in redox potential affect ligand affinity and that π-stacking may provide a novel route to engineer heme protein properties for new functions.
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Affiliation(s)
- Emily E Weinert
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
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34
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Petruk AA, Vergara A, Estrin D, Merlino A. Molecular basis of the NO trans influence in quaternary T-state human hemoglobin: A computational study. FEBS Lett 2013; 587:2393-8. [DOI: 10.1016/j.febslet.2013.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 11/29/2022]
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35
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Banerjee R, Meier KK, Münck E, Lipscomb JD. Intermediate P* from soluble methane monooxygenase contains a diferrous cluster. Biochemistry 2013; 52:4331-42. [PMID: 23718184 DOI: 10.1021/bi400182y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the Fe(II)Fe(II) state (H(red)). O₂ binds rapidly at a site away from the cluster to form the Fe(II)Fe(II) intermediate O, which converts to an Fe(III)Fe(III)-peroxo intermediate P and finally to the Fe(IV)Fe(IV) intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of H(red) and O is lost. This was interpreted as signaling oxidation of the cluster, but a low level of accumulation of P* prevented further characterization. In this study, three methods for directly detecting and trapping P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of H(red) and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze-quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the Fe(II)Fe(II) state. Thus, the loss of the g = 16 EPR signal results from a change in the electronic structure of the Fe(II)Fe(II) center rather than oxidation. The similarity of the optical and Mössbauer spectra of H(red), O, and P* suggests that only subtle changes occur in the electronic and physical structure of the diiron cluster as P* forms. Nevertheless, the changes that do occur are necessary for O₂ to be activated for hydrocarbon oxidation.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Watanabe K, Kitagishi H, Kano K. Supramolecular Iron Porphyrin/Cyclodextrin Dimer Complex that Mimics the Functions of Hemoglobin and Methemoglobin. Angew Chem Int Ed Engl 2013; 52:6894-7. [DOI: 10.1002/anie.201302470] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/22/2013] [Indexed: 11/12/2022]
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Watanabe K, Kitagishi H, Kano K. Supramolecular Iron Porphyrin/Cyclodextrin Dimer Complex that Mimics the Functions of Hemoglobin and Methemoglobin. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Dickson CF, Rich AM, D'Avigdor WMH, Collins DAT, Lowry JA, Mollan TL, Khandros E, Olson JS, Weiss MJ, Mackay JP, Lay PA, Gell DA. α-Hemoglobin-stabilizing protein (AHSP) perturbs the proximal heme pocket of oxy-α-hemoglobin and weakens the iron-oxygen bond. J Biol Chem 2013; 288:19986-20001. [PMID: 23696640 DOI: 10.1074/jbc.m112.437509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
α-Hemoglobin (αHb)-stabilizing protein (AHSP) is a molecular chaperone that assists hemoglobin assembly. AHSP induces changes in αHb heme coordination, but how these changes are facilitated by interactions at the αHb·AHSP interface is not well understood. To address this question we have used NMR, x-ray absorption spectroscopy, and ligand binding measurements to probe αHb conformational changes induced by AHSP binding. NMR chemical shift analyses of free CO-αHb and CO-αHb·AHSP indicated that the seven helical elements of the native αHb structure are retained and that the heme Fe(II) remains coordinated to the proximal His-87 side chain. However, chemical shift differences revealed alterations of the F, G, and H helices and the heme pocket of CO-αHb bound to AHSP. Comparisons of iron-ligand geometry using extended x-ray absorption fine structure spectroscopy showed that AHSP binding induces a small 0.03 Å lengthening of the Fe-O2 bond, explaining previous reports that AHSP decreases αHb O2 affinity roughly 4-fold and promotes autooxidation due primarily to a 3-4-fold increase in the rate of O2 dissociation. Pro-30 mutations diminished NMR chemical shift changes in the proximal heme pocket, restored normal O2 dissociation rate and equilibrium constants, and reduced O2-αHb autooxidation rates. Thus, the contacts mediated by Pro-30 in wild-type AHSP promote αHb autooxidation by introducing strain into the proximal heme pocket. As a chaperone, AHSP facilitates rapid assembly of αHb into Hb when βHb is abundant but diverts αHb to a redox resistant holding state when βHb is limiting.
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Affiliation(s)
- Claire F Dickson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, TAS 7000, Australia
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Small ligand-globin interactions: reviewing lessons derived from computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1722-38. [PMID: 23470499 DOI: 10.1016/j.bbapap.2013.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 11/24/2022]
Abstract
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Nishimura R, Shibata T, Tai H, Ishigami I, Ogura T, Nagao S, Matsuo T, Hirota S, Imai K, Neya S, Suzuki A, Yamamoto Y. Relationship between the Electron Density of the Heme Fe Atom and the Vibrational Frequencies of the Fe-Bound Carbon Monoxide in Myoglobin. Inorg Chem 2013; 52:3349-55. [DOI: 10.1021/ic3028447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience,
Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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Boechi L, Arrar M, Martí MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. J Biol Chem 2013; 288:6754-62. [PMID: 23297402 DOI: 10.1074/jbc.m112.426056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis.
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Affiliation(s)
- Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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42
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Ferreiro DN, Boechi L, Estrin DA, Martí MA. The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin. J Inorg Biochem 2012; 119:75-84. [PMID: 23220591 DOI: 10.1016/j.jinorgbio.2012.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
Flavohemoglobins (FHbs) are members of the globin superfamily, widely distributed among prokaryotes and eukaryotes that have been shown to carry out nitric oxide dioxygenase (NOD) activity. In prokaryotes, such as Escherichia coli, NOD activity is a defence mechanism against the NO release by the macrophages of the hosts' immune system during infection. Because of that, FHbs have been studied thoroughly and several drugs have been developed in an effort to fight infectious processes. Nevertheless, the protein's structural determinants involved in the NOD activity are still poorly understood. In this context, the aim of the present work is to unravel the molecular basis of FHbs structural dynamics-to-function relationship using state of the art computer simulation tools. In an effort to fulfill this goal, we studied three key processes that determine NOD activity, namely i) ligand migration into the active site ii) stabilization of the coordinated oxygen and iii) intra-protein electron transfer (ET). Our results allowed us to determine key factors related to all three processes like the presence of a long hydrophobic tunnel for ligand migration, the presence of a water mediated hydrogen bond to stabilize the coordinated oxygen and therefore achieve a high affinity, and the best possible ET paths between the FAD and the heme, where water molecules play an important role. Taken together the presented results close an important gap in our understanding of the wide and diverse globin structural-functional relationships.
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Affiliation(s)
- Dardo N Ferreiro
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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43
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Shibata T, Matsumoto D, Nishimura R, Tai H, Matsuoka A, Nagao S, Matsuo T, Hirota S, Imai K, Neya S, Suzuki A, Yamamoto Y. Relationship between oxygen affinity and autoxidation of myoglobin. Inorg Chem 2012; 51:11955-60. [PMID: 23082875 DOI: 10.1021/ic301848t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies using myoglobins reconstituted with a variety of chemically modified heme cofactors revealed that the oxygen affinity and autoxidation reaction rate of the proteins are highly correlated to each other, both decreasing with decreasing the electron density of the heme iron atom. An Fe(3+)-O(2)(-)-like species has been expected for the Fe(2+)-O(2) bond in the protein, and the electron density of the heme iron atom influences the resonance process between the two forms. A shift of the resonance toward the Fe(2+)-O(2) form results in lowering of the O(2) affinity due to an increase in the O(2) dissociation rate. On the other hand, a shift of the resonance toward the Fe(3+)-O(2)(-)-like species results in acceleration of the autoxidation through increasing H(+) affinity of the bound ligand.
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Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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44
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Capece L, Lewis-Ballester A, Yeh SR, Estrin DA, Marti MA. Complete reaction mechanism of indoleamine 2,3-dioxygenase as revealed by QM/MM simulations. J Phys Chem B 2012; 116:1401-13. [PMID: 22196056 PMCID: PMC3304497 DOI: 10.1021/jp2082825] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indoleamine 2,3-dioxygenase (IDO) and tryptophan dioxygenase (TDO) are two heme proteins that catalyze the oxidation reaction of tryptophan (Trp) to N-formylkynurenine (NFK). Human IDO (hIDO) has recently been recognized as a potent anticancer drug target, a fact that triggered intense research on the reaction and inhibition mechanisms of hIDO. Our recent studies revealed that the dioxygenase reaction catalyzed by hIDO and TDO is initiated by addition of the ferric iron-bound superoxide to the C(2)═C(3) bond of Trp to form a ferryl and Trp-epoxide intermediate, via a 2-indolenylperoxo radical transition state. The data demonstrate that the two atoms of dioxygen are inserted into the substrate in a stepwise fashion, challenging the paradigm of heme-based dioxygenase chemistry. In the current study, we used QM/MM methods to decipher the mechanism by which the second ferryl oxygen is inserted into the Trp-epoxide to form the NFK product in hIDO. Our results show that the most energetically favored pathway involves proton transfer from Trp-NH(3)(+) to the epoxide oxygen, triggering epoxide ring opening and a concerted nucleophilic attack of the ferryl oxygen to the C(2) of Trp that leads to a metastable reaction intermediate. This intermediate subsequently converts to NFK, following C(2)-C(3) bond cleavage and the associated back proton transfer from the oxygen to the amino group of Trp. A comparative study with Xantomonas campestris TDO (xcTDO) indicates that the reaction follows a similar pathway, although subtle differences distinguishing the two enzyme reactions are evident. The results underscore the importance of the NH(3)(+) group of Trp in the two-step ferryl-based mechanism of hIDO and xcTDO, by acting as an acid catalyst to facilitate the epoxide ring-opening reaction and ferryl oxygen addition to the indole ring.
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Affiliation(s)
- Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461 USA
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461 USA
| | - Dario A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET
| | - Marcelo A. Marti
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina
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45
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Jorge SEDC, Petruk AA, Kimura EM, Oliveira DM, Caire L, Suemasu CN, Silveira PAA, Albuquerque DM, Costa FF, Skaf MS, Martínez L, Sonati MDF. Hb S-São Paulo: a new sickling hemoglobin with stable polymers and decreased oxygen affinity. Arch Biochem Biophys 2012; 519:23-31. [PMID: 22244832 DOI: 10.1016/j.abb.2012.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 12/22/2011] [Accepted: 01/01/2012] [Indexed: 01/19/2023]
Abstract
Hb S-São Paulo (SP) [HBB:c.20A>T p.Glu6Val; c.196A>G p.Lys65Glu] is a new double-mutant hemoglobin that was found in heterozygosis in an 18-month-old Brazilian male with moderate anemia. It behaves like Hb S in acid electrophoresis, isoelectric focusing and solubility testing but shows different behavior in alkaline electrophoresis, cation-exchange HPLC and RP-HPLC. The variant is slightly unstable, showed reduced oxygen affinity and also appeared to form polymers more stable than the Hb S. Molecular dynamics simulation suggests that the polymerization is favored by interfacial electrostatic interactions. This provides a plausible explanation for some of the reported experimental observations.
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Affiliation(s)
- Susan E D C Jorge
- Department of Clinical Pathology, School of Medical Sciences, State University of Campinas, Campinas, State of São Paulo, Brazil
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46
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Kano K, Chimoto S, Tamaki M, Itoh Y, Kitagishi H. Supramolecular dioxygen receptors composed of an anionic water-soluble porphinatoiron(ii) and cyclodextrin dimers. Dalton Trans 2012; 41:453-61. [DOI: 10.1039/c1dt11596k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Nagatomo S, Hamada H, Yoshikawa H. Elongation of the Fe–His Bond in the α Subunit Induced by Binding of the Allosteric Effector Bezafibrate to Hemoglobins. J Phys Chem B 2011; 115:12971-7. [DOI: 10.1021/jp205010m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiromi Hamada
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroyuki Yoshikawa
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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Li J, Peng Q, Barabanschikov A, Pavlik JW, Alp EE, Sturhahn W, Zhao J, Schulz CE, Sage JT, Scheidt WR. New perspectives on iron-ligand vibrations of oxyheme complexes. Chemistry 2011; 17:11178-85. [PMID: 21922552 PMCID: PMC3234299 DOI: 10.1002/chem.201101352] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Indexed: 11/12/2022]
Abstract
We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations.
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Affiliation(s)
- Jianfeng Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
| | - Qian Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
| | - Alexander Barabanschikov
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115 (USA)
| | - Jeffrey W. Pavlik
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
| | - E. Ercan Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (USA)
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (USA)
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (USA)
| | - Charles E. Schulz
- Department of Physics, Knox College, Galesburg, Illinois 61401 (USA)
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115 (USA)
| | - W. Robert Scheidt
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (USA), Fax (574) 631-6652
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A protective protein matrix improves the discrimination of nitroxyl from nitric oxide by MnIII protoporphyrinate IX in aerobic media. J Inorg Biochem 2011; 105:1044-9. [DOI: 10.1016/j.jinorgbio.2011.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 04/25/2011] [Accepted: 05/02/2011] [Indexed: 11/20/2022]
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50
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Weinert EE, Phillips-Piro CM, Tran R, Mathies RA, Marletta MA. Controlling conformational flexibility of an O₂-binding H-NOX domain. Biochemistry 2011; 50:6832-40. [PMID: 21721586 DOI: 10.1021/bi200788x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heme Nitric oxide/OXygen binding (H-NOX) domains have provided a novel scaffold to probe ligand affinity in hemoproteins. Mutation of isoleucine 5, a conserved residue located in the heme-binding pocket of the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX), was carried out to examine changes in oxygen (O(2))-binding properties. A series of I5 mutants (I5F, I5F/I75F, I5F/L144F, I5F/I75F/L144F) were investigated to probe the role of steric bulk within the heme pocket. The mutations significantly increased O(2) association rates (1.5-2.5-fold) and dissociation rates (8-190-fold) as compared to wild-type Tt H-NOX. Structural changes that accompanied the I5F mutation were characterized using X-ray crystallography and resonance Raman spectroscopy. A 1.67 Å crystal structure of the I5F mutant indicated that introducing a phenylalanine at position 5 resulted in a significant shift of the N-terminal domain of the protein, causing an opening of the heme pocket. This movement also resulted in an increased amount of flexibility at the N-terminus and the loop covering the N-terminal helix as indicated by the two conformations of the first six N-terminal amino acids, high B-factors in this region of the protein, and partially discontinuous electron density. In addition, introduction of a phenylalanine at position 5 resulted in increased flexibility of the heme within the pocket and weakened hydrogen bonding to the bound O(2) as measured by resonance Raman spectroscopy. This study provides insight into the critical role of I5 in controlling conformational flexibility and ligand affinity in H-NOX proteins.
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Affiliation(s)
- Emily E Weinert
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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