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De Simone G, di Masi A, Pasquadibisceglie A, Coletta A, Sebastiani F, Smulevich G, Coletta M, Ascenzi P. Nitrobindin versus myoglobin: A comparative structural and functional study. J Inorg Biochem 2024; 250:112387. [PMID: 37914583 DOI: 10.1016/j.jinorgbio.2023.112387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 11/03/2023]
Abstract
Most hemoproteins display an all-α-helical fold, showing the classical three on three (3/3) globin structural arrangement characterized by seven or eight α-helical segments that form a sandwich around the heme. Over the last decade, a completely distinct class of heme-proteins called nitrobindins (Nbs), which display an all-β-barrel fold, has been identified and characterized from both structural and functional perspectives. Nbs are ten-stranded anti-parallel all-β-barrel heme-proteins found across the evolutionary ladder, from bacteria to Homo sapiens. Myoglobin (Mb), commonly regarded as the prototype of monomeric all-α-helical globins, is involved along with the oligomeric hemoglobin (Hb) in diatomic gas transport, storage, and sensing, as well as in the detoxification of reactive nitrogen and oxygen species. On the other hand, the function(s) of Nbs is still obscure, even though it has been postulated that they might participate to O2/NO signaling and metabolism. This function might be of the utmost importance in poorly oxygenated tissues, such as the eye's retina, where a delicate balance between oxygenation and blood flow (regulated by NO) is crucial. Dysfunction in this balance is associated with several pathological conditions, such as glaucoma and diabetic retinopathy. Here a detailed comparison of the structural, spectroscopic, and functional properties of Mb and Nbs is reported to shed light on the similarities and differences between all-α-helical and all-β-barrel heme-proteins.
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Affiliation(s)
| | | | | | | | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy.
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2
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Messias A, Pasquadibisceglie A, Alonso de Armiño D, De Simone G, Polticelli F, Coletta M, Ascenzi P, Estrin DA. Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation. J Inorg Biochem 2023; 248:112336. [PMID: 37572543 DOI: 10.1016/j.jinorgbio.2023.112336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/28/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Nitrobindins (Nbs) represent an evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom, coordinated by a proximal His residue. Interestingly, even if the distal side is exposed to the solvent, the value of the second order rate constants for ligand binding to the ferrous derivative is almost one order of magnitude lower than those reported for myoglobins (Mbs). Noteworthy, nitric oxide binding to the sixth coordination position of the heme-Fe(II)-atom causes the cleavage or the severe weakening of the proximal His-Fe(II) bond. Here, we provide a computer simulation investigation to shed light on the molecular basis of ligand binding kinetics, by dissecting the ligand binding process into the ligand migration and the bond formation steps. Classical molecular dynamics simulations were performed employing a steered molecular dynamics approach and the Jarzinski equality to obtain ligand migration free energy profiles. The formation of the heme-Fe(II)-NO bond took into consideration the iron atom displacement from the heme plane. The ligand migration is almost unhindered, and the low rate constant for NO binding is due to the large displacement of the Fe(II) atom with respect to the heme plane responsible for the barrier for the Fe(II)-NO bond formation. In addition, we investigated the weakening and breaking of the proximal His-Fe(II) bond, observed experimentally upon NO binding, by means of a combination of classical molecular dynamics simulations and quantum-classical (QM-MM) optimizations. In both human and M. tuberculosis Nbs, a stable alternative conformation of the proximal His residue interacting with a network of water molecules was observed.
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Affiliation(s)
- Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | | | - Diego Alonso de Armiño
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Roma, Italy
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Roma, Italy
| | | | - Paolo Ascenzi
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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3
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Shalom B, Salaymeh Y, Risling M, Katzav S. Unraveling the Oncogenic Potential of VAV1 in Human Cancer: Lessons from Mouse Models. Cells 2023; 12:cells12091276. [PMID: 37174676 PMCID: PMC10177506 DOI: 10.3390/cells12091276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
VAV1 is a hematopoietic signal transducer that possesses a GDP/GTP nucleotide exchange factor (GEF) that is tightly regulated by tyrosine phosphorylation, along with adapter protein domains, such as SH2 and SH3. Research on VAV1 has advanced over the years since its discovery as an in vitro activated oncogene in an NIH3T3 screen for oncogenes. Although the oncogenic form of VAV1 first identified in the screen has not been detected in human clinical tumors, its wild-type and mutant forms have been implicated in mammalian malignancies of various tissue origins, as well as those of the hematopoietic system. This review article addresses the activity of human VAV1 as an overexpressed or mutated gene and also describes the differences in the distribution of VAV1 mutations in the hematopoietic system and in other tissues. The knowledge accumulated thus far from GEMMs expressing VAV1 is described, with the conclusion that GEMMs of both wild-type VAV1 and mutant VAV1 do not form tumors, yet these will be generated when additional molecular insults, such as loss of p53 or KRAS mutation, occur.
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Affiliation(s)
- Batel Shalom
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Yaser Salaymeh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Matan Risling
- Department of Military Medicine and "Tzameret", Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
- Medical Corps, Israel Defense Forces, Tel-Hashomer 02149, Israel
| | - Shulamit Katzav
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
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Turilli-Ghisolfi ES, Lualdi M, Fasano M. Ligand-Based Regulation of Dynamics and Reactivity of Hemoproteins. Biomolecules 2023; 13:683. [PMID: 37189430 PMCID: PMC10135655 DOI: 10.3390/biom13040683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
Hemoproteins include several heme-binding proteins with distinct structure and function. The presence of the heme group confers specific reactivity and spectroscopic properties to hemoproteins. In this review, we provide an overview of five families of hemoproteins in terms of dynamics and reactivity. First, we describe how ligands modulate cooperativity and reactivity in globins, such as myoglobin and hemoglobin. Second, we move on to another family of hemoproteins devoted to electron transport, such as cytochromes. Later, we consider heme-based reactivity in hemopexin, the main heme-scavenging protein. Then, we focus on heme-albumin, a chronosteric hemoprotein with peculiar spectroscopic and enzymatic properties. Eventually, we analyze the reactivity and dynamics of the most recently discovered family of hemoproteins, i.e., nitrobindins.
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Affiliation(s)
| | | | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, 22100 Como, Italy
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5
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De Simone G, di Masi A, Tundo GR, Coletta M, Ascenzi P. Nitrite Reductase Activity of Ferrous Nitrobindins: A Comparative Study. Int J Mol Sci 2023; 24:ijms24076553. [PMID: 37047528 PMCID: PMC10094804 DOI: 10.3390/ijms24076553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Nitrobindins (Nbs) are all-β-barrel heme proteins spanning from bacteria to Homo sapiens. They inactivate reactive nitrogen species by sequestering NO, converting NO to HNO2, and promoting peroxynitrite isomerization to NO3−. Here, the nitrite reductase activity of Nb(II) from Mycobacterium tuberculosis (Mt-Nb(II)), Arabidopsis thaliana (At-Nb(II)), Danio rerio (Dr-Nb(II)), and Homo sapiens (Hs-Nb(II)) is reported. This activity is crucial for the in vivo production of NO, and thus for the regulation of blood pressure, being of the utmost importance for the blood supply to poorly oxygenated tissues, such as the eye retina. At pH 7.3 and 20.0 °C, the values of the second-order rate constants (i.e., kon) for the reduction of NO2− to NO and the concomitant formation of nitrosylated Mt-Nb(II), At-Nb(II), Dr-Nb(II), and Hs-Nb(II) (Nb(II)-NO) were 7.6 M−1 s−1, 9.3 M−1 s−1, 1.4 × 101 M−1 s−1, and 5.8 M−1 s−1, respectively. The values of kon increased linearly with decreasing pH, thus indicating that the NO2−-based conversion of Nb(II) to Nb(II)-NO requires the involvement of one proton. These results represent the first evidence for the NO2 reductase activity of Nbs(II), strongly supporting the view that Nbs are involved in NO metabolism. Interestingly, the nitrite reductase reactivity of all-β-barrel Nbs and of all-α-helical globins (e.g., myoglobin) was very similar despite the very different three-dimensional fold; however, differences between all-α-helical globins and all-β-barrel Nbs suggest that nitrite reductase activity appears to be controlled by distal steric barriers, even though a more complex regulatory mechanism can be also envisaged.
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Affiliation(s)
| | | | - Grazia R. Tundo
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, 00133 Roma, Italy
| | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy
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6
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Nitrosylation of ferric zebrafish nitrobindin: A spectroscopic, kinetic, and thermodynamic study. J Inorg Biochem 2022; 237:111996. [PMID: 36150290 DOI: 10.1016/j.jinorgbio.2022.111996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/30/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023]
Abstract
Nitrobindins (Nbs) are all-β-barrel heme-proteins present in all the living kingdoms. Nbs inactivate reactive nitrogen species by sequestering NO, converting NO to HNO2, and isomerizing peroxynitrite to NO3- and NO2-. Here, the spectroscopic characterization of ferric Danio rerio Nb (Dr-Nb(III)) and NO scavenging through the reductive nitrosylation of the metal center are reported, both processes being relevant for the regulation of blood flow in fishes through poorly oxygenated tissues, such as retina. Both UV-Vis and resonance Raman spectroscopies indicate that Dr-Nb(III) is a mixture of a six-coordinated aquo- and a five-coordinated species, whose relative abundancies depend on pH. At pH ≤ 7.0, Dr-Nb(III) binds reversibly NO, whereas at pH ≥ 7.8 NO induces the conversion of Dr-Nb(III) to Dr-Nb(II)-NO. The conversion of Dr-Nb(III) to Dr-Nb(II)-NO is a monophasic process, suggesting that the formation of the transient Dr-Nb(III)-NO species is lost in the mixing time of the rapid-mixing stopped-flow apparatus (∼ 1.5 ms). The pseudo-first-order rate constant for the reductive nitrosylation of Dr-Nb(III) is not linearly dependent on the NO concentration but tends to level off. Values of the rate-limiting constant (i.e., klim) increase linearly with the OH- concentration, indicating that the conversion of Dr-Nb(III) to Dr-Nb(II)-NO is limited by the OH--based catalysis. From the dependence of klim on [OH-], the value of the second-order rate constant kOH- was obtained (5.2 × 103 M-1 s-1). Reductive nitrosylation of Dr-Nb(III) leads to the inactivation of two NO molecules: one being converted to HNO2, and the other being tightly bound to the heme-Fe(II) atom.
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7
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De Simone G, Fattibene P, Sebastiani F, Smulevich G, Coletta M, Ascenzi P. Dissociation of the proximal His-Fe bond upon NO binding to ferrous zebrafish nitrobindin. J Inorg Biochem 2022; 236:111962. [PMID: 36075159 DOI: 10.1016/j.jinorgbio.2022.111962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Nitrobindins (Nbs) are all-β-barrel heme-proteins present in prokaryotes and eukaryotes. Although the physiological role(s) of Nbs are still unclear, it has been postulated that they are involved in the NO/O2 metabolism, which is particularly relevant in fishes for the oxygen supply. Here, the reactivity of ferrous Danio rerio Nb (Dr-Nb(II)) towards NO has been investigated from the spectroscopic and kinetic viewpoints and compared with those of Mycobacterium tuberculosis Nb, Arabidopsis thaliana Nb, Homo sapiens Nb, and Equus ferus caballus myoglobin. Between pH 5.5 and 9.1 at 22.0 °C, Dr-Nb(II) nitrosylation is a monophasic process; values of the second-order rate constant for Dr-Nb(II) nitrosylation and of the first-order rate constant for Dr-Nb(II)-NO denitrosylation are pH-independent ranging between 1.6 × 106 M-1 s-1 and 2.3 × 106 M-1 s-1 and between 5.3 × 10-2 s-1 and 8.2 × 10-2 s-1, respectively. Interestingly, both UV-Vis and EPR spectroscopies indicate that the heme-Fe(II) atom of Dr-Nb(II)-NO is five-coordinated. Kinetics of Dr-Nb(II) nitrosylation may reflect the ligand accessibility to the metal center, which is likely impaired by the crowded network of water molecules which shields the heme pocket from the bulk solvent. On the other hand, kinetics of Dr-Nb(II)-NO denitrosylation may reflect an easy pathway for the ligand escape into the outer solvent.
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Affiliation(s)
| | - Paola Fattibene
- Servizio Grandi Strumentazioni e Core Facilities, Istituto Superiore di Sanità, Roma, Italy
| | | | | | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy.
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De Simone G, Coletta A, di Masi A, Coletta M, Ascenzi P. The Balancing of Peroxynitrite Detoxification between Ferric Heme-Proteins and CO2: The Case of Zebrafish Nitrobindin. Antioxidants (Basel) 2022; 11:antiox11101932. [PMID: 36290653 PMCID: PMC9599043 DOI: 10.3390/antiox11101932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrobindins (Nbs) are all-β-barrel heme proteins and are present in prokaryotes and eukaryotes. Although their function(s) is still obscure, Nbs trap NO and inactivate peroxynitrite. Here, the kinetics of peroxynitrite scavenging by ferric Danio rerio Nb (Dr-Nb(III)) in the absence and presence of CO2 is reported. The Dr-Nb(III)-catalyzed scavenging of peroxynitrite is facilitated by a low pH, indicating that the heme protein interacts preferentially with peroxynitrous acid, leading to the formation of nitrate (~91%) and nitrite (~9%). The physiological levels of CO2 dramatically facilitate the spontaneous decay of peroxynitrite, overwhelming the scavenging activity of Dr-Nb(III). The effect of Dr-Nb(III) on the peroxynitrite-induced nitration of L-tyrosine was also investigated. Dr-Nb(III) inhibits the peroxynitrite-mediated nitration of free L-tyrosine, while, in the presence of CO2, Dr-Nb(III) does not impair nitro-L-tyrosine formation. The comparative analysis of the present results with data reported in the literature indicates that, to act as efficient peroxynitrite scavengers in vivo, i.e., in the presence of physiological levels of CO2, the ferric heme protein concentration must be higher than 10−4 M. Thus, only the circulating ferric hemoglobin levels appear to be high enough to efficiently compete with CO2/HCO3− in peroxynitrite inactivation. The present results are of the utmost importance for tissues, like the eye retina in fish, where blood circulation is critical for adaptation to diving conditions.
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Affiliation(s)
| | - Andrea Coletta
- Dipartimento di Scienze, Università Roma Tre, 00146 Roma, Italy
| | | | - Massimo Coletta
- IRCCS Fondazione Bietti, 00198 Roma, Italy
- Correspondence: (M.C.); (P.A.)
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, 00146 Roma, Italy
- Correspondence: (M.C.); (P.A.)
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9
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Hydroxylamine-induced oxidation of ferrous nitrobindins. J Biol Inorg Chem 2022; 27:443-453. [PMID: 35543759 DOI: 10.1007/s00775-022-01940-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/21/2022] [Indexed: 12/19/2022]
Abstract
Hemoglobin and myoglobin are generally taken as molecular models of all-α-helical heme-proteins. On the other hand, nitrophorins and nitrobindins (Nb), which are arranged in 8 and 10 β-strands, respectively, represent the molecular models of all-β-barrel heme-proteins. Here, kinetics of the hydroxylamine- (HA-) mediated oxidation of ferrous Mycobacterium tuberculosis, Arabidopsis thaliana, and Homo sapiens nitrobindins (Mt-Nb(II), At-Nb(II), and Hs-Nb(II), respectively), at pH 7.0 and 20.0 °C, are reported. Of note, HA displays antibacterial properties and is a good candidate for the treatment and/or prevention of reactive nitrogen species- (RNS-) linked aging-related pathologies, such as macular degeneration. Under anaerobic conditions, mixing the Mt-Nb(II), At-Nb(II), and Hs-Nb(II) solutions with the HA solutions brings about absorbance spectral changes reflecting the formation of the ferric derivative (i.e., Mt-Nb(III), At-Nb(III), and Hs-Nb(III), respectively). Values of the second order rate constant for the HA-mediated oxidation of Mt-Nb(II), At-Nb(II), and Hs-Nb(II) are 1.1 × 104 M-1 s-1, 6.5 × 104 M-1 s-1, and 2.2 × 104 M-1 s-1, respectively. Moreover, the HA:Nb(II) stoichiometry is 1:2 as reported for ferrous deoxygenated and carbonylated all-α-helical heme-proteins. A comparative look of the HA reduction kinetics by several ferrous heme-proteins suggests that an important role might be played by residues (such as His or Tyr) in the proximity of the heme-Fe atom either coordinating it or not. In this respect, Nbs seem to exploit somewhat different structural aspects, indicating that redox mechanisms for the heme-Fe(II)-to-heme-Fe(III) conversion might differ between all-α-helical and all-β-barrel heme-proteins.
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De Simone G, di Masi A, Fattibene P, Ciaccio C, Platas-Iglesias C, Coletta M, Pesce A, Ascenzi P. Oxygen-mediated oxidation of ferrous nitrosylated nitrobindins. J Inorg Biochem 2021; 224:111579. [PMID: 34479003 DOI: 10.1016/j.jinorgbio.2021.111579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/23/2021] [Accepted: 08/10/2021] [Indexed: 01/25/2023]
Abstract
The O2-mediated oxidation of all-β-barrel ferrous nitrosylated nitrobindin from Arabidopsis thaliana (At-Nb(II)-NO), Mycobacterium tuberculosis (Mt-Nb(II)-NO), and Homo sapiens (Hs-Nb(II)-NO) to ferric derivative (At-Nb(III), Mt-Nb(III), and Hs-Nb(III), respectively) has been investigated at pH 7.0 and 20.0 °C. Unlike ferrous nitrosylated horse myoglobin, human serum heme-albumin and human hemoglobin, the process in Nb(II)-NO is mono-exponential and linearly dependent on the O2 concentration, displaying a bimolecular behavior, characterized by kon = (6.3 ± 0.8) × 103 M-1 s-1, (1.4 ± 0.2) × 103 M-1 s-1, and (3.9 ± 0.5) × 103 M-1 s-1 for At-Nb(II)-NO, Mt-Nb(II)-NO, and Hs-Nb(II)-NO, respectively. No intermediate is detected, indicating that the O2 reaction with Nb(II)-NO is the rate-limiting step and that the subsequent conversion of the heme-Fe(III)-N(O)OO- species (i.e., N-bound peroxynitrite to heme-Fe(III)) to heme-Fe(III) and NO3- is much faster. A similar mechanism can be invoked for ferrous nitrosylated human neuroglobin and rabbit hemopexin, in which the heme-Fe(III)-N(O)OO- species is formed as well, although the rate-limiting step seems represented by the reshaping of the six-coordinated heme-Fe(III) complex. Although At-Nb(II)-NO and Mt-Nb(II)-NO are partially (while Hs-Nb(II)-NO is almost completely) penta-coordinated, density functional theory (DFT) calculations rule out that the cleavage of the proximal heme-Fe-His bond in Nb(II)-NO is responsible for the more stable heme-Fe(III)-N(O)OO- species. Moreover, the oxidation of the penta-coordinated heme-Fe(II)-NO adduct does not depend on O2 binding at the proximal side of the metal center. These features may instead reflect the peculiarity of Nb folding and of the heme environment, with a reduced steric constraint for the formation of the heme-Fe(III)-N(O)OO- complex.
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Affiliation(s)
- Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy
| | - Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy
| | - Paola Fattibene
- Technical Scientific Service and Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133 Roma, Italy
| | - Carlos Platas-Iglesias
- Centro de Investigatiòns Cientìficas Avanzadas (CIA), Departamento de Quìmica, Facultade de Ciencias, Universidad da Coruña, 15071 A Coruña, Galicia, Spain
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133 Roma, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, 16100 Genova, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy; Interdepartmental Laboratory of Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy.
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11
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Markel U, Sauer DF, Wittwer M, Schiffels J, Cui H, Davari MD, Kröckert KW, Herres-Pawlis S, Okuda J, Schwaneberg U. Chemogenetic Evolution of a Peroxidase-like Artificial Metalloenzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Daniel F. Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Malte Wittwer
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Johannes Schiffels
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Konstantin W. Kröckert
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Sonja Herres-Pawlis
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI—Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
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12
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Kaur G, Vikal Y, Kaur L, Kalia A, Mittal A, Kaur D, Yadav I. Elucidating the morpho-physiological adaptations and molecular responses under long-term waterlogging stress in maize through gene expression analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110823. [PMID: 33568312 DOI: 10.1016/j.plantsci.2021.110823] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 05/25/2023]
Abstract
Waterlogging stress in maize is one of the emerging abiotic stresses in the current climate change scenario. To gain insights in transcriptional reprogramming during late hours of waterlogging stress under field conditions, we aimed to elucidate the transcriptional and anatomical changes in two contrasting maize inbreds viz. I110 (susceptible) and I172 (tolerant). Waterlogging stress reduced dry matter translocations from leaves and stems to ears, resulting in a lack of sink capacity and inadequate grain filling in I110, thus decreased the grain yield drastically. The development of aerenchyma cells within 48 h in I172 enabled hypoxia tolerance. The upregulation of alanine aminotransferase, ubiquitin activating enzyme E1, putative mitogen activated protein kinase and pyruvate kinase in I172 suggested that genes involved in protein degradation, signal transduction and carbon metabolism provided adaptive mechanisms during waterlogging. Overexpression of alcohol dehydrogenase, sucrose synthase, aspartate aminotransferase, NADP dependent malic enzyme and many miRNA targets in I110 indicated that more oxygen and energy consumption might have shortened plant survival during long-term waterlogging exposure. To the best of our knowledge, this is the first report of transcript profiling at late stage (24-96 h) of waterlogging stress under field conditions and provides new visions to understand the molecular basis of waterlogging tolerance in maize.
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Affiliation(s)
- Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Loveleen Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Anu Kalia
- Department of Nanoscience, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Dasmeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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13
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Mycobacterial and Human Ferrous Nitrobindins: Spectroscopic and Reactivity Properties. Int J Mol Sci 2021; 22:ijms22041674. [PMID: 33562340 PMCID: PMC7915275 DOI: 10.3390/ijms22041674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022] Open
Abstract
Structural and functional properties of ferrous Mycobacterium tuberculosis (Mt-Nb) and human (Hs-Nb) nitrobindins (Nbs) were investigated. At pH 7.0 and 25.0 °C, the unliganded Fe(II) species is penta-coordinated and unlike most other hemoproteins no pH-dependence of its coordination was detected over the pH range between 2.2 and 7.0. Further, despite a very open distal side of the heme pocket (as also indicated by the vanishingly small geminate recombination of CO for both Nbs), which exposes the heme pocket to the bulk solvent, their reactivity toward ligands, such as CO and NO, is significantly slower than in most hemoproteins, envisaging either a proximal barrier for ligand binding and/or crowding of H2O molecules in the distal side of the heme pocket which impairs ligand binding to the heme Fe-atom. On the other hand, liganded species display already at pH 7.0 and 25 °C a severe weakening (in the case of CO) and a cleavage (in the case of NO) of the proximal Fe-His bond, suggesting that the ligand-linked movement of the Fe(II) atom onto the heme plane brings about a marked lengthening of the proximal Fe-imidazole bond, eventually leading to its rupture. This structural evidence is accompanied by a marked enhancement of both ligands dissociation rate constants. As a whole, these data clearly indicate that structural–functional relationships in Nbs strongly differ from what observed in mammalian and truncated hemoproteins, suggesting that Nbs play a functional role clearly distinct from other eukaryotic and prokaryotic hemoproteins.
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14
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Sauer DF, Wittwer M, Markel U, Minges A, Spiertz M, Schiffels J, Davari MD, Groth G, Okuda J, Schwaneberg U. Chemogenetic engineering of nitrobindin toward an artificial epoxygenase. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00609f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemogenetic engineering turned the heme protein nitrobindin into an artificial epoxygenase: MnPPIX was introduced and subsequent protein engineering increased the activity in the epoxidation of styrene derivatives by overall 7-fold.
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Affiliation(s)
- Daniel F. Sauer
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Malte Wittwer
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Markel
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Alexander Minges
- Institute of Biochemical Plant Physiology
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Markus Spiertz
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | | | - Mehdi D. Davari
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Georg Groth
- Institute of Biochemical Plant Physiology
- Heinrich Heine University Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI – Leibniz Institute for Interactive Materials
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15
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NO Scavenging through Reductive Nitrosylation of Ferric Mycobacterium tuberculosis and Homo sapiens Nitrobindins. Int J Mol Sci 2020; 21:ijms21249395. [PMID: 33321752 PMCID: PMC7763097 DOI: 10.3390/ijms21249395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022] Open
Abstract
Ferric nitrobindins (Nbs) selectively bind NO and catalyze the conversion of peroxynitrite to nitrate. In this study, we show that NO scavenging occurs through the reductive nitrosylation of ferric Mycobacterium tuberculosis and Homo sapiens nitrobindins (Mt-Nb(III) and Hs-Nb(III), respectively). The conversion of Mt-Nb(III) and Hs-Nb(III) to Mt-Nb(II)-NO and Hs-Nb(II)-NO, respectively, is a monophasic process, suggesting that over the explored NO concentration range (between 2.5 × 10−5 and 1.0 × 10−3 M), NO binding is lost in the mixing time (i.e., NOkon ≥ 1.0 × 106 M−1 s−1). The pseudo-first-order rate constant for the reductive nitrosylation of Mt-Nb(III) and Hs-Nb(III) (i.e., k) is not linearly dependent on the NO concentration but tends to level off, with a rate-limiting step (i.e., klim) whose values increase linearly with [OH−]. This indicates that the conversion of Mt-Nb(III) and Hs-Nb(III) to Mt-Nb(II)-NO and Hs-Nb(II)-NO, respectively, is limited by the OH−-based catalysis. From the dependence of klim on [OH−], the values of the second-order rate constant kOH− for the reductive nitrosylation of Mt-Nb(III)-NO and Hs-Nb(III)-NO were obtained (4.9 (±0.5) × 103 M−1 s−1 and 6.9 (±0.8) × 103 M−1 s−1, respectively). This process leads to the inactivation of two NO molecules: one being converted to HNO2 and another being tightly bound to the ferrous heme-Fe(II) atom.
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16
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Bozhanova NG, Calcutt MW, Beavers WN, Brown BP, Skaar EP, Meiler J. Lipocalin Blc is a potential heme-binding protein. FEBS Lett 2020; 595:206-219. [PMID: 33210733 PMCID: PMC8177097 DOI: 10.1002/1873-3468.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022]
Abstract
Lipocalins are a superfamily of functionally diverse proteins defined by a well-conserved tertiary structure despite variation in sequence. Lipocalins bind and transport small hydrophobic molecules in organisms of all kingdoms. However, there is still uncertainty regarding the function of some members of the family, including bacterial lipocalin Blc from Escherichia coli. Here, we present evidence that lipocalin Blc may be involved in heme binding, trans-periplasmic transport, or heme storage. This conclusion is supported by a cocrystal structure, mass-spectrometric data, absorption titration, and in silico analysis. Binding of heme is observed at low micromolar range with one-to-one ligand-to-protein stoichiometry. However, the absence of classical coordination to the iron atom leaves the possibility that the primary ligand of Blc is another tetrapyrrole.
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Affiliation(s)
- Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin P Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Discovery, Medical School, Leipzig University, Germany
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17
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De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P. Mycobacterial and Human Nitrobindins: Structure and Function. Antioxid Redox Signal 2020; 33:229-246. [PMID: 32295384 DOI: 10.1089/ars.2019.7874] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aims: Nitrobindins (Nbs) are evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom. The physiological role(s) of Nbs is almost unknown. Here, the structural and functional properties of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) and ferric Homo sapiens Nb (Hs-Nb(III)) have been investigated and compared with those of ferric Arabidopsis thaliana Nb (At-Nb(III), Rhodnius prolixus nitrophorins (Rp-NP(III)s), and mammalian myoglobins. Results: Data here reported demonstrate that Mt-Nb(III), At-Nb(III), and Hs-Nb(III) share with Rp-NP(III)s the capability to bind selectively nitric oxide, but display a very low reactivity, if any, toward histamine. Data obtained overexpressing Hs-Nb in human embryonic kidney 293 cells indicate that Hs-Nb localizes mainly in the cytoplasm and partially in the nucleus, thanks to a nuclear localization sequence encompassing residues Glu124-Leu154. Human Hs-Nb corresponds to the C-terminal domain of the human nuclear protein THAP4 suggesting that Nb may act as a sensor possibly modulating the THAP4 transcriptional activity residing in the N-terminal region. Finally, we provide strong evidence that both Mt-Nb(III) and Hs-Nb(III) are able to scavenge peroxynitrite and to protect free l-tyrosine against peroxynitrite-mediated nitration. Innovation: Data here reported suggest an evolutionarily conserved function of Nbs related to their role as nitric oxide sensors and components of antioxidant systems. Conclusion: Human THAP4 may act as a sensing protein that couples the heme-based Nb(III) reactivity with gene transcription. Mt-Nb(III) seems to be part of the pool of proteins required to scavenge reactive nitrogen and oxygen species produced by the host during the immunity response.
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Affiliation(s)
| | | | | | - Fabio Polticelli
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy.,Istituto Nazionale di Fisica Nucleare, Sezione di Roma Tre, Roma, Italy
| | | | - Marco Nardini
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy.,Centro di Ricerche Pediatriche R.E. Invernizzi, Università di Milano, Milano, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
| | - Emily Samuela Turilli
- Dipartimento di Scienza ed Alta Tecnologia, Università dell'Insubria, Busto Arsizio, Italy
| | - Mauro Fasano
- Dipartimento di Scienza ed Alta Tecnologia, Università dell'Insubria, Busto Arsizio, Italy
| | - Lorenzo Tognaccini
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
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18
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Foglia NO, Bari SE, Estrin DA. In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins. Inorg Chem 2020; 59:3631-3641. [DOI: 10.1021/acs.inorgchem.9b03198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nicolás O. Foglia
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica, Buenos Aires, Argentina
| | - Sara E. Bari
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - Darío A. Estrin
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica, Buenos Aires, Argentina
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19
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Nazemi Z, Prasad P, Chakraborty S. Kinetics of Oxygen Reduction by a Beta Barrel Heme Protein on Hyrid Bioelectrodes. ChemElectroChem 2020. [DOI: 10.1002/celc.201901945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zahra Nazemi
- Department of Chemistry and BiochemistryUniversity of Mississippi, University Mississippi MS 38677 USA
| | - Pallavi Prasad
- Department of Chemistry and BiochemistryUniversity of Mississippi, University Mississippi MS 38677 USA
| | - Saumen Chakraborty
- Department of Chemistry and BiochemistryUniversity of Mississippi, University Mississippi MS 38677 USA
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20
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Sauer DF, Schiffels J, Hayashi T, Schwaneberg U, Okuda J. Olefin metathesis catalysts embedded in β-barrel proteins: creating artificial metalloproteins for olefin metathesis. Beilstein J Org Chem 2018; 14:2861-2871. [PMID: 30546470 PMCID: PMC6278764 DOI: 10.3762/bjoc.14.265] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
This review summarizes the recent progress of Grubbs-Hoveyda (GH) type olefin metathesis catalysts incorporated into the robust fold of β-barrel proteins. Anchoring strategies are discussed and challenges and opportunities in this emerging field are shown from simple small-molecule transformations over ring-opening metathesis polymerizations to in vivo olefin metathesis.
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Affiliation(s)
- Daniel F Sauer
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
| | - Johannes Schiffels
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany
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21
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De Simone G, di Masi A, Polticelli F, Ascenzi P. Human nitrobindin: the first example of an all-β-barrel ferric heme-protein that catalyzes peroxynitrite detoxification. FEBS Open Bio 2018; 8:2002-2010. [PMID: 30524950 PMCID: PMC6275384 DOI: 10.1002/2211-5463.12534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/29/2018] [Accepted: 09/26/2018] [Indexed: 11/12/2022] Open
Abstract
Nitrobindins (Nbs), constituting a heme‐protein family spanning from bacteria to Homo sapiens, display an all‐β‐barrel structural organization. Human Nb has been described as a domain of the nuclear protein named THAP4, whose physiological function is still unknown. We report the first evidence of the heme‐Fe(III)‐based detoxification of peroxynitrite by the all‐β‐barrel C‐terminal Nb‐like domain of THAP4. Ferric human Nb (Nb(III)) catalyzes the conversion of peroxynitrite to NO3− and impairs the nitration of free l‐tyrosine. The rate of human Nb(III)‐mediated scavenging of peroxynitrite is similar to those of all‐α‐helical horse heart and sperm whale myoglobin and human hemoglobin, generally taken as the prototypes of all‐α‐helical heme‐proteins. The heme‐Fe(III) reactivity of all‐β‐barrel human Nb(III) and all‐α‐helical prototypical heme‐proteins possibly reflects the out‐to‐in‐plane transition of the heme‐Fe(III)‐atom preceding peroxynitrite binding. Human Nb(III) not only catalyzes the detoxification of peroxynitrite but also binds NO, possibly representing a target of reactive nitrogen species.
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Affiliation(s)
| | | | - Fabio Polticelli
- Department of Sciences Roma Tre University Italy.,National Institute of Nuclear Physics Roma Tre Section Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy Roma Tre University Italy
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22
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Reductive nitrosylation of ferric microperoxidase-11. J Biol Inorg Chem 2018; 24:21-29. [PMID: 30390140 DOI: 10.1007/s00775-018-1623-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Microperoxidase-11 (MP11) is an undecapeptide derived from horse heart cytochrome c, which is considered as a heme-protein model. Here, the reductive nitrosylation of ferric MP11 (MP11(III)) under anaerobic conditions has been investigated between pH 7.4 and 9.2, at T = 20.0 °C. At pH ≤ 7.7, NO binds reversibly to MP11(III) leading to the formation of the MP11(III)-NO complex. However, between pH 8.2 and 9.2, the addition of NO to MP11(III) leads to the formation of ferrous nitrosylated MP11(II) (MP11(II)-NO). In fact, the transient MP11{FeNO}6 species is converted to ferrous deoxygenated MP11 (MP11(II)) by OH-- and H2O-based catalysis, which represents the rate-limiting step of the whole reaction. Then, MP11(II) binds NO very rapidly leading to MP11(II)-NO formation. Over the whole pH range explored, the apparent values of kon, koff, and K (= koff/kon) for MP11(III)(-NO) (de)nitrosylation are essentially pH independent, ranging between 5.8 × 105 M-1 s-1 and 1.6 × 106 M-1 s-1, between 1.9 s-1 and 3.7 s-1, and between 1.4 × 10-6 M and 4.6 × 10-6 M, respectively. Values of the apparent pseudo-first-order rate constant for the MP11{FeNO}6 conversion to MP11(II) (i.e., h) increase linearly with pH; the apparent values [Formula: see text] and [Formula: see text] are 7.2 × 102 M-1 s-1 and 2.5 × 10-4 s-1, respectively. Present data confirm that MP11 is a useful molecular model to highlight the role of the protein matrix on the heme-based reactivity.
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23
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Esmieu C, Raleiras P, Berggren G. From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production. SUSTAINABLE ENERGY & FUELS 2018; 2:724-750. [PMID: 31497651 PMCID: PMC6695573 DOI: 10.1039/c7se00582b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/31/2018] [Indexed: 06/09/2023]
Abstract
Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.
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Affiliation(s)
- C Esmieu
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - P Raleiras
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
| | - G Berggren
- Department of Chemistry , Ångström Laboratory , Uppsala University , Box 523 , SE-75120 Uppsala , Sweden .
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24
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De Simone G, Ascenzi P, di Masi A, Polticelli F. Nitrophorins and nitrobindins: structure and function. Biomol Concepts 2018; 8:105-118. [PMID: 28574374 DOI: 10.1515/bmc-2017-0013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/03/2017] [Indexed: 12/23/2022] Open
Abstract
Classical all α-helical globins are present in all living organisms and are ordered in three lineages: (i) flavohemoglobins and single domain globins, (ii) protoglobins and globin coupled sensors and (iii) truncated hemoglobins, displaying the 3/3 or the 2/2 all α-helical fold. However, over the last two decades, all β-barrel and mixed α-helical-β-barrel heme-proteins displaying heme-based functional properties (e.g. ligand binding, transport and sensing) closely similar to those of all α-helical globins have been reported. Monomeric nitrophorins (NPs) and α1-microglobulin (α1-m), belonging to the lipocalin superfamily and nitrobindins (Nbs) represent prototypical heme-proteins displaying the all β-barrel and mixed α-helical-β-barrel folds. NPs are confined to the Reduviidae and Cimicidae families of Heteroptera, whereas α1-m and Nbs constitute heme-protein families spanning bacteria to Homo sapiens. The structural organization and the reactivity of the stable ferric solvent-exposed heme-Fe atom suggest that NPs and Nbs are devoted to NO transport, storage and sensing, whereas Hs-α1-m participates in heme metabolism. Here, the structural and functional properties of NPs and Nbs are reviewed in parallel with those of sperm whale myoglobin, which is generally taken as the prototype of monomeric globins.
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25
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Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas. Proc Natl Acad Sci U S A 2017; 114:764-769. [PMID: 28062691 DOI: 10.1073/pnas.1608839114] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) are a heterogeneous group of non-Hodgkin lymphomas frequently associated with poor prognosis and for which genetic mechanisms of transformation remain incompletely understood. Using RNA sequencing and targeted sequencing, here we identify a recurrent in-frame deletion (VAV1 Δ778-786) generated by a focal deletion-driven alternative splicing mechanism as well as novel VAV1 gene fusions (VAV1-THAP4, VAV1-MYO1F, and VAV1-S100A7) in PTCL. Mechanistically these genetic lesions result in increased activation of VAV1 catalytic-dependent (MAPK, JNK) and non-catalytic-dependent (nuclear factor of activated T cells, NFAT) VAV1 effector pathways. These results support a driver oncogenic role for VAV1 signaling in the pathogenesis of PTCL.
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26
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De Simone G, Ascenzi P, Polticelli F. Nitrobindin: An Ubiquitous Family of All β-Barrel Heme-proteins. IUBMB Life 2016; 68:423-8. [PMID: 27080126 DOI: 10.1002/iub.1500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/21/2016] [Indexed: 11/10/2022]
Abstract
Rhodnius prolixus nitrophorins (Rp-NPs), Arabidopsis thaliana nitrobindin (At-Nb), and Homo sapiens THAP4 (Hs-THAP4) are the unique known proteins that use a β-barrel fold to bind ferric heme, which is devoted to NO transport and/or catalysis. The eight-stranded antiparallel β-barrel Rp-NPs, which represent the only heme-binding lipocalins, are devoted to deliver NO into the blood vessel of the host and to scavenge histamine during blood sucking. Regarding Nbs, crystallographic data suggest the ability of At-Nb and Hs-THAP4 to bind ferric heme; however, no data are available with respect to these functions in the natural host. Here, a bioinformatics investigation based on the amino acid sequences and three-dimensional structures of At-Nb and Hs-THAP4 suggests a conservation of the 10-stranded antiparallel β-barrel Nb structural module in all life kingdoms of the evolutionary ladder. In particular, amino acid residues involved in the heme recognition and in the structure stabilization of the Nb structural module are highly conserved (identity > 29%; homology > 83%). Moreover, molecular models of putative Nbs from different organisms match very well with each other and known three-dimensional structures of Nbs. Furthermore, phylogenetic tree reconstruction indicates that NPs and Nbs group in distinct clades. These data indicate that 10-stranded β-barrel Nbs constitute a new ubiquitous heme protein family spanning from bacteria to Homo sapiens. © 2016 IUBMB Life, 68(6):423-428, 2016.
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Affiliation(s)
- Giovanna De Simone
- Department of Sciences, Roma Tre University, Roma, Italy.,Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Roma, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Roma, Italy.,Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Roma, Italy
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, Roma, Italy.,National Institute of Nuclear Physics, Roma Tre Section, Roma Tre University, Roma, Italy
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Sauer DF, Gotzen S, Okuda J. Metatheases: artificial metalloproteins for olefin metathesis. Org Biomol Chem 2016; 14:9174-9183. [DOI: 10.1039/c6ob01475e] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent advance in the design of artificial metalloproteins for olefin metathesis is presented.
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Affiliation(s)
- D. F. Sauer
- Institute of Inorganic Chemistry
- RWTH Aachen University
- 52056 Aachen
- Germany
| | - S. Gotzen
- Institute of Inorganic Chemistry
- RWTH Aachen University
- 52056 Aachen
- Germany
| | - J. Okuda
- Institute of Inorganic Chemistry
- RWTH Aachen University
- 52056 Aachen
- Germany
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28
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Sauer DF, Himiyama T, Tachikawa K, Fukumoto K, Onoda A, Mizohata E, Inoue T, Bocola M, Schwaneberg U, Hayashi T, Okuda J. A Highly Active Biohybrid Catalyst for Olefin Metathesis in Water: Impact of a Hydrophobic Cavity in a β-Barrel Protein. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01792] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel F. Sauer
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Tomoki Himiyama
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Kengo Tachikawa
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Kazuki Fukumoto
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Akira Onoda
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Eiichi Mizohata
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Tsuyoshi Inoue
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Marco Bocola
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52056 Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 1, D-52056 Aachen, Germany
| | - Takashi Hayashi
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita 565-0871, Japan
| | - Jun Okuda
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
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Lakshmi B, Mishra M, Srinivasan N, Archunan G. Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily. PLoS One 2015; 10:e0135507. [PMID: 26263546 PMCID: PMC4532494 DOI: 10.1371/journal.pone.0135507] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/22/2015] [Indexed: 01/26/2023] Open
Abstract
Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.
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Affiliation(s)
- Balasubramanian Lakshmi
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, 620024, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Madhulika Mishra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Narayanaswamy Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
- * E-mail: (NS); (GA)
| | - Govindaraju Archunan
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, 620024, India
- * E-mail: (NS); (GA)
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30
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Onoda A, Kihara Y, Fukumoto K, Sano Y, Hayashi T. Photoinduced Hydrogen Evolution Catalyzed by a Synthetic Diiron Dithiolate Complex Embedded within a Protein Matrix. ACS Catal 2014. [DOI: 10.1021/cs500392e] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akira Onoda
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshihiko Kihara
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuki Fukumoto
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yohei Sano
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry,
Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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31
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Zhang C, Srivastava P, Ellis-Guardiola K, Lewis JC. Manganese terpyridine artificial metalloenzymes for benzylic oxygenation and olefin epoxidation. Tetrahedron 2014; 70:4245-4249. [PMID: 24904188 DOI: 10.1016/j.tet.2014.03.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
New catalysts for non-directed hydrocarbon functionalization have great potential in organic synthesis. We hypothesized that incorporating a Mn-terpyridine cofactor into a protein scaffold would lead to artificial metalloenzymes (ArMs) in which the selectivity of the Mn cofactor could be controlled by the protein scaffold. We designed and synthesized a maleimide-substituted Mn-terpyridine cofactor and demonstrated that this cofactor could be incorporated into two different scaffold proteins to generate the desired ArMs. The structure and reactivity of one of these ArMs was explored, and the broad oxygenation capability of the Mn-terpyridine catalyst was maintained, providing a robust platform for optimization of ArMs for selective hydrocarbon functionalization.
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Affiliation(s)
- Chen Zhang
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
| | - Poonam Srivastava
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
| | - Ken Ellis-Guardiola
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
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32
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Chandra G, Chater KF. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 2014; 38:345-79. [PMID: 24164321 PMCID: PMC4255298 DOI: 10.1111/1574-6976.12047] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022] Open
Abstract
To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.
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33
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Fukumoto K, Onoda A, Mizohata E, Bocola M, Inoue T, Schwaneberg U, Hayashi T. Rhodium-Complex-Linked Hybrid Biocatalyst: Stereo-Controlled Phenylacetylene Polymerization within an Engineered Protein Cavity. ChemCatChem 2014. [DOI: 10.1002/cctc.201301055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Lamont EA, Xu WW, Sreevatsan S. Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection. BMC Genomics 2013; 14:694. [PMID: 24112552 PMCID: PMC3832399 DOI: 10.1186/1471-2164-14-694] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 10/02/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The initial interaction between host cell and pathogen sets the stage for the ensuing infection and ultimately determine the course of disease. However, there is limited knowledge of the transcripts utilized by host and pathogen and how they may impact one another during this critical step. The purpose of this study was to create a host-Mycobacterium avium subsp. paratuberculosis (MAP) interactome for early infection in an epithelium-macrophage co-culture system using RNA-seq. RESULTS Establishment of the host-MAP interactome revealed a novel iron assimilation system for carboxymycobactin. Iron assimilation is linked to nitric oxide synthase-2 production by the host and subsequent nitric oxide buildup. Iron limitation as well as nitric oxide is a prompt for MAP to enter into an iron sequestration program. This new iron sequestration program provides an explanation for mycobactin independence in some MAP strains grown in vitro as well as during infection within the host cell. Utilization of such a pathway is likely to aid MAP establishment and long-term survival within the host. CONCLUSIONS The host-MAP interactome identified a number of metabolic, DNA repair and virulence genes worthy for consideration as novel drug targets as well as future pathogenesis studies. Reported interactome data may also be utilized to conduct focused, hypothesis-driven research. Co-culture of uninfected bovine epithelial cells (MAC-T) and primary bovine macrophages creates a tolerant genotype as demonstrated by downregulation of inflammatory pathways. This co-culture system may serve as a model to investigate other bovine enteric pathogens.
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Affiliation(s)
- Elise A Lamont
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
| | - Wayne W Xu
- Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - Srinand Sreevatsan
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
- Department of Veterinary Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
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35
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Onoda A, Fukumoto K, Arlt M, Bocola M, Schwaneberg U, Hayashi T. A rhodium complex-linked β-barrel protein as a hybrid biocatalyst for phenylacetylene polymerization. Chem Commun (Camb) 2013; 48:9756-8. [PMID: 22918399 DOI: 10.1039/c2cc35165j] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our group recently prepared a hybrid catalyst containing a rhodium complex, Rh(Cp)(cod), with a maleimide moiety at the peripheral position of the Cp ligand. This compound was then inserted into a β-barrel protein scaffold of a mutant of aponitrobindin (Q96C) via a covalent linkage. The hybrid protein is found to act as a polymerization catalyst and preferentially yields trans-poly(phenylacetylene) (PPA), although the rhodium complex without the protein scaffold normally produces cis PPA.
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Affiliation(s)
- Akira Onoda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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36
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Onoda A, Hayashi T. Complimenting a Metal Complex with Protein Environment toward a New Hybrid Biocatalyst. J SYN ORG CHEM JPN 2013. [DOI: 10.5059/yukigoseikyokaishi.71.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Koch I, Kreuchwig A, May P. Hierarchical representation of supersecondary structures using a graph-theoretical approach. Methods Mol Biol 2013; 932:7-33. [PMID: 22987344 DOI: 10.1007/978-1-62703-065-6_2] [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: 06/01/2023]
Abstract
The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for comparison and classification of protein structures. Here, we describe a graph-theoretical modeling approach of the protein supersecondary structure. The resulting linear notations are intuitive and can be used to find common substructures very fast and easily. We illustrate the necessary definitions by biological examples and discuss the representation of various supersecondary structure motifs.
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Affiliation(s)
- Ina Koch
- Molecular Bioinformatics Group, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
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38
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Lehnert N, Scheidt WR, Wolf MW. Structure and Bonding in Heme–Nitrosyl Complexes and Implications for Biology. NITROSYL COMPLEXES IN INORGANIC CHEMISTRY, BIOCHEMISTRY AND MEDICINE II 2013. [DOI: 10.1007/430_2013_92] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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39
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Nalepa AI, Taing JJ, Savitsky A, Knipp M. Preparation of cysteine-34-nitroxide spin labeled human α₁-microglobulin. Protein Expr Purif 2012. [PMID: 23201281 DOI: 10.1016/j.pep.2012.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
α(1)-Microglobulin (α(1)m) is a protein of yet unresolved function occurring in blood plasma and urine. It consists of a lipocaline type of fold with two cysteine residues forming a disulfide bridge and the third cysteine-34 remaining a free, somewhat reactive thiol. A number of investigations point to an interaction with heme and we have recently reported, that heme binding triggers the formation of a stable α(1)m trimer upon modification of cysteine-34 with 2-iodoacetamide, i.e., [α(1)m(heme)(2)](3) [J.F. Siebel, R.L. Kosinsky, B. Åkerström, M. Knipp, Insertion of heme b into the structure of the Cys34-carbamidomethylated human lipocalin α(1)-microglobulin-formation of a [(heme)(2)(α(1)-microglobulin)](3) complex, ChemBioChem 13 (2012) 879-887]. For further structural and functional investigations, an improved purification protocol for α(1)m was sought, in particular yielding an untagged amino acid sequence. The method reported herein improves the speed and the yield of the protein production even when an expression plasmid without tag was applied. Furthermore, for the purpose of future structural studies using electron paramagnetic resonance (EPR) techniques, in accordance to the modification with 2-iodoacetamide (α(1)m(AM)), the protein was modified with 3-(2-iodoacetamido)-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (3-(2-iodoacetamido)-PROXYL) yielding the nitroxide spin labeled α(1)m(N-O). The extinction coefficient of the protein was calibrated using magnetic circular dichroism (MCD) spectroscopy of tryptophan (ε(280nm)=40,625M(-1)cm(-1)). The parallel quantification by absorbance spectroscopy (protein) and cw-EPR spectroscopy (radical spin) determined the degree of spin labeling to 90%. Characterization of the protein by circular dichroism (CD) spectroscopy and matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) upon tryptic digestion further demonstrated the similar fold of α(1)m(AM) and α(1)m(N-O), but also established the modification of cystein-34 as well as the formation of the cysteine-72-cysteine-169 disulfide bond.
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Affiliation(s)
- Anna I Nalepa
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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40
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Siebel JF, Kosinsky RL, Åkerström B, Knipp M. Insertion of heme b into the structure of the Cys34-carbamidomethylated human lipocalin α(1)-microglobulin: formation of a [(heme)(2) (α(1)-Microglobulin)](3) complex. Chembiochem 2012; 13:879-87. [PMID: 22492620 DOI: 10.1002/cbic.201100808] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
α(1)-Microglobulin (α(1)m) is a 26 kDa plasma and tissue protein belonging to the lipocalin protein family. Previous investigations indicate that the protein interacts with heme and suggest that it has a function in heme metabolism. However, detailed characterizations of the α(1)m-heme interactions are lacking. Here, we report for the first time the preparation and analysis of a stable α(1)m-heme complex upon carbamidomethylation of the reactive Cys34 by using recombinantly expressed human α(1)m. Analytical size-exclusion chromatography coupled with a diode-array absorbance spectrophotometry demonstrates that at first an α(1)m-heme monomer is formed. Subsequently, a second heme triggers oligomerization that leads to trimerization. The resulting (α(1)m[heme](2))(3) complex was characterized by resonance Raman and EPR spectroscopy, which support the presence of two ferrihemes, thus indicating an unusual spin-state admixed ground state with S=(3)/(2), (5)/(2).
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Affiliation(s)
- Judith F Siebel
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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Hannibal L, Collins D, Brassard J, Chakravarti R, Vempati R, Dorlet P, Santolini J, Dawson JH, Stuehr DJ. Heme binding properties of glyceraldehyde-3-phosphate dehydrogenase. Biochemistry 2012; 51:8514-29. [PMID: 22957700 DOI: 10.1021/bi300863a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic enzyme that also functions in transcriptional regulation, oxidative stress, vesicular trafficking, and apoptosis. Because GAPDH is required for the insertion of cellular heme into inducible nitric oxide synthase [Chakravarti, R., et al. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 18004-18009], we extensively characterized the heme binding properties of GAPDH. Substoichiometric amounts of ferric heme bound to GAPDH (one heme per GAPDH tetramer) to form a low-spin complex with UV-visible maxima at 362, 418, and 537 nm and when reduced to ferrous gave maxima at 424, 527, and 559 nm. Ferric heme association and dissociation rate constants at 10 °C were as follows: k(on) = 17800 M(-1) s(-1), k(off1) = 7.0 × 10(-3) s(-1), and k(off2) = 3.3 × 10(-4) s(-1) (giving approximate affinities of 19-390 nM). Ferrous heme bound more poorly to GAPDH and dissociated with a k(off) of 4.2 × 10(-3) s(-1). Magnetic circular dichroism, resonance Raman, and electron paramagnetic resonance spectroscopic data on the ferric, ferrous, and ferrous-CO complexes of GAPDH showed that the heme is bis-ligated with His as the proximal ligand. The distal ligand in the ferric complex was not displaced by CN(-) or N(3)(-) but in the ferrous complex could be displaced by CO at a rate of 1.75 s(-1) (for >0.2 mM CO). Studies with heme analogues revealed selectivity toward the coordinating metal and porphyrin ring structure. The GAPDH-heme complex was isolated from bacteria induced to express rabbit GAPDH in the presence of δ-aminolevulinic acid. Our finding of heme binding to GAPDH expands the protein's potential roles. The strength, selectivity, reversibility, and redox sensitivity of heme binding to GAPDH are consistent with it performing heme sensing or heme chaperone-like functions in cells.
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Affiliation(s)
- Luciana Hannibal
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Bhuyan J, Sarkar S. Nitrous‐Acid‐Mediated Synthesis of Iron–Nitrosyl–Porphyrin: pH‐Dependent Release of Nitric Oxide. Chem Asian J 2012; 7:2690-5. [DOI: 10.1002/asia.201200518] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/01/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Jagannath Bhuyan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur‐208016, U.P. (India)
| | - Sabyasachi Sarkar
- Department of Chemistry, Bengal Engineering and Science University, Shibpur, Howrah‐711103 (West Bengal)
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43
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Gottstein D, Kirchner DK, Güntert P. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. JOURNAL OF BIOMOLECULAR NMR 2012; 52:351-64. [PMID: 22351031 DOI: 10.1007/s10858-012-9615-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/03/2012] [Indexed: 05/18/2023]
Abstract
A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative 'regmean structure' is obtained by simulated annealing in torsion angle space with the program CYANA using as input data the experimental restraints, restraints for the atom positions relative to the average Cartesian coordinates, and restraints for the torsion angles relative to the corresponding principal cluster average values of the ensemble. The method was applied to 11 proteins for which NMR structure ensembles are available, and compared to alternative, commonly used simple approaches for selecting a single representative structure, e.g. the structure from the ensemble that best fulfills the experimental and steric restraints, or the structure from the ensemble that has the lowest RMSD value to the average Cartesian coordinates. In all cases our method found a structure in torsion angle space that is significantly closer to the mean coordinates than the alternatives while maintaining the same quality as individual conformers. The method is thus suitable to generate representative single structure representations of protein structure ensembles in torsion angle space. Since in the case of NMR structure calculations with CYANA the single structure is calculated in the same way as the individual conformers except that weak positional and torsion angle restraints are added, we propose to represent new NMR structures by a 'regmean bundle' consisting of the single representative structure as the first conformer and all but one original individual conformers (the original conformer with the highest target function value is discarded in order to keep the number of conformers in the bundle constant). In this way, analyses that require a single structure can be carried out in the most meaningful way using the first model, while at the same time the additional information contained in the ensemble remains available.
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Affiliation(s)
- Daniel Gottstein
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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Knipp M, He C. Nitrophorins: nitrite disproportionation reaction and other novel functionalities of insect heme-based nitric oxide transport proteins. IUBMB Life 2011; 63:304-12. [PMID: 21491557 DOI: 10.1002/iub.451] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 02/15/2011] [Indexed: 01/14/2023]
Abstract
Nitrophorins (NPs) comprise a unique class of heme proteins used by the blood-sucking insect Rhodnius prolixus to deliver the signaling gas molecule NO into the blood vessel of a host during feeding. Upon NO release, histamine can be scavenged by coordination to the heme iron. Although the protein is of similar size as the mammalian globin monomers and shares the same cofactor and proximal histidine coordination, nitrophorin structure, in contrast, is almost entirely composed of a β-barrel. Comparison of the NO and histamine association constants with the concentrations of both compounds invivo raises concerns about the very simple ligand release model in case of at least some of the NPs. Therefore, novel functionalities of the NPs were sought. As a result, catalysis of the nitrite disproportionation reaction was found, which leads to the formation of NO with nitrite as the sole substrate. This is the first example of a ferriheme protein that can perform this reaction. Furthermore, although NPs stabilize the ferriheme state, a peroxidase reactivity of the cofactor involving the higher oxidation state iron (Compound I/II) was studied with the potential to catalyze the oxidation of histamine and norepinephrine. In contrast to many other heme proteins including the globins, the ferroheme state was found to be extremely sensitive to O(2) , which is a consequence of the much lower reduction potential of the NPs, so that the 1-electron reduction of O(2) to O (•-)(2) becomes a thermodynamically favored process. Altogether, the detailed study of the NPs gives insight into the structure-function relationships required for the targeted delivery of diatomic gas molecules in biology. Moreover, the comparison of the structure-function relationships of the NPs (NO transporters) with those of the globins (O(2) transporters) will help to elucidate the architectural requirement for the respective tasks.
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Affiliation(s)
- Markus Knipp
- Max-Planck-Institut für Bioanorganische Chemie, Mülheim an der Ruhr, Germany.
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Bianchetti CM, Bingman CA, Phillips GN. Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens. Proteins 2011; 79:1337-41. [PMID: 21387410 PMCID: PMC3179982 DOI: 10.1002/prot.22944] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/05/2010] [Indexed: 01/07/2023]
Affiliation(s)
- Christopher M. Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA,Centers for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
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He C, Ogata H, Knipp M. Formation of the Complex of Nitrite with the Ferriheme b β-Barrel Proteins Nitrophorin 4 and Nitrophorin 7,. Biochemistry 2010; 49:5841-51. [DOI: 10.1021/bi100324z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Chunmao He
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Knipp
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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