1
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Nardini M, Pesce A, Bolognesi M. Truncated (2/2) hemoglobin: Unconventional structures and functional roles in vivo and in human pathogenesis. Mol Aspects Med 2021; 84:101049. [PMID: 34776271 DOI: 10.1016/j.mam.2021.101049] [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: 10/22/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022]
Abstract
Truncated hemoglobins (trHbs) build a sub-class of the globin family, found in eubacteria, cyanobacteria, unicellular eukaryotes, and in higher plants; among these, selected human pathogens are found. The trHb fold is based on a 2/2 α-helical sandwich, consisting of a simplified and reduced-size version of the classical 3/3 α-helical sandwich of vertebrate and invertebrate globins. Phylogenetic analysis indicates that trHbs further branch into three groups: group I (or trHbN), group II (or trHbO), and group III (or trHbP), each group being characterized by specific structural features. Among these, a protein matrix tunnel, or a cavity system implicated in diatomic ligand diffusion through the protein matrix, is typical of group I and group II, respectively. In general, a highly intertwined network of hydrogen bonds stabilizes the heme bound ligand, despite variability of the heme distal residues in the different trHb groups. Notably, some organisms display genes from more than one trHb group, suggesting that trHbN, trHbO, and trHbP may support different functions in vivo, such as detoxification of reactive nitrogen and oxygen species, respiration, oxygen storage/sensoring, thus aiding survival of an invading microorganism. Here, structural features and proposed functions of trHbs from human pathogens are reviewed.
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Affiliation(s)
- Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
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2
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Johnson EA, Russo MM, Nye DB, Schlessman JL, Lecomte JTJ. Lysine as a heme iron ligand: A property common to three truncated hemoglobins from Chlamydomonas reinhardtii. Biochim Biophys Acta Gen Subj 2018; 1862:2660-2673. [PMID: 30251657 DOI: 10.1016/j.bbagen.2018.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND The nuclear genome of Chlamydomonas reinhardtii encodes a dozen hemoglobins of the truncated lineage. Four of these, named THB1-4, contain a single ~130-residue globin unit. THB1, which is cytoplasmic and capable of nitric oxide dioxygenation activity, uses a histidine and a lysine as axial ligands to the heme iron. In the present report, we compared THB2, THB3, and THB4 to THB1 to gain structural and functional insights into algal globins. METHODS We inspected properties of the globin domains prepared by recombinant means through site-directed mutagenesis, electronic absorption, CD, and NMR spectroscopies, and X-ray crystallography. RESULTS Recombinant THB3, which lacks the proximal histidine but has a distal histidine, binds heme weakly. NMR data demonstrate that the recombinant domains of THB2 and THB4 coordinate the ferrous heme iron with the proximal histidine and a lysine from the distal helix. An X-ray structure of ferric THB4 confirms lysine coordination. THB1, THB2, and THB4 have reduction potentials between -65 and -100 mV, are capable of nitric oxide dioxygenation, are reduced at different rates by the diaphorase domain of C. reinhardtii nitrate reductase, and show different response to peroxide treatment. CONCLUSIONS Three single-domain C. reinhardtii hemoglobins use lysine as a distal heme ligand in both Fe(III) and Fe(II) oxidation states. This common feature is likely related to enzymatic activity in the management of reactive oxygen species. GENERAL SIGNIFICANCE Primary structure analysis of hemoglobins has limited power in the prediction of heme ligation. Experimental determination reveals variations in this essential property across the superfamily.
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Affiliation(s)
- Eric A Johnson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Miranda M Russo
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Dillon B Nye
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Jamie L Schlessman
- Chemistry Department, U.S. Naval Academy, Annapolis, MD 21402, United States
| | - Juliette T J Lecomte
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, United States.
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3
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Feis A, Howes BD, Milazzo L, Coppola D, Smulevich G. Structural determinants of ligand binding in truncated hemoglobins: Resonance Raman spectroscopy of the native states and their carbon monoxide and hydroxide complexes. Biopolymers 2018; 109:e23114. [DOI: 10.1002/bip.23114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Barry D. Howes
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Lisa Milazzo
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
| | - Daniela Coppola
- Dipartimento di Scienze bio-agroalimentari del CNR (DiSBA-CNR), CNR, Via Pietro Castellino 111; Naples I-80131 Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff,”; Università di Firenze, Via della Lastruccia 3-13; Sesto Fiorentino 50019 Italy
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4
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Coexistence of multiple globin genes conferring protection against nitrosative stress to the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Nitric Oxide 2018; 73:39-51. [DOI: 10.1016/j.niox.2017.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/07/2017] [Accepted: 12/18/2017] [Indexed: 11/20/2022]
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5
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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6
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Liao F, Yuan H, Du KJ, You Y, Gao SQ, Wen GB, Lin YW, Tan X. Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin. MOLECULAR BIOSYSTEMS 2016; 12:3139-45. [PMID: 27476534 DOI: 10.1039/c6mb00537c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A hydrogen-bond (H-bond) network, specifically a Tyr-associated H-bond network, plays key roles in regulating the structure and function of proteins, as exemplified by abundant heme proteins in nature. To explore an approach for fine-tuning the structure and function of artificial heme proteins, we herein used myoglobin (Mb) as a model protein and introduced a Tyr residue in the secondary sphere of the heme active site at two different positions (107 and 138). We performed X-ray crystallography, UV-Vis spectroscopy, stopped-flow kinetics, and electron paramagnetic resonance (EPR) studies for the two single mutants, I107Y Mb and F138Y Mb, and compared to that of wild-type Mb under the same conditions. The results showed that both Tyr107 and Tyr138 form a distinct H-bond network involving water molecules and neighboring residues, which fine-tunes ligand binding to the heme iron and enhances the protein stability, respectively. Moreover, the Tyr107-associated H-bond network was shown to fine-tune both H2O2 binding and activation. With two cases demonstrated for Mb, this study suggests that the Tyr-associated H-bond network has distinct roles in regulating the protein structure, properties and functions, depending on its location in the protein scaffold. Therefore, it is possible to design a Tyr-associated H-bond network in general to create other artificial heme proteins with improved properties and functions.
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Affiliation(s)
- Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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7
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Deng Y, Lin J, Mao Y, Zhang X. Systematic analysis of an evolved Thermobifida fusca muC producing malic acid on organic and inorganic nitrogen sources. Sci Rep 2016; 6:30025. [PMID: 27424527 PMCID: PMC4948018 DOI: 10.1038/srep30025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Thermobifida fusca is a thermophilic actinobacterium. T. fusca muC obtained by adaptive evolution preferred yeast extract to ammonium sulfate for accumulating malic acid and ammonium sulfate for cell growth. We did transcriptome analysis of T. fusca muC on Avicel and cellobiose with addition of ammonium sulfate or yeast extract, respectively by RNAseq. The transcriptional results indicate that ammonium sulfate induced the transcriptions of the genes related to carbohydrate metabolisms significantly more than yeast extract. Importantly, Tfu_2487, encoding histidine-containing protein (HPr), didn’t transcribe on yeast extract at all, while it transcribed highly on ammonium sulfate. In order to understand the impact of HPr on malate production and cell growth of the muC strain, we deleted Tfu_2487 to get a mutant strain: muCΔ2487, which had 1.33 mole/mole-glucose equivalent malate yield, much higher than that on yeast extract. We then developed an E. coli-T. fusca shuttle plasmid for over-expressing HPr in muCΔ2487, a strain without HPr background, forming the muCΔ2487S strain. The muCΔ2487S strain had a much lower malate yield but faster cell growth than the muC strain. The results of both mutant strains confirmed that HPr was the key regulatory protein for T. fusca’s metabolisms on nitrogen sources.
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Affiliation(s)
- Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jia Lin
- College of Life Science, North China University of Science and Technology, Tangshan 063000, China
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xiaojuan Zhang
- School of pharmaceutical science, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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8
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Yan DJ, Yuan H, Li W, Xiang Y, He B, Nie CM, Wen GB, Lin YW, Tan X. How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin. Dalton Trans 2016; 44:18815-22. [PMID: 26458300 DOI: 10.1039/c5dt03040d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.
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Affiliation(s)
- Dao-Jing Yan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Wei Li
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
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9
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Bustamante JP, Szretter ME, Sued M, Martí MA, Estrin DA, Boechi L. A quantitative model for oxygen uptake and release in a family of hemeproteins. Bioinformatics 2016; 32:1805-13. [PMID: 27153569 DOI: 10.1093/bioinformatics/btw083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/30/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. RESULTS We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. CONTACT lboechi@ic.fcen.uba.ar SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - María E Szretter
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires Departamento De Matemática, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Mariela Sued
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Marcelo A Martí
- Departamento De Química Biológica E Instituto De Química Biológica De La Facultad De Ciencias Exactas Y Naturales (IQUIBICEN), Universidad De Buenos Aires, Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Leonardo Boechi
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
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10
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Giordano D, Pesce A, Boechi L, Bustamante JP, Caldelli E, Howes BD, Riccio A, di Prisco G, Nardini M, Estrin D, Smulevich G, Bolognesi M, Verde C. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. FEBS J 2015; 282:2948-65. [PMID: 26040838 DOI: 10.1111/febs.13335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/17/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | | | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Juan Pablo Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Elena Caldelli
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Barry D Howes
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Alessia Riccio
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Giulietta Smulevich
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Italy.,CNR-Institute of Biophysics and CIMAINA, University of Milano, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy.,Department of Biology, Roma 3 University, Italy
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11
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Howes BD, Boechi L, Boffi A, Estrin DE, Smulevich G. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO. Adv Microb Physiol 2015; 67:85-126. [PMID: 26616516 DOI: 10.1016/bs.ampbs.2015.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
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Affiliation(s)
- Barry D Howes
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alberto Boffi
- Dipartimento di Scienze Biochimiche, Università "Sapienza", Rome, Italy
| | - Dario E Estrin
- Departamento de Química Inorgánica, Analítica y Química Física and Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy.
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12
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Abstract
In the last few years, advances in algal research have identified the participation of haemoglobins in nitrogen metabolism and the management of reactive nitrogen and oxygen species. This chapter summarises the state of knowledge concerning algal haemoglobins with a focus on the most widely used model system, namely, Chlamydomonas reinhardtii. Genetic, physiologic, structural, and chemical information is compiled to provide a framework for further studies.
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Affiliation(s)
- Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
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13
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Bieza SA, Boubeta F, Feis A, Smulevich G, Estrin DA, Boechi L, Bari SE. Reactivity of inorganic sulfide species toward a heme protein model. Inorg Chem 2014; 54:527-33. [PMID: 25537304 DOI: 10.1021/ic502294z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The reactivity of inorganic sulfide species toward heme peptides was explored under biorelevant conditions in order to unravel the molecular details of the reactivity of the endogenous hydrogen sulfide toward heme proteins. Unlike ferric porphyrinates, which are reduced by inorganic sulfide, some heme proteins can form stable Fe(III)-sulfide adducts. To isolate the protein factors ruling the redox chemistry, we used as a system model, the undecapeptide microperoxidase (MP11), a heme peptide derived from cytochrome c proteolysis that retains the proximal histidine bound to the Fe(III) atom. Upon addition of gaseous hydrogen sulfide (H2S) at pH 6.8, the UV-vis spectra of MP11 closely resembled those of the low-spin ferric hydroxo complex (only attained at an alkaline pH) and cysteine or alkylthiol derivatives, suggesting that the Fe(III) reduction was prevented. The low-frequency region of the resonance Raman spectrum revealed the presence of an Fe(III)-S band at 366 cm(-1) and the general features of a low-spin hexacoordinated heme. Anhydrous sodium sulfide (Na2S) was the source of sulfide of choice for the kinetic evaluation of the process. Theoretical calculations showed no distal stabilization mechanisms for bound sulfide species in MP11, highlighting a key role of the proximal histidine for the stabilization of the Fe(III)-S adducts of heme compounds devoid of distal counterparts, which is significant with regard to the biochemical reactivity of endogenous hydrogen sulfide.
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Affiliation(s)
- Silvina A Bieza
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Ciudad Universitaria , Buenos Aires C1428EHA, Argentina
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14
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Nicoletti FP, Bustamante JP, Droghetti E, Howes BD, Fittipaldi M, Bonamore A, Baiocco P, Feis A, Boffi A, Estrin DA, Smulevich G. Interplay of the H-Bond Donor–Acceptor Role of the Distal Residues in Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin. Biochemistry 2014; 53:8021-30. [DOI: 10.1021/bi501132a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | | | - Enrica Droghetti
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Barry D. Howes
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Maria Fittipaldi
- INSTM
and Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - Alessandra Bonamore
- Institute
Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences
and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Paola Baiocco
- Center of
Life Nano Sciences, Italian Institute of Technology, Viale Regina
Elena 291, I-00161 Rome, Italy
| | - Alessandro Feis
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute
Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences
and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | | | - Giulietta Smulevich
- Dipartimento
di Chimica “Ugo Schiff”, Università di Firenze, Via della
Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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15
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Patrizi B, Lapini A, Di Donato M, Marcelli A, Lima M, Righini R, Foggi P, Baiocco P, Bonamore A, Boffi A. Role of local structure and dynamics of small ligand migration in proteins: a study of a mutated truncated hemoprotein from Thermobifida fusca by time resolved MIR spectroscopy. J Phys Chem B 2014; 118:9209-17. [PMID: 25019316 DOI: 10.1021/jp504499b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Carbon monoxide recombination dynamics in a mutant of the truncated hemoglobin from Thermobida fusca (3F-Tf-trHb) has been analyzed by means of ultrafast Visible-pump/MidIR-probe spectroscopy and compared with that of the wild-type protein. In 3F-Tf-trHb, three topologically relevant amino acids, responsible for the ligand stabilization through the formation of a H-bond network (TyrB10 TyrCD1 and TrpG8), have been replaced by Phe residues. X-ray diffraction data show that Phe residues in positions B10 and G8 maintain the same rotameric arrangements as Tyr and Trp in the wild-type protein, while Phe in position CD1 displays significant rotameric heterogeneity. Photodissociation of the ligand has been induced by exciting the sample with 550 nm pump pulses and the CO rebinding has been monitored in two mid-IR regions respectively corresponding to the ν(CO) stretching vibration of the iron-bound CO (1880-1980 cm(-1)) and of the dissociated free CO (2050-2200 cm(-1)). In both the mutant and wild-type protein, a significant amount of geminate CO rebinding is observed on a subnanosecond time scale. Despite the absence of the distal pocket hydrogen-bonding network, the kinetics of geminate rebinding in 3F-Tf-trHb is very similar to the wild-type, showing how the reactivity of dissociated CO toward the heme is primarily regulated by the effective volume and flexibility of the distal pocket and by caging effects exerted on the free CO on the analyzed time scale.
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Affiliation(s)
- Barbara Patrizi
- LENS (European Laboratory for Nonlinear Spectroscopy) Via N. Carrara 1, Sesto Fiorentino, Florence 50019, Italy
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16
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Reeder BJ, Hough MA. The structure of a class 3 nonsymbiotic plant haemoglobin from Arabidopsis thaliana reveals a novel N-terminal helical extension. ACTA ACUST UNITED AC 2014; 70:1411-8. [PMID: 24816109 DOI: 10.1107/s1399004714004878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/03/2014] [Indexed: 12/25/2022]
Abstract
Plant nonsymbiotic haemoglobins fall into three classes, each with distinct properties but all with largely unresolved physiological functions. Here, the first crystal structure of a class 3 nonsymbiotic plant haemoglobin, that from Arabidopsis thaliana, is reported to 1.77 Å resolution. The protein forms a homodimer, with each monomer containing a two-over-two α-helical domain similar to that observed in bacterial truncated haemoglobins. A novel N-terminal extension comprising two α-helices plays a major role in the dimer interface, which occupies the periphery of the dimer-dimer face, surrounding an open central cavity. The haem pocket contains a proximal histidine ligand and an open sixth iron-coordination site with potential for a ligand, in this structure hydroxide, to form hydrogen bonds to a tyrosine or a tryptophan residue. The haem pocket appears to be unusually open to the external environment, with another cavity spanning the entrance of the two haem pockets. The final 23 residues of the C-terminal domain are disordered in the structure; however, these domains in the functional dimer are adjacent and include the only two cysteine residues in the protein sequence. It is likely that these residues form disulfide bonds in vitro and it is conceivable that this C-terminal region may act in a putative complex with a partner molecule in vivo.
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Affiliation(s)
- Brandon J Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, England
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, England
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17
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Jamil F, Teh AH, Schadich E, Saito JA, Najimudin N, Alam M. Crystal structure of truncated haemoglobin from an extremely thermophilic and acidophilic bacterium. J Biochem 2014; 156:97-106. [PMID: 24733432 DOI: 10.1093/jb/mvu023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A truncated haemoglobin (tHb) has been identified in an acidophilic and thermophilic methanotroph Methylacidiphilium infernorum. Hell's Gate Globin IV (HGbIV) and its related tHbs differ from all other bacterial tHbs due to their distinctively large sequence and polar distal haem pocket residues. Here we report the crystal structure of HGbIV determined at 1.96 Å resolution. The HGbIV structure has the distinctive 2/2 α-helical structure with extensions at both termini. It has a large distal site cavity in the haem pocket surrounded by four polar residues: His70(B9), His71(B10), Ser97(E11) and Trp137(G8). This cavity can bind bulky ligands such as a phosphate ion. Conformational shifts of His71(B10), Leu90(E4) and Leu93(E7) can also provide more space to accommodate larger ligands than the phosphate ion. The entrance/exit of such bulky ligands might be facilitated by positional flexibility in the CD1 loop, E helix and haem-propionate A. Therefore, the large cavity in HGbIV with polar His70(B9) and His71(B10), in contrast to the distal sites of other bacterial tHbs surrounded by non-polar residues, suggests its distinct physiological functions.
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Affiliation(s)
- Farrukh Jamil
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Ermin Schadich
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Jennifer A Saito
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Nazalan Najimudin
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Maqsudul Alam
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USACentre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, 2565 McCarthy Mall, Honolulu, HI 96822, USA; School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; and Department of Microbiology, University of Hawaii, 2538 McCarthy Mall, Honolulu, HI 96822, USA
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18
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Molecular basis of thermal stability in truncated (2/2) hemoglobins. Biochim Biophys Acta Gen Subj 2014; 1840:2281-8. [PMID: 24704259 DOI: 10.1016/j.bbagen.2014.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/14/2014] [Accepted: 03/25/2014] [Indexed: 11/23/2022]
Abstract
BACKGROUND Understanding the molecular mechanism through which proteins are functional at extreme high and low temperatures is one of the key issues in structural biology. To investigate this phenomenon, we have focused on two instructive truncated hemoglobins from Thermobifida fusca (Tf-trHbO) and Mycobacterium tuberculosis (Mt-trHbO); although the two proteins are structurally nearly identical, only the former is stable at high temperatures. METHODS We used molecular dynamics simulations at different temperatures as well as thermal melting profile measurements of both wild type proteins and two mutants designed to interchange the amino acid residue, either Pro or Gly, at E3 position. RESULTS The results show that the presence of a Pro at the E3 position is able to increase (by 8°) or decrease (by 4°) the melting temperature of Mt-trHbO and Tf-trHbO, respectively. We observed that the ProE3 alters the structure of the CD loop, making it more flexible. CONCLUSIONS This gain in flexibility allows the protein to concentrate its fluctuations in this single loop and avoid unfolding. The alternate conformations of the CD loop also favor the formation of more salt-bridge interactions, together augmenting the protein's thermostability. GENERAL SIGNIFICANCE These results indicate a clear structural and dynamical role of a key residue for thermal stability in truncated hemoglobins.
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19
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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20
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Abstract
Small size globins that have been defined as 'truncated haemoglobins' or as '2/2 haemoglobins' have increasingly been discovered in microorganisms since the early 1990s. Analysis of amino acid sequences allowed to distinguish three groups that collect proteins with specific and common structural properties. All three groups display 3D structures that are based on four main α-helices, which are a subset of the conventional eight-helices globin fold. Specific features, such as the presence of protein matrix tunnels that are held to promote diffusion of functional ligands to/from the haem, distinguish members of the three groups. Haem distal sites vary for their accessibility, local structures, polarity, and ligand stabilization mechanisms, suggesting functional roles that are related to O2/NO chemistry. In a few cases, such activities have been proven in vitro and in vivo through deletion mutants. The issue of 2/2 haemoglobin varied biological functions throughout the three groups remains however fully open.
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21
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Dumont E, Jokipii-Lukkari S, Parkash V, Vuosku J, Sundström R, Nymalm Y, Sutela S, Taskinen K, Kallio PT, Salminen TA, Häggman H. Evolution, three-dimensional model and localization of truncated hemoglobin PttTrHb of hybrid aspen. PLoS One 2014; 9:e88573. [PMID: 24520401 PMCID: PMC3919811 DOI: 10.1371/journal.pone.0088573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 01/09/2014] [Indexed: 11/19/2022] Open
Abstract
Thus far, research on plant hemoglobins (Hbs) has mainly concentrated on symbiotic and non-symbiotic Hbs, and information on truncated Hbs (TrHbs) is scarce. The aim of this study was to examine the origin, structure and localization of the truncated Hb (PttTrHb) of hybrid aspen (Populus tremula L. × tremuloides Michx.), the model system of tree biology. Additionally, we studied the PttTrHb expression in relation to non-symbiotic class1 Hb gene (PttHb1) using RNAi-silenced hybrid aspen lines. Both the phylogenetic analysis and the three-dimensional (3D) model of PttTrHb supported the view that plant TrHbs evolved vertically from a bacterial TrHb. The 3D model suggested that PttTrHb adopts a 2-on-2 sandwich of α-helices and has a Bacillus subtilis -like ligand-binding pocket in which E11Gln and B10Tyr form hydrogen bonds to a ligand. However, due to differences in tunnel cavity and gate residue (E7Ala), it might not show similar ligand-binding kinetics as in Bs-HbO (E7Thr). The immunolocalization showed that PttTrHb protein was present in roots, stems as well as leaves of in vitro -grown hybrid aspens. In mature organs, PttTrHb was predominantly found in the vascular bundles and specifically at the site of lateral root formation, overlapping consistently with areas of nitric oxide (NO) production in plants. Furthermore, the NO donor sodium nitroprusside treatment increased the amount of PttTrHb in stems. The observed PttTrHb localization suggests that PttTrHb plays a role in the NO metabolism.
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Affiliation(s)
- Estelle Dumont
- Department of Biology, University of Oulu, Oulu, Finland
- UMR-MD1, Transporteurs Membranaires, Chimiorésistance et Drug-Design, Aix-Marseille Université, Marseille, France
| | | | - Vimal Parkash
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Jaana Vuosku
- Department of Biology, University of Oulu, Oulu, Finland
| | - Robin Sundström
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Yvonne Nymalm
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Suvi Sutela
- Department of Biology, University of Oulu, Oulu, Finland
| | | | | | - Tiina A. Salminen
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Hely Häggman
- Department of Biology, University of Oulu, Oulu, Finland
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22
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Bustamante JP, Abbruzzetti S, Marcelli A, Gauto D, Boechi L, Bonamore A, Boffi A, Bruno S, Feis A, Foggi P, Estrin DA, Viappiani C. Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins. J Phys Chem B 2014; 118:1234-45. [PMID: 24410478 DOI: 10.1021/jp410724z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
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23
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Vinogradov SN, Tinajero-Trejo M, Poole RK, Hoogewijs D. Bacterial and archaeal globins — A revised perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1789-800. [DOI: 10.1016/j.bbapap.2013.03.021] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/12/2013] [Accepted: 03/16/2013] [Indexed: 12/17/2022]
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24
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Nicoletti FP, Droghetti E, Howes BD, Bustamante JP, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1901-9. [PMID: 23467007 DOI: 10.1016/j.bbapap.2013.02.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
Abstract
The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN(-) have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH(-) and Fe-CN(-) frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH(-) ligand, CN(-) binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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25
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Lapini A, Di Donato M, Patrizi B, Marcelli A, Lima M, Righini R, Foggi P, Sciamanna N, Boffi A. Carbon monoxide recombination dynamics in truncated hemoglobins studied with visible-pump midIR-probe spectroscopy. J Phys Chem B 2012; 116:8753-61. [PMID: 22759230 DOI: 10.1021/jp3019149] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobifida fusca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron-CO coordination band located at 1850-1950 cm(-1) and the free CO absorption band in the region 2050-2200 cm(-1) have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850-1950 cm(-1) reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.
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Affiliation(s)
- Andrea Lapini
- LENS (European Laboratory for Nonlinear Spectroscopy), via N. Carrara 1, 50019 Sesto Fiorentino (FI), Italy
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26
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Marcelli A, Abbruzzetti S, Bustamante JP, Feis A, Bonamore A, Boffi A, Gellini C, Salvi PR, Estrin DA, Bruno S, Viappiani C, Foggi P. Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca. PLoS One 2012; 7:e39884. [PMID: 22792194 PMCID: PMC3391200 DOI: 10.1371/journal.pone.0039884] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022] Open
Abstract
CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ∼100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ∼2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ∼100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ∼3 to ∼100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.
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Affiliation(s)
- Agnese Marcelli
- LENS, European Laboratory for Non-linear Spectroscopy, Florence, Italy.
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27
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Giordano D, Russo R, Ciaccio C, Howes BD, di Prisco G, Marden MC, Hui Bon Hoa G, Smulevich G, Coletta M, Verde C. Ligand- and proton-linked conformational changes of the ferrous 2/2 hemoglobin of Pseudoalteromonas haloplanktis TAC125. IUBMB Life 2012; 63:566-73. [PMID: 21698762 DOI: 10.1002/iub.492] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The spectroscopic and ligand-binding properties of a 2/2 globin from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 have been studied in the ferrous state. It displays two major conformations characterized by CO-association rates that differ by a factor of 20, with relative fractions that depend on pH. A dynamic equilibrium is found between the two conformations, as indicated by an enhanced slower phase when lower CO levels were used to allow a longer time to facilitate the transition. The deoxy form, in the absence of external ligands, is a mixture of a predominant six-coordinate low spin form and a five-coordinate high-spin state; the proportion of low spin increasing at alkaline pH. In addition, at temperatures above the physiological temperature of 1 °C, an enhanced tendency of the protein to oxidize is observed.
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28
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Nicoletti FP, Droghetti E, Boechi L, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin. J Am Chem Soc 2011; 133:20970-80. [DOI: 10.1021/ja209312k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Enrica Droghetti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandra Bonamore
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Natascia Sciamanna
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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Droghetti E, Nicoletti FP, Bonamore A, Sciamanna N, Boffi A, Feis A, Smulevich G. The optical spectra of fluoride complexes can effectively probe H-bonding interactions in the distal cavity of heme proteins. J Inorg Biochem 2011; 105:1338-43. [DOI: 10.1016/j.jinorgbio.2011.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 06/17/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
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30
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Teh AH, Saito JA, Baharuddin A, Tuckerman JR, Newhouse JS, Kanbe M, Newhouse EI, Rahim RA, Favier F, Didierjean C, Sousa EH, Stott MB, Dunfield PF, Gonzalez G, Gilles-Gonzalez MA, Najimudin N, Alam M. Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin. FEBS Lett 2011; 585:3250-8. [DOI: 10.1016/j.febslet.2011.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 08/17/2011] [Accepted: 09/01/2011] [Indexed: 11/27/2022]
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31
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Pietri R, Román-Morales E, López-Garriga J. Hydrogen sulfide and hemeproteins: knowledge and mysteries. Antioxid Redox Signal 2011; 15:393-404. [PMID: 21050142 PMCID: PMC3118656 DOI: 10.1089/ars.2010.3698] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Historically, hydrogen sulfide (H(2)S) has been regarded as a poisonous gas, with a wide spectrum of toxic effects. However, like ·NO and CO, H(2)S is now referred to as a signaling gas involved in numerous physiological processes. The list of reports highlighting the physiological effects of H(2)S is rapidly expanding and several drug candidates are now being developed. As with ·NO and CO, not a single H(2)S target responsible for all the biological effects has been found till now. Nevertheless, it has been suggested that H(2)S can bind to hemeproteins, inducing different responses that can mediate its effects. For instance, the interaction of H(2)S with cytochrome c oxidase has been associated with the activation of the ATP-sensitive potassium channels, regulating muscle relaxation. Inhibition of cytochrome c oxidase by H(2)S has also been related to inducing a hibernation-like state. Although H(2)S might induce these effects by interacting with hemeproteins, the mechanisms underlying these interactions are obscure. Therefore, in this review we discuss the current state of knowledge about the interaction of H(2)S with vertebrate and invertebrate hemeproteins and postulate a generalized mechanism. Our goal is to stimulate further research aimed at evaluating plausible mechanisms that explain H(2)S reactivity with hemeproteins.
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Affiliation(s)
- Ruth Pietri
- Department of Chemistry, University of Puerto Rico, Mayagüez, Puerto Rico
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32
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A hydrogen-bonding network formed by the B10–E7–E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification. J Biol Inorg Chem 2011; 16:599-609. [DOI: 10.1007/s00775-011-0761-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
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33
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Droghetti E, Nicoletti FP, Bonamore A, Boechi L, Arroyo Mañez P, Estrin DA, Boffi A, Smulevich G, Feis A. Heme pocket structural properties of a bacterial truncated hemoglobin from Thermobifida fusca. Biochemistry 2010; 49:10394-402. [PMID: 21049911 DOI: 10.1021/bi101452k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An acidic surface variant (ASV) of the "truncated" hemoglobin from Thermobifida fusca was designed with the aim of creating a versatile globin scaffold endowed with thermostability and a high level of recombinant expression in its soluble form while keeping the active site unmodified. This engineered protein was obtained by mutating the surface-exposed residues Phe107 and Arg91 to Glu. Molecular dynamics simulations showed that the mutated residues remain solvent-exposed, not affecting the overall protein structure. Thus, the ASV was used in a combinatorial mutagenesis of the distal heme pocket residues in which one, two, or three of the conserved polar residues [TyrB10(54), TyrCD1(67), and TrpG8(119)] were substituted with Phe. Mutants were characterized by infrared and resonance Raman spectroscopy and compared with the wild-type protein. Similar Fe-proximal His stretching frequencies suggest that none of the mutations alters the proximal side of the heme cavity. Two conformers were observed in the spectra of the CO complexes of both wild-type and ASV protein: form 1 with ν(FeC) and ν(CO) at 509 and 1938 cm(-1) and form 2 with ν(FeC) and ν(CO) at 518 and 1920 cm(-1), respectively. Molecular dynamics simulations were performed for the wild-type and ASV forms, as well as for the TyrB10 mutant. The spectroscopic and computational results demonstrate that CO interacts with TrpG8 in form 1 and interacts with both TrpG8 and TyrCD1 in form 2. TyrB10 does not directly interact with the bound CO.
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Affiliation(s)
- Enrica Droghetti
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
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34
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Pesce A, Nardini M, Labarre M, Richard C, Wittenberg JB, Wittenberg BA, Guertin M, Bolognesi M. Structural characterization of a group II 2/2 hemoglobin from the plant pathogen Agrobacterium tumefaciens. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:810-6. [PMID: 21070893 DOI: 10.1016/j.bbapap.2010.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 10/27/2010] [Accepted: 11/02/2010] [Indexed: 11/18/2022]
Abstract
Within the 2/2 hemoglobin sub-family, no group II 2/2Hbs from proteobacteria have been so far studied. Here we present the first structural characterization of a group II 2/2Hb from the soil and phytopathogenic bacterium Agrobacterium tumefaciens (At-2/2HbO). The crystal structure of ferric At-2/2HbO (reported at 2.1Å resolution) shows the location of specific/unique heme distal site residues (e.g., His(42)CD1, a residue distinctive of proteobacteria group II 2/2Hbs) that surround a heme-liganded water molecule. A highly intertwined hydrogen-bonded network, involving residues Tyr(26)B10, His(42)CD1, Ser(49)E7, Trp(93)G8, and three distal site water molecules, stabilizes the heme-bound ligand. Such a structural organization suggests a path for diatomic ligand diffusion to/from the heme. Neither a similar distal site structuring effect nor the presence of distal site water molecules has been so far observed in group I and group III 2/2Hbs, thus adding new distinctive information to the complex picture of currently available 2/2Hb structural and functional data. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, University of Genova, I-16146 Genova, Italy
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35
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Nicoletti FP, Comandini A, Bonamore A, Boechi L, Boubeta FM, Feis A, Smulevich G, Boffi A. Sulfide binding properties of truncated hemoglobins. Biochemistry 2010; 49:2269-78. [PMID: 20102180 DOI: 10.1021/bi901671d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The truncated hemoglobins from Bacillus subtilis (Bs-trHb) and Thermobifida fusca (Tf-trHb) have been shown to form high-affinity complexes with hydrogen sulfide in their ferric state. The recombinant proteins, as extracted from Escherichia coli cells after overexpression, are indeed partially saturated with sulfide, and even highly purified samples still contain a small but significant amount of iron-bound sulfide. Thus, a complete thermodynamic and kinetic study has been undertaken by means of equilibrium and kinetic displacement experiments to assess the relevant sulfide binding parameters. The body of experimental data indicates that both proteins possess a high affinity for hydrogen sulfide (K = 5.0 x 10(6) and 2.8 x 10(6) M(-1) for Bs-trHb and Tf-trHb, respectively, at pH 7.0), though lower with respect to that reported previously for the sulfide avid Lucina pectinata I hemoglobins (2.9 x 10(8) M(-1)). From the kinetic point of view, the overall high affinity resides in the slow rate of sulfide release, attributed to hydrogen bonding stabilization of the bound ligand by distal residue WG8. A set of point mutants in which these residues have been replaced with Phe indicates that the WG8 residue represents the major kinetic barrier to the escape of the bound sulfide species. Accordingly, classical molecular dynamics simulations of SH(-)-bound ferric Tf-trHb show that WG8 plays a key role in the stabilization of coordinated SH(-) whereas the YCD1 and YB10 contributions are negligible. Interestingly, the triple Tf-trHb mutant bearing only Phe residues in the relevant B10, G8, and CD1 positions is endowed with a higher overall affinity for sulfide characterized by a very fast second-order rate constant and 2 order of magnitude faster kinetics of sulfide release with respect to the wild-type protein. Resonance Raman spectroscopy data indicate that the sulfide adducts are typical of a ferric iron low-spin derivative. In analogy with other low-spin ferric sulfide adducts, the strong band at 375 cm(-1) is tentatively assigned to a Fe-S stretching band. The high affinity for hydrogen sulfide is thought to have a possible physiological significance as H(2)S is produced in bacteria at metabolic steps involved in cysteine biosynthesis and hence in thiol redox homeostasis.
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Affiliation(s)
- Francesco P Nicoletti
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
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36
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Unusual proximal heme pocket geometry in the deoxygenated Thermobifida fusca: A combined spectroscopic investigation. Biophys Chem 2010; 147:1-7. [DOI: 10.1016/j.bpc.2009.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 11/25/2009] [Accepted: 11/25/2009] [Indexed: 11/19/2022]
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37
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Kuwada T, Hasegawa T, Takagi T, Sato I, Shishikura F. pH-dependent structural changes in haemoglobin component V from the midge larvaPropsilocerus akamusi(Orthocladiinae, Diptera). ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:258-67. [DOI: 10.1107/s0907444909055760] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 12/30/2009] [Indexed: 11/10/2022]
Abstract
Haemoglobin component V (Hb V) from the midge larvaPropsilocerus akamusiexhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb V retains its functional properties by adapting to the structural changes caused by amino-acid replacements.
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38
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Torge R, Comandini A, Catacchio B, Bonamore A, Botta B, Boffi A. Peroxidase-like activity of Thermobifida fusca hemoglobin: The oxidation of dibenzylbutanolide. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Razzera G, Vernal J, Baruh D, Serpa VI, Tavares C, Lara F, Souza EM, Pedrosa FO, Almeida FCL, Terenzi H, Valente AP. Spectroscopic characterization of a truncated hemoglobin from the nitrogen-fixing bacterium Herbaspirillum seropedicae. J Biol Inorg Chem 2008; 13:1085-96. [DOI: 10.1007/s00775-008-0394-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 05/29/2008] [Indexed: 11/28/2022]
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40
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Pesce A, Milani M, Nardini M, Bolognesi M. Mapping Heme‐Ligand Tunnels in Group I Truncated(2/2) Hemoglobins. Methods Enzymol 2008; 436:303-15. [DOI: 10.1016/s0076-6879(08)36017-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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41
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Feis A, Lapini A, Catacchio B, Brogioni S, Foggi P, Chiancone E, Boffi A, Smulevich G. Unusually Strong H-Bonding to the Heme Ligand and Fast Geminate Recombination Dynamics of the Carbon Monoxide Complex of Bacillus subtilis Truncated Hemoglobin. Biochemistry 2007; 47:902-10. [DOI: 10.1021/bi701297f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro Feis
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Andrea Lapini
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Bruno Catacchio
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Silvia Brogioni
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Paolo Foggi
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Emilia Chiancone
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Alberto Boffi
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, European Laboratory for Non-linear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino (FI), Italy, Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy, and Dipartimento di Chimica, Università di Perugia, Via Elce di Sotto 8, I-06100 Perugia, Italy
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42
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Ouellet H, Milani M, LaBarre M, Bolognesi M, Couture M, Guertin M. The roles of Tyr(CD1) and Trp(G8) in Mycobacterium tuberculosis truncated hemoglobin O in ligand binding and on the heme distal site architecture. Biochemistry 2007; 46:11440-50. [PMID: 17887774 DOI: 10.1021/bi7010288] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure of the cyano-met form of Mt-trHbO revealed two unusual distal residues Y(CD1) and W(G8) forming a hydrogen-bond network with the heme-bound ligand [Milani, M., et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 5766-5771]. W(G8) is an invariant residue in group II and group III trHbs and has no counterpart in other globins. A previous study reported that changing Y(CD1) for a Phe causes a significant increase in the O2 combination rate, but almost no change in the O2 dissociation rate [Ouellet, H., et al. (2003) Biochemistry 42, 5764-5774]. Here we investigated the role of the W(G8) in ligand binding by using resonance Raman spectroscopy, stopped-flow spectrophotometry, and X-ray crystallography. For this purpose, W(G8) was changed, by site-directed mutagenesis, to a Phe in both the wild-type protein and the mutant Y(CD1)F to create the single mutant W(G8)F and the double mutant Y(CD1)F/W(G8)F, respectively. Resonance Raman results suggest that W(G8) interacts with the heme-bound O2 and CO, as evidenced by the increase of the Fe-O2 stretching mode from 559 to 564 cm-1 and by the lower frequency of the Fe-CO stretching modes (514 and 497 cm-1) compared to that of the wild-type protein. Mutation of W(G8) to Phe indicates that this residue controls ligand binding, as evidenced by a dramatic increase of the combination rates of both O2 and CO. Also, the rate of O2 dissociation showed a 90-1000-fold increase in the W(G8)F and Y(CD1)F/W(G8)F mutants, that is in sharp contrast with the values obtained for the other distal mutants Y(B10)F and Y(CD1)F [Ouellet, H., et al. (2003) Biochemistry 42, 5764-5774]. Taken together, these data indicate a pivotal role for the W(G8) residue in O2 binding and stabilization.
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Affiliation(s)
- Hugues Ouellet
- Department of Biochemistry and Microbiology, Laval University, Quebec, Canada, G1K 7P4
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43
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Giordano D, Parrilli E, Dettaï A, Russo R, Barbiero G, Marino G, Lecointre G, di Prisco G, Tutino L, Verde C. The truncated hemoglobins in the Antarctic psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Gene 2007; 398:69-77. [PMID: 17582708 DOI: 10.1016/j.gene.2007.02.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 01/23/2007] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
The genome sequence of the Antarctic Gram-negative marine eubacterium Pseudoalteromonas haloplanktis TAC125 is a potential source of useful data on proteins from a cold-adapted microorganism. Identifying the bases of protein adaptation to higher or lower temperatures is important to understand the relationship between structure/function and life history on the Earth. The P. haloplanktis TAC125 genome contains three genes in distinct positions on chromosome I, named PSHAa0030, PSHAa2217 and PSHAa0458. These genes encode three truncated hemoglobins. The amino-acid identity between the three hemoglobins is less than 25% suggesting that these proteins may have different function(s) in bacterial cellular metabolism. The hemoglobin encoded by the PSHAa0030 gene has been cloned, expressed in Escherichia coli, purified and structurally characterised. This truncated hemoglobin is monomeric; circular dichroism shows high temperature resistance. The optical spectra of oxygenated and CO forms are similar to those of other truncated hemoglobins. Phylogenetic analyses show that two truncated globins encoded by the PSHAa0030 and PSHAa2217 genes belong to group II, and the third one encoded by PSHAa0458 to group I.
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Affiliation(s)
- Daniela Giordano
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy
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44
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Bonamore A, Attili A, Arenghi F, Catacchio B, Chiancone E, Morea V, Boffi A. A novel chimera: the "truncated hemoglobin-antibiotic monooxygenase" from Streptomyces avermitilis. Gene 2007; 398:52-61. [PMID: 17574781 DOI: 10.1016/j.gene.2007.01.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 01/24/2007] [Accepted: 01/30/2007] [Indexed: 10/23/2022]
Abstract
Novel chimeric proteins made of a globin domain fused with a "cofactor free" monooxygenase domain have been identified within the Streptomyces avermitilis and Frankia sp. genomes by means of bioinformatics methods. Structure based sequence alignments show that the globin domains of both proteins can be unambiguously assigned to the truncated hemoglobin family, in view of the striking similarity to the truncated hemoglobins from Mycobacterium tuberculosis, Thermobifida fusca and Bacillus subtilis. In turn, the non-heme domains belong to a family of small (about 100 aminoacids) homodimeric proteins annotated as antibiotic biosynthesis monooxygenases, despite the lack of a cofactor (e.g., a metal, a flavin or a heme) necessary for oxygen activation. The chimeric protein from S. avermitilis has been cloned, expressed and characterized. The protein is a stable dimer in solution based on analytical ultracentrifugation experiments. The heme ligand binding properties with oxygen and carbonmonoxide resemble those of other Group II truncated hemoglobins. In addition, an oxygen dependent redox activity has been demonstrated towards easily oxidizable substrates such as menadiol and p-aminophenol. These findings suggest novel functional roles of truncated hemoglobins, which might represent a vast class of multipurpose oxygen activating/scavenging proteins whose catalytic action is mediated by the interaction with cofactor free monooxygenases.
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Affiliation(s)
- Alessandra Bonamore
- Department of Biochemical Sciences, University of Rome La Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy
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Ilari A, Kjelgaard P, von Wachenfeldt C, Catacchio B, Chiancone E, Boffi A. Crystal structure and ligand binding properties of the truncated hemoglobin from Geobacillus stearothermophilus. Arch Biochem Biophys 2007; 457:85-94. [PMID: 17126283 DOI: 10.1016/j.abb.2006.09.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Revised: 09/14/2006] [Accepted: 09/15/2006] [Indexed: 11/22/2022]
Abstract
A novel truncated hemoglobin has been identified in the thermophilic bacterium Geobacillus stearothermophilus (Gs-trHb). The protein has been expressed in Escherichia coli, the 3D crystal structure (at 1.5 Angstroms resolution) and the ligand binding properties have been determined. The distal heme pocket displays an array of hydrogen bonding donors to the iron-bound ligands, including Tyr-B10 on one side of the heme pocket and Trp-G8 indole nitrogen on the opposite side. At variance with the highly similar Bacillus subtilis hemoglobin, Gs-trHb is dimeric both in the crystal and in solution and displays several unique structural properties. In the crystal cell, the iron-bound ligand is not homogeneously distributed within each distal site such that oxygen and an acetate anion can be resolved with relative occupancies of 50% each. Accordingly, equilibrium titrations of the oxygenated derivative in solution with acetate anion yield a partially saturated ferric acetate adduct. Moreover, the asymmetric unit contains two subunits and sedimentation velocity ultracentrifugation data confirm that the protein is dimeric.
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Affiliation(s)
- Andrea Ilari
- Department of Biochemical Sciences and CNR Institute of Molecular Biology and Pathology, University of Rome La Sapienza, P le Aldo Moro 5, 00185 Rome, Italy
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