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Reeder BJ, Svistunenko DA, Wilson MT. Hell's Gate Globin-I from Methylacidiphilum infernorum Displays a Unique Temperature-Independent pH Sensing Mechanism Utililized a Lipid-Induced Conformational Change. Int J Mol Sci 2024; 25:6794. [PMID: 38928500 PMCID: PMC11203436 DOI: 10.3390/ijms25126794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Hell's Gate globin-I (HGb-I) is a thermally stable globin from the aerobic methanotroph Methylacidiphilium infernorum. Here we report that HGb-I interacts with lipids stoichiometrically to induce structural changes in the heme pocket, changing the heme iron distal ligation coordination from hexacoordinate to pentacoordinate. Such changes in heme geometry have only been previously reported for cytochrome c and cytoglobin, linked to apoptosis regulation and enhanced lipid peroxidation activity, respectively. However, unlike cytoglobin and cytochrome c, the heme iron of HGb-I is altered by lipids in ferrous as well as ferric oxidation states. The apparent affinity for lipids in this thermally stable globin is highly pH-dependent but essentially temperature-independent within the range of 20-60 °C. We propose a mechanism to explain these observations, in which lipid binding and stability of the distal endogenous ligand are juxtaposed as a function of temperature. Additionally, we propose that these coupled equilibria may constitute a mechanism through which this acidophilic thermophile senses the pH of its environment.
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Affiliation(s)
- Brandon J. Reeder
- School of Biological Sciences, University of Essex, Wivenhoe Park Colchester, Essex CO4 3SQ, UK; (D.A.S.); (M.T.W.)
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2
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Mathur S, Yadav SK, Yadav K, Bhatt S, Kundu S. A novel single sensor hemoglobin domain from the thermophilic cyanobacteria Thermosynechococcus elongatus BP-1 exhibits higher pH but lower thermal stability compared to globins from mesophilic organisms. Int J Biol Macromol 2023; 240:124471. [PMID: 37076076 DOI: 10.1016/j.ijbiomac.2023.124471] [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: 02/19/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Thermosynechococcus elongatus-BP1 belongs to the class of photoautotrophic cyanobacterial organisms. The presence of chlorophyll a, carotenoids, and phycocyanobilin are the characteristics that categorize T. elongatus as a photosynthetic organism. Here, we report the structural and spectroscopic characteristics of novel hemoglobin (Hb) Synel Hb from T.elongatus, synonymous with Thermosynechococcus vestitus BP-1. The X-ray crystal structure (2.15 Å) of Synel Hb suggests the presence of a globin domain with a pre-A helix similar to the sensor domain (S) family of Hbs. The rich hydrophobic core accommodates heme in a penta-coordinated state and readily binds an extraneous ligand(imidazole). The absorption and circular dichroic spectral analysis of Synel Hb reiteratedthat the heme is in FeIII+ state with a predominantly α-helical structure similar to myoglobin. Synel Hb displays higher resistance to structural perturbations induced via external stresses like pH and guanidium hydrochloride, which is comparable to Synechocystis Hb. However, Synel Hb exhibited lower thermal stability compared to mesophilic hemoglobins. Overall, the data is suggestive of the structural sturdiness of Synel Hb, which probably corroborates its origin in extreme thermophilic conditions. The stable globin provides scope for further investigation and may lead to new insights with scope for engineering stability in hemoglobin-based oxygen carriers.
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Affiliation(s)
- Shruti Mathur
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi 110007, India
| | - Sanjeev Kumar Yadav
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Kajal Yadav
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Delhi School of Public Health, Institute of Eminence, University of Delhi, Delhi 110007, India; Birla Institute of Technology and Science Pilani, K.K.Birla Goa Campus, Goa 403726, India.
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3
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Gilles-Gonzalez MA, Sousa EHS. Measurement of O 2 Binding by Sensory Hemeproteins. Methods Mol Biol 2023; 2648:11-25. [PMID: 37039982 DOI: 10.1007/978-1-0716-3080-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The discovery of an increasing number of proteins that function in the detoxification and sensing of gaseous ligands has renewed interest in hemeproteins. It is critical to measure the affinities of these proteins for ligands like O2, CO, and NO, know with confidence when a protein is fully saturated with a specific ligand, and be able to estimate how well a ligand will compete against other ligands for a specific protein. Below we describe how to obtain an intact O2-binding hemeprotein with a full complement of heme, how to evaluate the factors that can impact its affinity for O2, and how to determine accurately the equilibrium and kinetic parameters Kd, kon, and koff for O2 binding.
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Affiliation(s)
- Marie A Gilles-Gonzalez
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Eduardo H S Sousa
- Department of Organic and Inorganic Chemistry, Federal University of Ceara, Center for Sciences, Fortaleza, Ceara, Brazil.
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4
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GLB-3: A resilient, cysteine-rich, membrane-tethered globin expressed in the reproductive and nervous system of Caenorhabditis elegans. J Inorg Biochem 2023; 238:112063. [PMID: 36370505 DOI: 10.1016/j.jinorgbio.2022.112063] [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: 09/14/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
Abstract
The popular genetic model organism Caenorhabditis elegans (C. elegans) encodes 34 globins, whereby the few that are well-characterized show divergent properties besides the typical oxygen carrier function. Here, we present a biophysical characterization and expression analysis of C. elegans globin-3 (GLB-3). GLB-3 is predicted to exist in two isoforms and is expressed in the reproductive and nervous system. Knockout of this globin causes a 99% reduction in fertility and reduced motility. Spectroscopic analysis reveals that GLB-3 exists as a bis-histidyl-ligated low-spin form in both the ferrous and ferric heme form. A function in binding of diatomic gases is excluded on the basis of the slow CO-binding kinetics. Unlike other globins, GLB-3 is also not capable of reacting with H2O2, H2S, and nitrite. Intriguingly, not only does GLB-3 contain a high number of cysteine residues, it is also highly stable under harsh conditions (pH = 2 and high concentrations of H2O2). The resilience diminishes when the N- and C-terminal extensions are removed. Redox potentiometric measurements reveal a slightly positive redox potential (+8 ± 19 mV vs. SHE), suggesting that the heme iron may be able to oxidize cysteines. Electron paramagnetic resonance shows that formation of an intramolecular disulphide bridge, involving Cys70, affects the heme-pocket region. The results suggest an involvement of the globin in (cysteine) redox chemistry.
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5
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Redox potential determination of the Hell’s gate globin I protein facing multiple exogenous ligands. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Schneider T, Tan Y, Li H, Fisher JS, Zhang D. Photoglobin, a distinct family of non-heme binding globins, defines a potential photosensor in prokaryotic signal transduction systems. Comput Struct Biotechnol J 2022; 20:261-273. [PMID: 35024098 PMCID: PMC8717448 DOI: 10.1016/j.csbj.2021.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Globins constitute an ancient superfamily of proteins, exhibiting enormous structural and functional diversity, as demonstrated by many heme-binding families and two non-heme binding families that were discovered in bacterial stressosome component RsbR and in light-harvesting phycobiliproteins (phycocyanin) in cyanobacteria and red algae. By comprehensively exploring the globin repertoire using sensitive computational analyses of sequences, structures, and genomes, we present the identification of the third family of non-heme binding globins—the photoglobin. By conducting profile-based comparisons, clustering analyses, and structural modeling, we demonstrate that photoglobin is related to, but distinct from, the phycocyanin family. Photoglobin preserves a potential ligand-binding pocket, whose residue configuration closely resembles that of phycocyanin, indicating that photoglobin potentially binds to a comparable linear tetrapyrrole. By exploring the contextual information provided by the photoglobin’s domain architectures and gene-neighborhoods, we found that photoglobin is frequently associated with the B12-binding light sensor domain and many domains typical of prokaryotic signal transduction systems. Structural modeling using AlphaFold2 demonstrated that photoglobin and B12-binding domains form a structurally conserved hub among different domain architecture contexts. Based on these strong associations, we predict that the coupled photoglobin and B12-binding domains act as a light-sensing regulatory bundle, with each domain sensing different wavelengths of light resulting in switch-like regulation of downstream signaling effectors. Thus, based on the above lines of evidence, we present a distinct non-heme binding globin family and propose that it may define a new type of light sensor, by means of a linear tetrapyrrole, in complex prokaryotic signal transduction systems.
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Affiliation(s)
- Theresa Schneider
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Jonathan S Fisher
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States.,Program of Bioinformatics and Computational Biology, College of Arts & Sciences, Saint Louis University, MO 63103, United States
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7
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Muraki N, Takeda K, Nam D, Muraki M, Aono S. Structural Characterization of Y29F Mutant of Thermoglobin from a Hyperthermophilic Bacterium Aquifex aeolicus. CHEM LETT 2021. [DOI: 10.1246/cl.200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Norifumi Muraki
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Kouta Takeda
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Dayeon Nam
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Megumi Muraki
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shigetoshi Aono
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
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9
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Lessons from the post-genomic era: Globin diversity beyond oxygen binding and transport. Redox Biol 2020; 37:101687. [PMID: 32863222 PMCID: PMC7475203 DOI: 10.1016/j.redox.2020.101687] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Vertebrate hemoglobin (Hb) and myoglobin (Mb) were among the first proteins whose structures and sequences were determined over 50 years ago. In the subsequent pregenomic period, numerous related proteins came to light in plants, invertebrates and bacteria, that shared the myoglobin fold, a signature sequence motif characteristic of a 3-on-3 α-helical sandwich. Concomitantly, eukaryote and bacterial globins with a truncated 2-on-2 α-helical fold were discovered. Genomic information over the last 20 years has dramatically expanded the list of known globins, demonstrating their existence in a limited number of archaeal genomes, a majority of bacterial genomes and an overwhelming majority of eukaryote genomes. In vertebrates, 6 additional globin types were identified, namely neuroglobin (Ngb), cytoglobin (Cygb), globin E (GbE), globin X (GbX), globin Y (GbY) and androglobin (Adgb). Furthermore, functions beyond the familiar oxygen transport and storage have been discovered within the vertebrate globin family, including NO metabolism, peroxidase activity, scavenging of free radicals, and signaling functions. The extension of the knowledge on globin functions suggests that the original roles of bacterial globins must have been enzymatic, involved in defense against NO toxicity, and perhaps also as sensors of O2, regulating taxis away or towards high O2 concentrations. In this review, we aimed to discuss the evolution and remarkable functional diversity of vertebrate globins with particular focus on the variety of non-canonical expression sites of mammalian globins and their according impressive variability of atypical functions.
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10
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Cooper CE, Silkstone GGA, Simons M, Gretton S, Rajagopal BS, Allen-Baume V, Syrett N, Shaik T, Popa G, Sheng X, Bird M, Choi JW, Piano R, Ronda L, Bettati S, Paredi G, Mozzarelli A, Reeder BJ. Engineering hemoglobin to enable homogenous PEGylation without modifying protein functionality. Biomater Sci 2020; 8:3896-3906. [PMID: 32539053 DOI: 10.1039/c9bm01773a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to infuse hemoglobin into the vasculature as an oxygen therapeutic or blood substitute, it is necessary to increase the size of the molecule to enhance vascular retention. This aim can be achieved by PEGylation. However, using non-specific conjugation methods creates heterogenous mixtures and alters protein function. Site-specific PEGylation at the naturally reactive thiol on human hemoglobin (βCys93) alters hemoglobin oxygen binding affinity and increases its autooxidation rate. In order to avoid this issue, new reactive thiol residues were therefore engineered at sites distant to the heme group and the α/β dimer/dimer interface. The two mutants were βCys93Ala/αAla19Cys and βCys93Ala/βAla13Cys. Gel electrophoresis, size exclusion chromatography and mass spectrometry revealed efficient PEGylation at both αAla19Cys and βAla13Cys, with over 80% of the thiols PEGylated in the case of αAla19Cys. For both mutants there was no significant effect on the oxygen affinity or the cooperativity of oxygen binding. PEGylation at αAla19Cys had the additional benefit of decreasing the rates of autoxidation and heme release, properties that have been considered contributory factors to the adverse clinical side effects exhibited by previous hemoglobin based oxygen carriers. PEGylation at αAla19Cys may therefore be a useful component of future clinical products.
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Affiliation(s)
- Chris E Cooper
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
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11
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Crystal structure of a neoagarobiose-producing GH16 family β-agarase from Persicobacter sp. CCB-QB2. Appl Microbiol Biotechnol 2019; 104:633-641. [PMID: 31784792 DOI: 10.1007/s00253-019-10237-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
PdAgaC from the marine bacterium Persicobacter sp. CCB-QB2 is a β-agarase belonging to the glycoside hydrolase family 16 (GH16). It is one of only a handful of endo-acting GH16 β-agarases able to degrade agar completely to produce neoagarobiose (NA2). The crystal structure of PdAgaC's catalytic domain, which has one of the highest Vmax value at 2.9 × 103 U/mg, was determined in order to understand its unique mechanism. The catalytic domain is made up of a typical β-jelly roll fold with two additional insertions, and a well-conserved but wider substrate-binding cleft with some minor changes. Among the unique differences, two unconserved residues, Asn226 and Arg286, may potentially contribute additional hydrogen bonds to subsites -1 and +2, respectively, while a third, His185 from one of the additional insertions, may further contribute another bond to subsite +2. These additional hydrogen bonds may probably have enhanced PdAgaC's affinity for short agaro-oligosaccharides such as neoagarotetraose (NA4), rendering it capable of binding NA4 strongly enough for rapid degradation into NA2.
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12
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Kim T, Kassim AM, Botejue A, Zhang C, Forte J, Rozzell D, Huffman MA, Devine PN, McIntosh JA. Hemoprotein-Catalyzed Cyclopropanation En Route to the Chiral Cyclopropanol Fragment of Grazoprevir. Chembiochem 2019; 20:1129-1132. [PMID: 30666768 DOI: 10.1002/cbic.201800652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/14/2019] [Indexed: 11/07/2022]
Abstract
Reactions that were once the exclusive province of synthetic catalysts can increasingly be addressed using biocatalysis. Through discovery of unnatural enzyme reactions, biochemists have significantly expanded the reach of enzymatic catalysis to include carbene transfer chemistries including olefin cyclopropanation. Here we describe hemoprotein cyclopropanation catalysts derived from thermophilic bacterial globins that react with diazoacetone and an unactivated olefin substrate to furnish a cyclopropyl ketone, a previously unreported reaction for enzyme catalysts. We further demonstrate that the resulting cyclopropyl ketone can be converted to a key cyclopropanol intermediate that occurs en route to the anti-hepatitis C drug grazoprevir.
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Affiliation(s)
- Taejin Kim
- Provivi Inc., 1701 Colorado Avenue, Santa Monica, CA, 90404, USA
| | - Amude M Kassim
- Merck & Co., Inc., Enabling Technologies, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Ajit Botejue
- Provivi Inc., 1701 Colorado Avenue, Santa Monica, CA, 90404, USA
| | - Chen Zhang
- Provivi Inc., 1701 Colorado Avenue, Santa Monica, CA, 90404, USA
| | - Jared Forte
- Provivi Inc., 1701 Colorado Avenue, Santa Monica, CA, 90404, USA
| | - David Rozzell
- Provivi Inc., 1701 Colorado Avenue, Santa Monica, CA, 90404, USA
| | - Mark A Huffman
- Merck & Co., Inc., Enabling Technologies, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Paul N Devine
- Merck & Co., Inc., Enabling Technologies, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
| | - John A McIntosh
- Merck & Co., Inc., Enabling Technologies, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
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13
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Teixeira CS, Cabral MES, Carneiro RF, Brito SV, Nagano CS, Silva ALC, Garcia W, Almeida WO, Sampaio AH, Delatorre P, Carvalho JMS, Sousa EHS, Rocha BAM. Structural aspects and physiological implications of the hemoglobin of green iguana (Iguana iguana). Int J Biol Macromol 2018; 120:1275-1285. [PMID: 30171953 DOI: 10.1016/j.ijbiomac.2018.08.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Claudener S Teixeira
- Centro de Ciências Agrárias e Ambientais, Universidade Federal do Maranhão, Chapadinha, Maranhão, Brazil
| | - Mario E S Cabral
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Rômulo F Carneiro
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Samuel V Brito
- Centro de Ciências Agrárias e Ambientais, Universidade Federal do Maranhão, Chapadinha, Maranhão, Brazil
| | - Celso S Nagano
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - André L C Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | - Wanius Garcia
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Waltécio O Almeida
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
| | - Alexandre H Sampaio
- Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Plínio Delatorre
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - José M S Carvalho
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Eduardo H S Sousa
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Bruno A M Rocha
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, Brazil.
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14
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Correa-Aragunde N, Foresi N, Del Castello F, Lamattina L. A singular nitric oxide synthase with a globin domain found in Synechococcus PCC 7335 mobilizes N from arginine to nitrate. Sci Rep 2018; 8:12505. [PMID: 30131503 PMCID: PMC6104048 DOI: 10.1038/s41598-018-30889-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 08/07/2018] [Indexed: 12/11/2022] Open
Abstract
The enzyme nitric oxide synthase (NOS) oxidizes L-arginine to NO and citrulline. In this work, we characterise the NOS from the cyanobacteria Synechococcus PCC 7335 (SyNOS). SyNOS possesses a canonical mammalian NOS architecture consisting of oxygenase and reductase domains. In addition, SyNOS possesses an unusual globin domain at the N-terminus. Recombinant SyNOS expressed in bacteria is active, and its activity is suppressed by the NOS inhibitor L-NAME. SyNOS allows E. coli to grow in minimum media containing L-arginine as the sole N source, and has a higher growth rate during N deficiency. SyNOS is expressed in Synechococcus PCC 7335 where NO generation is dependent on L-arginine concentration. The growth of Synechococcus is dramatically inhibited by L-NAME, suggesting that SyNOS is essential for this cyanobacterium. Addition of arginine in Synechococcus increases the phycoerythrin content, an N reservoir. The role of the novel globin domain in SyNOS is discussed as an evolutionary advantage, conferring new functional capabilities for N metabolism.
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Affiliation(s)
- Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas. Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - CONICET, CC 1245, 7600, Mar del Plata, Argentina
| | - Noelia Foresi
- Instituto de Investigaciones Biológicas. Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - CONICET, CC 1245, 7600, Mar del Plata, Argentina
| | - Fiorella Del Castello
- Instituto de Investigaciones Biológicas. Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - CONICET, CC 1245, 7600, Mar del Plata, Argentina
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas. Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata - CONICET, CC 1245, 7600, Mar del Plata, Argentina.
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15
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Colloc'h N, Sacquin-Mora S, Avella G, Dhaussy AC, Prangé T, Vallone B, Girard E. Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep 2017; 7:1858. [PMID: 28500341 PMCID: PMC5431840 DOI: 10.1038/s41598-017-02097-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/20/2017] [Indexed: 11/09/2022] Open
Abstract
Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the “heme sliding mechanism”. Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie Univ., CERVOxy team, centre Cyceron, 14000, Caen, France.
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Giovanna Avella
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy.,BIOGEM Research Institute, Ariano Irpino, Italy
| | - Anne-Claire Dhaussy
- CRISTMAT UMR 6508 CNRS ENSICAEN UNICAEN Normandie Univ., 6 bd du Maréchal Juin, 14050, Caen, France
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, 4 avenue de l'Observatoire, 75270, Paris, France
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy
| | - Eric Girard
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
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16
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Reeder BJ. Redox and Peroxidase Activities of the Hemoglobin Superfamily: Relevance to Health and Disease. Antioxid Redox Signal 2017; 26:763-776. [PMID: 27637274 DOI: 10.1089/ars.2016.6803] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
SIGNIFICANCE Erythrocyte hemoglobin (Hb) and myocyte myoglobin, although primarily oxygen-carrying proteins, have the capacity to do redox chemistry. Such redox activity in the wider family of globins now appears to have important associations with the mechanisms of cell stress response. In turn, an understanding of such mechanisms in vivo may have a potential in the understanding of cancer therapy resistance and neurodegenerative disorders such as Alzheimer's. Recent Advances: There has been an enhanced understanding of the redox chemistry of the globin superfamily in recent years, leading to advances in development of Hb-based blood substitutes and in hypotheses relating to specific disease mechanisms. Neuroglobin (Ngb) and cytoglobin (Cygb) have been linked to cell protection mechanisms against hypoxia and oxidative stress, with implications in the onset and progression of neurodegenerative diseases for Ngb and cancer for Cygb. CRITICAL ISSUES Despite advances in the understanding of redox chemistry of globins, the physiological roles of many of these proteins still remain ambiguous at best. Confusion over potential physiological roles may relate to multifunctional roles for globins, which may be modulated by surface-exposed cysteine pairs in some globins. Such roles may be critical in deciphering the relationships of these globins in human diseases. FUTURE DIRECTIONS Further studies are required to connect the considerable knowledge on the mechanisms of globin redox chemistry in vitro with the physiological and pathological roles of globins in vivo. In doing so, new therapies for neurodegenerative disorders and cancer therapy resistance may be targeted. Antioxid. Redox Signal. 26, 763-776.
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Affiliation(s)
- Brandon J Reeder
- School of Biological Sciences, University of Essex , Essex, United Kingdom
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17
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Ascenzi P, di Masi A, Leboffe L, Fiocchetti M, Nuzzo MT, Brunori M, Marino M. Neuroglobin: From structure to function in health and disease. Mol Aspects Med 2016; 52:1-48. [DOI: 10.1016/j.mam.2016.10.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
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18
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Harish BM, Saraswathi R, Vinod D, Devaraju KS. Discovery of a latent calcineurin inhibitory peptide from its autoinhibitory domain by docking, dynamic simulation, and in vitro methods. J Biomol Struct Dyn 2015; 34:983-92. [DOI: 10.1080/07391102.2015.1064829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- B. M. Harish
- Department of Microbiology and Biotechnology, Bangalore University, JB Campus, Bangalore 560056, Karnataka, India
| | - R. Saraswathi
- Department of Microbiology and Biotechnology, Bangalore University, JB Campus, Bangalore 560056, Karnataka, India
| | - D. Vinod
- College of Pharmacy, Madras Medical College, Chennai 600003, India
| | - K. S. Devaraju
- Department of Microbiology and Biotechnology, Bangalore University, JB Campus, Bangalore 560056, Karnataka, India
- Department of Biochemistry, Karnatak University, Dharwad, Karnataka, India
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19
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Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites. Sci Rep 2015; 5:11407. [PMID: 26094577 PMCID: PMC4476040 DOI: 10.1038/srep11407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/22/2015] [Indexed: 11/24/2022] Open
Abstract
Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A–E, hence the distal site, from one subunit and helices F–H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys–His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions.
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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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21
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Herman JL, Challis CJ, Novák Á, Hein J, Schmidler SC. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Mol Biol Evol 2014; 31:2251-66. [PMID: 24899668 PMCID: PMC4137710 DOI: 10.1093/molbev/msu184] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence-structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.
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Affiliation(s)
- Joseph L Herman
- Department of Statistics, University of Oxford, Oxford, United KingdomDivision of Mathematical Biology, National Institute of Medical Research, London, United Kingdom
| | | | - Ádám Novák
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Scott C Schmidler
- Department of Statistical Science, Duke UniversityDepartment of Computer Science, Duke University
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22
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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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23
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Pechkova E, Bragazzi NL, Nicolini C. Advances in nanocrystallography as a proteomic tool. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:163-91. [PMID: 24985772 DOI: 10.1016/b978-0-12-800453-1.00005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In order to overcome the difficulties and hurdles too much often encountered in crystallizing a protein with the conventional techniques, our group has introduced the innovative Langmuir-Blodgett (LB)-based crystallization, as a major advance in the field of both structural and functional proteomics, thus pioneering the emerging field of the so-called nanocrystallography or nanobiocrystallography. This approach uniquely combines protein crystallography and nanotechnologies within an integrated, coherent framework that allows one to obtain highly stable protein crystals and to fully characterize them at a nano- and subnanoscale. A variety of experimental techniques and theoretical/semi-theoretical approaches, ranging from atomic force microscopy, circular dichroism, Raman spectroscopy and other spectroscopic methods, microbeam grazing-incidence small-angle X-ray scattering to in silico simulations, bioinformatics, and molecular dynamics, has been exploited in order to study the LB-films and to investigate the kinetics and the main features of LB-grown crystals. When compared to classical hanging-drop crystallization, LB technique appears strikingly superior and yields results comparable with crystallization in microgravity environments. Therefore, the achievement of LB-based crystallography can have a tremendous impact in the field of industrial and clinical/therapeutic applications, opening new perspectives for personalized medicine. These implications are envisaged and discussed in the present contribution.
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Affiliation(s)
- Eugenia Pechkova
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy
| | - Nicola Luigi Bragazzi
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; School of Public Health, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Claudio Nicolini
- Nanobiotechnology and Biophysics Laboratories (NBL), Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Nanoworld Institute Fondazione ELBA Nicolini (FEN), Pradalunga, Bergamo, Italy; Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
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24
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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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25
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Fuerst JA. The PVC superphylum: exceptions to the bacterial definition? Antonie van Leeuwenhoek 2013; 104:451-66. [PMID: 23912444 DOI: 10.1007/s10482-013-9986-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/22/2013] [Indexed: 11/30/2022]
Abstract
The PVC superphylum is a grouping of distinct phyla of the domain bacteria proposed initially on the basis of 16S rRNA gene sequence analysis. It consists of a core of phyla Planctomycetes, Verrucomicrobia and Chlamydiae, but several other phyla have been considered to be members, including phylum Lentisphaerae and several other phyla consisting only of yet-to-be cultured members. The genomics-based links between Planctomycetes, Verrucomicrobia and Chlamydiae have been recently strengthened, but there appear to be other features which may confirm the relationship at least of Planctomycetes, Verrucomicrobia and Lentisphaerae. Remarkably these include the unique planctomycetal compartmentalized cell plan differing from the cell organization typical for bacteria. Such a shared cell plan suggests that the common ancestor of the PVC superphylum members may also have been compartmentalized, suggesting this is an evolutionarily homologous feature at least within the superphylum. Both the PVC endomembranes and the eukaryote-homologous membrane-coating MC proteins linked to endocytosis ability in Gemmata obscuriglobus and shared by PVC members suggest such homology may extend beyond the bacteria to the Eukarya. If so, either our definition of bacteria may have to change or PVC members admitted to be exceptions. The cases for and against considering the PVC superphylum members as exceptions to the bacteria are discussed, and arguments for them as exceptions presented. Recent critical analysis has favoured convergence and analogy for explaining eukaryote-like features in planctomycetes and other PVC organisms. The case is made for constructing hypotheses leaving the possibility of homology and evolutionary links to eukaryote features open. As the case of discovery of endocytosis-like protein uptake in planctomycetes has suggested, this may prove a strong basis for the immediate future of experimental research programs in the PVC scientific community.
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Affiliation(s)
- John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia,
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26
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Newhouse EI, Newhouse JS, Alam M. Molecular dynamics study of hell's gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity. J Mol Model 2013; 19:2265-71. [PMID: 23377896 DOI: 10.1007/s00894-012-1739-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 12/14/2012] [Indexed: 11/24/2022]
Abstract
Hell's gate globin I (HGbI), a heme-containing protein from the extremophile Methylacidiphilum infernorum, has fast oxygen-binding/slow release characteristics due to its distal residues Gln and Tyr. The combination of Gln/Tyr distal iron coordination, adaptation to extreme environmental conditions, and lack of a D helix suggests that ligand migration in HGbI differs from other previously studied globins. Locally enhanced molecular dynamics trajectories of oxygen migration indicate a large internal cavity. This may increase the tendency of oxygen to exit from portals other than the most direct exit from the space near the heme. Oxygen may reside transiently in shallow surface depressions around the exits. Such surface trapping may enhance both oxygen uptake by increasing contact time between molecules, and decrease release by increasing the probability of oxygen reentry from the vicinity of the portal.
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Abstract
Approximately, 20 years ago, a haemoglobin gene was identified within the genome of the cyanobacterium Nostoc commune. Haemoglobins have now been confirmed in multiple species of photosynthetic microbes beyond N. commune, and the diversity of these proteins has recently come under increased scrutiny. This chapter summarizes the state of knowledge concerning the phylogeny, physiology and chemistry of globins in cyanobacteria and green algae. Sequence information is by far the best developed and the most rapidly expanding aspect of the field. Structural and ligand-binding properties have been described for just a few proteins. Physiological data are available for even fewer. Although activities such as nitric oxide dioxygenation and oxygen scavenging are strong candidates for cellular function, dedicated studies will be required to complete the story on this intriguing and ancient group of proteins.
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Vázquez-Limón C, Hoogewijs D, Vinogradov SN, Arredondo-Peter R. The evolution of land plant hemoglobins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:71-81. [PMID: 22682566 DOI: 10.1016/j.plantsci.2012.04.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 04/24/2012] [Accepted: 04/25/2012] [Indexed: 05/04/2023]
Abstract
This review discusses the evolution of land plant hemoglobins within the broader context of eukaryote hemoglobins and the three families of bacterial globins. Most eukaryote hemoglobins, including metazoan globins and the symbiotic and non-symbiotic plant hemoglobins, are homologous to the bacterial 3/3-fold flavohemoglobins. The remaining plant hemoglobins are homologous to the bacterial 2/2-fold group 2 hemoglobins. We have proposed that all eukaryote globins were acquired via horizontal gene transfer concomitant with the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. Although the 3/3 hemoglobins originated in the ancestor of green algae and plants prior to the emergence of embryophytes at about 450 mya, the 2/2 hemoglobins appear to have originated via horizontal gene transfer from a bacterium ancestral to present day Chloroflexi. Unlike the 2/2 hemoglobins, the evolution of the 3/3 hemoglobins was accompanied by duplication, diversification, and functional adaptations. Duplication of the ancestral plant nshb gene into the nshb-1 and nshb-2 lineages occurred prior to the monocot-dicot divergence at ca. 140 mya. It was followed by the emergence of symbiotic hemoglobins from a non-symbiotic hemoglobin precursor and further specialization, leading to leghemoglobins in N₂-fixing legume nodules concomitant with the origin of nodulation at ca. 60 mya. The transition of non-symbiotic to symbiotic hemoglobins (including to leghemoglobins) was accompanied by the alteration of heme-Fe coordination from hexa- to penta-coordination. Additional genomic information about Charophyte algae, the sister group to land plants, is required for the further clarification of plant globin phylogeny.
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Affiliation(s)
- Consuelo Vázquez-Limón
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
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Pechkova E, Scudieri D, Belmonte L, Nicolini C. Oxygen-bound hell's gate globin I by classical versus LB nanotemplate method. J Cell Biochem 2012; 113:2543-8. [DOI: 10.1002/jcb.24131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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