Neuroglobins, Pivotal Proteins Associated with Emerging Neural Systems and Precursors of Metazoan Globin Diversity

Lechauve, Christophe; Jager, Muriel; Laguerre, Laurent; Kiger, Laurent; Correc, Gaëlle; Leroux, Cédric; Vinogradov, Serge N.; Czjzek, Mirjam; Marden, Michael C.; Bailly, Xavier

doi:10.1074/jbc.m112.407601

Cited by 34 publications

(58 citation statements)

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“…Kumaglobin is the first characterized globin protein from phylum Tardigrada and shows the unique coordination environment around heme. Evolution and functions of metazoan hexacoordinated globin proteins have been attracting researchers’ attention recently . Our study may provide a structural basis to understand relationships between tardigrade globin proteins and those from other phyla.…”

Section: Discussionmentioning

confidence: 89%

Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus

2018

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Tardigrades, also known as water bears, can survive extreme conditions. For example, tardigrades have high tolerance to extreme desiccation because they can enter an anhydrobiotic state, in which they show no or nearly undetectable metabolic processes. Proteins from anhydrobiotic tardigrades with low homology to known proteins from other organisms are new potential targets for structural genomics. Here, we present spectroscopic and structural characterization of an unprecedented globin protein (Kumaglobin: Kgb) found in an anhydrobiotic tardigrade. Spectroscopy reveals that Kgb contains hexacoordinated low‐spin heme, which is not capable of binding to hydrogen sulfide (H2S) unlike other globin proteins, such as neuroglobin. Interestingly however, when distal histidine is replaced with alanine, H2S is capable of binding to heme, implying that the distal histidine of Kgb binds tightly to heme. The overall structure of Kgb at 1.5 Å resolution shows high resemblance to well‐characterized eukaryotic globin proteins, such as myoglobin and cytoglobin. However, the heme coordination geometry in Kgb is unique because the distal histidinyl ligand is located at the 11th position of helix E while it is found at 7th position on helix E in many known globin proteins. The unusual conformation of distal histidine in Kgb is stabilized by a hydrogen bond with the carbonyl O atom of A103. Furthermore, bulky residues exist around the heme cofactor, resulting in a ruffling conformation of the porphyrin ring. Based on our study, Kgb is thought to be involved in electron transfer or enzymatic reactions rather than transporting or storing ligands. Database Structural data are available in the Protein Data Bank under the accession numbers http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5ZIQ (Kgb4‐SR) and http://www.rcsb.org/pdb/results/results.do?tabtoshow=Unreleased&qrid=D1773C9B (Kgb7‐house).

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Section: Discussionmentioning

confidence: 89%

Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus

2018

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“…A bona fide neuroglobin, SrNgb1, of the acoelomorph Symsagittifera roscoffensis, was amplified by PCR, cloned, crystallized, and structurally clarified by X-ray diffraction analysis [1]. Introduction 1 ).…”

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confidence: 99%

“…Of main concern was the orientation of the heme propanoate chains, with both carboxylate groups emerging from the distal side of heme in the crystal structure [1]. Symsagittifera roscoffensis Neuroglobin.…”

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confidence: 99%

“…The model for mNgb was based on X-ray diffraction data, at 1.8-resolution, for Escherichia coli-expressed mNgb/HEME, in complex with CO and Xe [6], accession code 3GLN on the PDB. The model for SrNgb1 was based on X-ray diffraction data, at 2.3-resolution, for the PCRamplified and then cloned protein, in complex with heme and O 2 (accession code 4B4Y) [1]. All crystallization H 2 O was retained, adding H-atoms with CHIMERA [25].…”

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confidence: 99%

“…Represented here is the structure of SrNgbÀO 2 (a-helices: A, yellow;, B, orange; C, cyan; D, forest green; E, dim gray;, F, cornflower blue; G, hot pink; H, red), fully-rebuilt from partial X-ray diffraction data[1], and MDequilibrated in solution. Represented here is the structure of SrNgbÀO 2 (a-helices: A, yellow;, B, orange; C, cyan; D, forest green; E, dim gray;, F, cornflower blue; G, hot pink; H, red), fully-rebuilt from partial X-ray diffraction data[1], and MDequilibrated in solution.…”

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confidence: 99%

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From Dioxygen Storing to Dioxygen Sensing with Neuroglobins: An Insight from Molecular Mechanics

Pietra

2013

Chemistry & Biodiversity

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This work deals with two neuroglobins from phylogenetically distant organisms. Deriving from the acoelomorph Symsagittifera roscoffensis, SrNgb is functionally pentacoordinated, and is assumed to function as a reserve of dioxygen (O₂). Obtained from mice, mNgb is functionally hexacoordinated, and presumably triggers signals from sensing O₂. Here, it is investigated how these two globins are permeated by diatomic gases, SrNgb by O₂ and mNgb by CO. With protein atomic coordinates available from high-resolution X-ray diffraction analysis, O₂ and CO pathways were traced from molecular-dynamics simulations in H₂O solution, which makes no difference between the two gases, accelerated by applying an external randomly-oriented minimal force to the center of mass of the diatomic gas molecule. This allowed us to explore a statistically significant large number of trajectories. It emerged that CO leaves mNgb from preferentially peripheral gates located on the side of the heme propionate chains, whereas O₂ leaves SrNgb from the opposite side. This shows no analogy with either the functionally pentacoordinated, O₂-transporting, myoglobin (Mgb), or the hexacoordinated, O₂-sensing, cytoglobin, despite the same three-over-three typical α-helical globin folding. The sole analogy that could be observed was a preference for the shortest diatomic gas pathways with both SrNgb and Mgb. It is tempting to speculate that this fulfills the need of being quick in delivering O₂ to depleted organs.

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Revised CHARMM force field parameters for iron‐containing cofactors of photosystem II

Adam

Knapp-Mohammady

et al. 2017

J Comput Chem

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Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor molecules. We present here CHARMM bonded and non-bonded parameters for the iron-containing cofactors of photosystem II that include a six-coordinated heme moiety coordinated by two histidine groups, and a non-heme iron complex coordinated by bicarbonate and four histidines. The force field parameters presented here give water interaction energies and geometries in good agreement with the quantum mechanical target data.

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Neuroglobins, Pivotal Proteins Associated with Emerging Neural Systems and Precursors of Metazoan Globin Diversity

Cited by 34 publications

References 61 publications

Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus

Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus

From Dioxygen Storing to Dioxygen Sensing with Neuroglobins: An Insight from Molecular Mechanics

Revised CHARMM force field parameters for iron‐containing cofactors of photosystem II

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