<scp>C</scp>
            hironomus

Bergtrom, Gerald

doi:10.1002/047120918x.emb0244

Cited by 2 publications

(8 citation statements)

References 27 publications

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“…Chironimids exhibit a stage-specific and tissue-specific synthesis of Hbs throughout larval and pupal stages. Twelve different globin chains, and more than 30 globin genes, have been identified in Chironomus thummi thummi (Goodman et al 1983;Green et al 1998;Bergstrom 1999), a similar situation being described for the Japanese midge species Tokunagayusurika akamusi (Yamamoto et al 2003). Extracellular Chironomus thummi thummi HbIII (CttHbIII) (Fig.…”

mentioning

confidence: 58%

Modulation of oxygen binding to insect hemoglobins: The structure of hemoglobin from the botfly Gasterophilus intestinalis

et al. 2005

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Hemoglobins (Hbs) reversibly bind gaseous diatomic ligands (e.g., O 2 ) as the sixth heme axial ligand of the penta-coordinate deoxygenated form. Selected members of the Hb superfamily, however, display a functionally relevant hexa-coordinate heme Fe atom in their deoxygenated state. Endogenous heme hexa-coordination is generally provided in these Hbs by the E7 residue (often His), which thus modulates accessibility to the heme distal pocket and reactivity of the heme toward exogenous ligands. Such a pivotal role of the E7 residue is prominently shown by analysis of the functional and structural properties of insect Hbs. Here, we report the 2.6 Å crystal structure of oxygenated Gasterophilus intestinalis Hb1, a Hb known to display a penta-coordinate heme in the deoxygenated form. The structure is analyzed in comparison with those of Drosophila melanogaster Hb, exhibiting a hexa-coordinate heme in its deoxygenated derivative, and of Chironomus thummi thummi HbIII, which displays a penta-coordinate heme in the deoxygenated form. Despite evident structural differences in the heme distal pockets, the distinct molecular mechanisms regulating O 2 binding to the three insect Hbs result in similar O 2 affinities (P 50 values ranging between 0.12 torr and 0.46 torr).

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confidence: 58%

Modulation of oxygen binding to insect hemoglobins: The structure of hemoglobin from the botfly Gasterophilus intestinalis

et al. 2005

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“…In a biological cell an amino-acyl tRNA synthetase (AARS) enzyme activates ATP and a cognate AA to form an amino acid AMP complex, charges the cognate tRNA with AA at the latter's C-terminal end and releases the AMP, then releases the charged or aminoacyl tRNA [10]. tRNA superspecificity [11] means an error rate of about 1 in 250 without error correction and 1 in 10000 with error correction [12].…”

Section: Stage 1: Charging Of Trna With An Amino Acid (Aa)mentioning

confidence: 99%

“…Here 20 is the number of standard AAs, and 61 the number of coding triplets in the genetic code. 'Wobble' in the third position [10] does not matter as only one tRNA type is used in each of the 1 to N cycles. With N = 20, the minimum number of cycles required is 1, the maximum 20, and the average 10.…”

Section: Stage 1: Charging Of Trna With An Amino Acid (Aa)mentioning

confidence: 99%

“…In in vivo translation the AA attached to a tRNA is effectively identified for attachment to a growing peptide when the anticodon in the amino-acyl tRNA binds with a codon in an mRNA by Chargaff base pairing [10]. There is no strict counterpart in the present case, so an ad hoc approach is used.…”

Section: Stage 2 Amino Acid Identification Based On Current Blockadementioning

confidence: 99%

“…Here a method of identifying free amino acid molecules is proposed and simulated in part. It combines nanopore-based measurements with chemical reactions that resemble those in the in vivo mRNA-to-protein translation process [10]. At its center is the superspecificity property of tRNAs: a tRNA molecule is almost always charged with its cognate amino acid [11].…”

Section: Introductionmentioning

confidence: 99%

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Label-free amino acid identification forde novoprotein sequencing via tRNA charging and current blockade in a nanopore

Sampath¹

2020

Preprint

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Label-free identification of amino acids (AAs) based on superspecific transfer RNAs (tRNAs) and amino-acyl tRNA synthetase (AARS) is explored. Molecules of a specific AA, a tRNA and its cognate AARS, and adenosine triphosphate (ATP) from a reservoir are confined to a micro-sized cavity by hydraulic pressure to counter the effects of diffusion. In this confined space a cognate tRNA in the cavity gets charged with AA and adenosine monophosphate (AMP) is released. The products are transferred to an electrolytic cell with a nanopore where AA, AMP, and ATP cause current blockades of different sizes. If an AMP-sized blockade occurs it means that a tRNA molecule has been charged with AA, this identifies AA; otherwise the procedure is repeated with a different tRNA and AARS until AA is identified. Unlike in most other nanopore-based methods, there is no need for precise measurement of current blockade levels. The efficacy of the procedure is assessed by simulating the movement of particles in a reservoir-cavity structure and analyzing the blockades that occur in the nanopore. In the former the probability of reactants escaping the cavity is found to be near 0. In the latter the probability of an error in identifying an AMP blockade is found to be less than 10% in the worst case (which occurs with the largest volume AA, namely Tryptophan). Detailed information and data are provided in a Supplementary File.

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C hironomus

Cited by 2 publications

References 27 publications

Modulation of oxygen binding to insect hemoglobins: The structure of hemoglobin from the botfly Gasterophilus intestinalis

Modulation of oxygen binding to insect hemoglobins: The structure of hemoglobin from the botfly Gasterophilus intestinalis

Label-free amino acid identification forde novoprotein sequencing via tRNA charging and current blockade in a nanopore

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