Reversible trifluoroacetic acid-induced conformational changes in glycophorin as detected by proton nuclear magnetic resonance spectroscopy

Cramer, John A.; Marchesi, V.; Armitage, Ian M.

doi:10.1016/0005-2736(80)90086-3

Cited by 15 publications

(14 citation statements)

References 15 publications

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“…In a previous study of micro-transcriptome analysis, 1,218 miRNAs were identified in flounder [ 31 ]. In the present study, all the 1,218 miRNAs were predicted to be the targets of DElncRNAs.…”

Section: Resultsmentioning

confidence: 99%

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Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

Ning

Sun

2021

BMC Genomics

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Background Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important marine fish susceptible to Vibrio anguillarum infection. To date, study on lncRNAs in flounder is scarce. Results Here, we reported the first systematic identification and characterization of flounder lncRNAs induced by V. anguillarum infection at different time points. A total of 2,368 lncRNAs were identified, 414 of which were differentially expressed lncRNAs (DElncRNAs) that responded significantly to V. anguillarum infection. For these DElncRNAs, 3,990 target genes (named DETGs) and 42 target miRNAs (named DETmiRs) were identified based on integrated analyses of lncRNA-mRNA and lncRNA-miRNA expressions, respectively. The DETGs were enriched in a cohort of functional pathways associated with immunity. In addition to modulating mRNAs, 36 DElncRNAs were also found to act as competitive endogenous RNAs (ceRNAs) that regulate 37 DETGs through 16 DETmiRs. The DETmiRs, DElncRNAs, and DETGs formed ceRNA regulatory networks consisting of 114 interacting DElncRNAs-DETmiRs-DETGs trinities spanning 10 immune pathways. Conclusions This study provides a comprehensive picture of lncRNAs involved in V. anguillarum infection. The identified lncRNAs and ceRNA networks add new insights into the anti-bacterial immunity of flounder.

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Section: Resultsmentioning

confidence: 99%

“…Recently, transcriptome and micro-transcriptome analyses revealed that V . anguillarum induced the expression of a large amount immune related genes and miRNAs in Japanese flounder [ 30 , 31 ]. However, no study on flounder lncRNA has been documented.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

Ning

Sun

2021

BMC Genomics

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“…A ]3C-NMR spectrum of the sample indicated that even though the carbohydrate residues appeared to have lost some intensity (broadened), the resonances at 38.1 ppm and 2.0 ppm remained intact. The only reagent which has been postulated to completely denature glycophorin A is trifluoroacetic acid [10]. Fig.2C shows a sample shown in fig.2B* which is now in TFA containing -0.5 M H202 (also 2.0 M H20).…”

Section: Resultsmentioning

confidence: 99%

“…Instead of observing a 13C spectrum of denatured glycoprotein containing well-resolved sharp resonances [16], we observe a 'washed-out' spectrum which probably results from glycophorin A which is in a high state of aggregation. It is known that urea, a common denaturing agent, does not have the ability to denature glycophorin A [10,12]. After treatment of this sample for -7 days in concentrated urea, it was extensively dialyzed, then freeze-dried.…”

Section: Methodsmentioning

confidence: 99%

“…Isolated glycophorin A in aqueous solution is known to aggregate [9][10][11] and it has been postulated that the site of aggregation involves the hy-*To whom correspondence should be addressed Abbreviations: 13C-NMR, carbon-13 nuclear magnetic resonance spectroscopy; TFA, trifluoroacetic acid: H202, hydrogen peroxide; IH-NMR, proton magnetic resonance spectroscopy; a-D-NeuAc, a-D-N-acetylneuraminic acid drophobic portion of the molecule (residues 71-92) [9]. Moreover, it is also known that modification of Met-81 affects the extent of glycophorin A aggregation [12].…”

Section: Introductionmentioning

confidence: 99%

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Preferential sulfoxidation of the methionine residues of glycophorin A

Hardy

Dill

1982

FEBS Letters

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Carbon-13 nuclear magnetic resonance spectroscopy was used to monitor the preferential sulfoxidation of the two methionine residues (8 and 81) of glycophorin A. In urea Met-8 is readily oxidized. However, Met-81 can only be oxidized in trifluoroacetic acid containing hydrogen peroxide. Our results also give some insight into the reagent accessibility of different portions of the protein molecule and the general stability of this glycoprotein.

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Polysaccharides

Govil¹,

Hosur²

1982

Conformation of Biological Molecules

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Reversible trifluoroacetic acid-induced conformational changes in glycophorin as detected by proton nuclear magnetic resonance spectroscopy

Cited by 15 publications

References 15 publications

Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

Preferential sulfoxidation of the methionine residues of glycophorin A

Polysaccharides

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