The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy
The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala−Ala−Thr*, in which Thr* is a glycosylated threonine with the disaccharide <i>beta-<span style="font-variant: small-caps;"&g...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-06-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/9/6/235 |
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| author | Cheenou Her Yin Yeh Viswanathan V. Krishnan |
| author_facet | Cheenou Her Yin Yeh Viswanathan V. Krishnan |
| author_sort | Cheenou Her |
| collection | DOAJ |
| description | The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala−Ala−Thr*, in which Thr* is a glycosylated threonine with the disaccharide <i>beta-<span style="font-variant: small-caps;">d</span>-galactosyl-(1,3)-alpha-N-acetyl-<span style="font-variant: small-caps;">d</span>-galactosamine.</i> AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod <i>Boreogadus</i> <i>saida</i> and the Antarctic notothenioid <i>Trematomus</i> <i>borchgrevinki</i>. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala−Thr*−Pro−Ala and Ala−Thr*−Ala−Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth. |
| first_indexed | 2024-12-11T22:51:22Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-12-11T22:51:22Z |
| publishDate | 2019-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-04b09a0252354b67819ec74f54fc12742022-12-22T00:47:25ZengMDPI AGBiomolecules2218-273X2019-06-019623510.3390/biom9060235biom9060235The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance SpectroscopyCheenou Her0Yin Yeh1Viswanathan V. Krishnan2Department of Chemistry, California State University, Fresno, CA 93740, USADepartment of Applied Science, University of California, Davis, CA 95616, USADepartment of Chemistry, California State University, Fresno, CA 93740, USAThe primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala−Ala−Thr*, in which Thr* is a glycosylated threonine with the disaccharide <i>beta-<span style="font-variant: small-caps;">d</span>-galactosyl-(1,3)-alpha-N-acetyl-<span style="font-variant: small-caps;">d</span>-galactosamine.</i> AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod <i>Boreogadus</i> <i>saida</i> and the Antarctic notothenioid <i>Trematomus</i> <i>borchgrevinki</i>. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala−Thr*−Pro−Ala and Ala−Thr*−Ala−Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.https://www.mdpi.com/2218-273X/9/6/235AFGPNMRensemble of structuresantifreeze proteins |
| spellingShingle | Cheenou Her Yin Yeh Viswanathan V. Krishnan The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy Biomolecules AFGP NMR ensemble of structures antifreeze proteins |
| title | The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy |
| title_full | The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy |
| title_fullStr | The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy |
| title_full_unstemmed | The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy |
| title_short | The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy |
| title_sort | ensemble of conformations of antifreeze glycoproteins afgp8 a study using nuclear magnetic resonance spectroscopy |
| topic | AFGP NMR ensemble of structures antifreeze proteins |
| url | https://www.mdpi.com/2218-273X/9/6/235 |
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