Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins
Abstract Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the 13C chemical shifts o...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Springer Netherlands
2021
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| Online Access: | https://hdl.handle.net/1721.1/136797 |
| _version_ | 1811089244395929600 |
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| author | Somberg, Noah H Gelenter, Martin D Hong, Mei |
| author_facet | Somberg, Noah H Gelenter, Martin D Hong, Mei |
| author_sort | Somberg, Noah H |
| collection | MIT |
| description | Abstract
Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the 13C chemical shifts of 17 amyloid proteins and 7 β-barrel membrane proteins whose high-resolution structures have been determined by NMR. These 24 proteins contain 373 β-sheet residues in amyloid fibrils and 521 β-sheet residues in β-barrel membrane proteins. The 13C chemical shifts are shown in 2D 13C–13C correlation maps, and the amino acid residues are categorized by two criteria: (1) whether they occur in β-strand segments or in loops and turns; (2) whether they are water-exposed or dry, facing other residues or lipids. We also examine the abundance of each amino acid in amyloid proteins and β-barrels and compare the sidechain rotameric populations. The 13C chemical shifts indicate that hydrophobic methyl-rich residues and aromatic residues exhibit larger static sidechain conformational disorder in amyloid fibrils than in β-barrels. In comparison, hydroxyl- and amide-containing polar residues have more ordered sidechains and more ordered backbones in amyloid fibrils than in β-barrels. These trends can be explained by steric zipper interactions between β-sheet planes in cross-β fibrils, and by the interactions of β-barrel residues with lipid and water in the membrane. These conformational trends should be useful for structural analysis of amyloid fibrils and β-barrels based principally on NMR chemical shifts. |
| first_indexed | 2024-09-23T14:16:07Z |
| format | Article |
| id | mit-1721.1/136797 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:16:07Z |
| publishDate | 2021 |
| publisher | Springer Netherlands |
| record_format | dspace |
| spelling | mit-1721.1/1367972022-04-18T04:00:54Z Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins Somberg, Noah H Gelenter, Martin D Hong, Mei Abstract Cross-β amyloid fibrils and membrane-bound β-barrels are two important classes of β-sheet proteins. To investigate whether there are systematic differences in the backbone and sidechain conformations of these two families of proteins, here we analyze the 13C chemical shifts of 17 amyloid proteins and 7 β-barrel membrane proteins whose high-resolution structures have been determined by NMR. These 24 proteins contain 373 β-sheet residues in amyloid fibrils and 521 β-sheet residues in β-barrel membrane proteins. The 13C chemical shifts are shown in 2D 13C–13C correlation maps, and the amino acid residues are categorized by two criteria: (1) whether they occur in β-strand segments or in loops and turns; (2) whether they are water-exposed or dry, facing other residues or lipids. We also examine the abundance of each amino acid in amyloid proteins and β-barrels and compare the sidechain rotameric populations. The 13C chemical shifts indicate that hydrophobic methyl-rich residues and aromatic residues exhibit larger static sidechain conformational disorder in amyloid fibrils than in β-barrels. In comparison, hydroxyl- and amide-containing polar residues have more ordered sidechains and more ordered backbones in amyloid fibrils than in β-barrels. These trends can be explained by steric zipper interactions between β-sheet planes in cross-β fibrils, and by the interactions of β-barrel residues with lipid and water in the membrane. These conformational trends should be useful for structural analysis of amyloid fibrils and β-barrels based principally on NMR chemical shifts. 2021-11-01T14:33:26Z 2021-11-01T14:33:26Z 2021-04-12 2021-05-19T03:24:00Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136797 en https://doi.org/10.1007/s10858-021-00364-y Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ The Author(s), under exclusive licence to Springer Nature B.V. application/pdf Springer Netherlands Springer Netherlands |
| spellingShingle | Somberg, Noah H Gelenter, Martin D Hong, Mei Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins |
| title | Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins |
| title_full | Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins |
| title_fullStr | Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins |
| title_full_unstemmed | Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins |
| title_short | Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins |
| title_sort | comparative analysis of 13c chemical shifts of β sheet amyloid proteins and outer membrane proteins |
| url | https://hdl.handle.net/1721.1/136797 |
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