Tandem domain structure determination based on a systematic enumeration of conformations
Abstract Protein structure determination is undergoing a change of perspective due to the larger importance taken in biology by the disordered regions of biomolecules. In such cases, the convergence criterion is more difficult to set up and the size of the conformational space is a obstacle to exhau...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-96370-z |
| _version_ | 1831631713792425984 |
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| author | Thérèse E. Malliavin |
| author_facet | Thérèse E. Malliavin |
| author_sort | Thérèse E. Malliavin |
| collection | DOAJ |
| description | Abstract Protein structure determination is undergoing a change of perspective due to the larger importance taken in biology by the disordered regions of biomolecules. In such cases, the convergence criterion is more difficult to set up and the size of the conformational space is a obstacle to exhaustive exploration. A pipeline is proposed here to exhaustively sample protein conformations using backbone angle limits obtained by nuclear magnetic resonance (NMR), and then to determine the populations of conformations. The pipeline is applied to a tandem domain of the protein whirlin. An original approach, derived from a reformulation of the Distance Geometry Problem is used to enumerate the conformations of the linker connecting the two domains. Specifically designed procedure then permit to assemble the domains to the linker conformations and to optimize the tandem domain conformations with respect to two sets of NMR measurements: residual dipolar couplings and paramagnetic resonance enhancements. The relative populations of optimized conformations are finally determined by fitting small angle X-ray scattering (SAXS) data. The most populated conformation of the tandem domain is a semi-closed one, fully closed and more extended conformations being in minority, in agreement with previous observations. The SAXS and NMR data show different influences on the determination of populations. |
| first_indexed | 2024-12-19T05:05:51Z |
| format | Article |
| id | doaj.art-5b859c69229b48e990be57a652283d2d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T05:05:51Z |
| publishDate | 2021-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-5b859c69229b48e990be57a652283d2d2022-12-21T20:34:57ZengNature PortfolioScientific Reports2045-23222021-08-0111111210.1038/s41598-021-96370-zTandem domain structure determination based on a systematic enumeration of conformationsThérèse E. Malliavin0Unité de Bioinformatique Structurale, Institut Pasteur, UMR 3528, CNRSAbstract Protein structure determination is undergoing a change of perspective due to the larger importance taken in biology by the disordered regions of biomolecules. In such cases, the convergence criterion is more difficult to set up and the size of the conformational space is a obstacle to exhaustive exploration. A pipeline is proposed here to exhaustively sample protein conformations using backbone angle limits obtained by nuclear magnetic resonance (NMR), and then to determine the populations of conformations. The pipeline is applied to a tandem domain of the protein whirlin. An original approach, derived from a reformulation of the Distance Geometry Problem is used to enumerate the conformations of the linker connecting the two domains. Specifically designed procedure then permit to assemble the domains to the linker conformations and to optimize the tandem domain conformations with respect to two sets of NMR measurements: residual dipolar couplings and paramagnetic resonance enhancements. The relative populations of optimized conformations are finally determined by fitting small angle X-ray scattering (SAXS) data. The most populated conformation of the tandem domain is a semi-closed one, fully closed and more extended conformations being in minority, in agreement with previous observations. The SAXS and NMR data show different influences on the determination of populations.https://doi.org/10.1038/s41598-021-96370-z |
| spellingShingle | Thérèse E. Malliavin Tandem domain structure determination based on a systematic enumeration of conformations Scientific Reports |
| title | Tandem domain structure determination based on a systematic enumeration of conformations |
| title_full | Tandem domain structure determination based on a systematic enumeration of conformations |
| title_fullStr | Tandem domain structure determination based on a systematic enumeration of conformations |
| title_full_unstemmed | Tandem domain structure determination based on a systematic enumeration of conformations |
| title_short | Tandem domain structure determination based on a systematic enumeration of conformations |
| title_sort | tandem domain structure determination based on a systematic enumeration of conformations |
| url | https://doi.org/10.1038/s41598-021-96370-z |
| work_keys_str_mv | AT thereseemalliavin tandemdomainstructuredeterminationbasedonasystematicenumerationofconformations |