Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion
Highly accurate protein structure prediction can generate accurate models of protein and protein–protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the...
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| Format: | Article |
| Language: | English |
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International Union of Crystallography
2024-03-01
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| Series: | IUCrJ |
| Subjects: | |
| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S2052252523010291 |
| _version_ | 1797271850769711104 |
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| author | Zengru Li Haifu Fan Wei Ding |
| author_facet | Zengru Li Haifu Fan Wei Ding |
| author_sort | Zengru Li |
| collection | DOAJ |
| description | Highly accurate protein structure prediction can generate accurate models of protein and protein–protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases. Following this strategy, full-length models or the conservative structural domains could be used directly as the starting model, and the phase error and the model bias between the starting model and the real structure would be modified in the direct-methods-based dual-space iteration. Many challenging cases (from CASP14) have been tested for the general applicability of this constructive strategy, and almost complete models have been generated with reasonable statistics. The hybrid strategy therefore provides a meaningful scheme for X-ray structure determination using a predicted model as the starting point. |
| first_indexed | 2024-03-07T14:16:07Z |
| format | Article |
| id | doaj.art-ff256dfa89a9497c908801f129be7b66 |
| institution | Directory Open Access Journal |
| issn | 2052-2525 |
| language | English |
| last_indexed | 2024-03-07T14:16:07Z |
| publishDate | 2024-03-01 |
| publisher | International Union of Crystallography |
| record_format | Article |
| series | IUCrJ |
| spelling | doaj.art-ff256dfa89a9497c908801f129be7b662024-03-06T12:41:13ZengInternational Union of CrystallographyIUCrJ2052-25252024-03-0111215216710.1107/S2052252523010291lz5066Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completionZengru Li0Haifu Fan1Wei Ding2Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of ChinaBeijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of ChinaBeijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of ChinaHighly accurate protein structure prediction can generate accurate models of protein and protein–protein complexes in X-ray crystallography. However, the question of how to make more effective use of predicted models for completing structure analysis, and which strategies should be employed for the more challenging cases such as multi-helical structures, multimeric structures and extremely large structures, both in the model preparation and in the completion steps, remains open for discussion. In this paper, a new strategy is proposed based on the framework of direct methods and dual-space iteration, which can greatly simplify the pre-processing steps of predicted models both in normal and in challenging cases. Following this strategy, full-length models or the conservative structural domains could be used directly as the starting model, and the phase error and the model bias between the starting model and the real structure would be modified in the direct-methods-based dual-space iteration. Many challenging cases (from CASP14) have been tested for the general applicability of this constructive strategy, and almost complete models have been generated with reasonable statistics. The hybrid strategy therefore provides a meaningful scheme for X-ray structure determination using a predicted model as the starting point.http://scripts.iucr.org/cgi-bin/paper?S2052252523010291ipcasalphafoldmolecular replacementdirect-methods-aided model completionphasingprotein structures |
| spellingShingle | Zengru Li Haifu Fan Wei Ding Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion IUCrJ ipcas alphafold molecular replacement direct-methods-aided model completion phasing protein structures |
| title | Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion |
| title_full | Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion |
| title_fullStr | Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion |
| title_full_unstemmed | Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion |
| title_short | Solving protein structures by combining structure prediction, molecular replacement and direct-methods-aided model completion |
| title_sort | solving protein structures by combining structure prediction molecular replacement and direct methods aided model completion |
| topic | ipcas alphafold molecular replacement direct-methods-aided model completion phasing protein structures |
| url | http://scripts.iucr.org/cgi-bin/paper?S2052252523010291 |
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