ArticleIUCrJ2015
Routine phasing of coiled-coil protein crystal structures with AMPLE.
Article in IUCrJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.Acta crystallographica. Section D, Structural biology · 2024Article
- ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.Protein science : a publication of the Protein Society · 2024Article
- Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Coiled-coil structure of meiosis protein TEX12 and conformational regulation by its C-terminal tip.Communications biology · 2022Article
- MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more.Acta crystallographica. Section D, Structural biology · 2022Article
- Implications of AlphaFold2 for crystallographic phasing by molecular replacement.Acta crystallographica. Section D, Structural biology · 2022Review
- Structural basis for the coiled-coil architecture of human CtIP.Open biology · 2021Article
- Phasertng: directed acyclic graphs for crystallographic phasing.Acta crystallographica. Section D, Structural biology · 2021Article
- Atypical chemoreceptor arrays accommodate high membrane curvature.Nature communications · 2020Article
- Helical ensembles outperform ideal helices in molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling.Acta crystallographica. Section D, Structural biology · 2020Article
- ALIXE: a phase-combination tool for fragment-based molecular replacement.Acta crystallographica. Section D, Structural biology · 2020Article
- Combinatorial use of disulfide bridges and native sulfur-SAD phasing for rapid structure determination of coiled-coils.Bioscience reports · 2018Article
- Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment.Acta crystallographica. Section D, Structural biology · 2018Article
- ARCIMBOLDO on coiled coils.Acta crystallographica. Section D, Structural biology · 2018Article
- Fragon: rapid high-resolution structure determination from ideal protein fragments.Acta crystallographica. Section D, Structural biology · 2018Article
- Approaches to ab initio molecular replacement of α-helical transmembrane proteins.Acta crystallographica. Section D, Structural biology · 2017Article
- Article
- Solving coiled-coil protein structures.IUCrJ · 2015Article
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6 authors.
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Abstract
Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallo-graphic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.
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