<i>ARCIMBOLDO</i>on coiled coils

Caballero, Iracema; Sammito, Massimo; Millán, Claudia; Лебедев, А. А.; Soler, Nicolas; Usón, Isabel

doi:10.1107/s2059798317017582

Cited by 44 publications

(40 citation statements)

References 71 publications

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“…ARCIMBOLDO combines the location of model fragments with Phaser (Read & McCoy, 2016) with density modification and autotracing with SHELXE (Usó n & Sheldrick, 2018) in a multisolution frame. This approach has been successful for test cases as well as for a novel protein (Rodríguez et al, 2009), for DNA-binding proteins (Prö pper et al, 2014) and for coiled coils (Caballero et al, 2018). Because this approach appears to work well at <2 Å resolution for proteins with a significant -helical content, it was applied to the 1.6 Å resolution data set.…”

Section: Resultsmentioning

confidence: 99%

Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO

et al. 2018

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Crystal structure determination requires solving the phase problem. This can be accomplished using ab initio direct methods for small molecules and macromolecules at resolutions higher than 1.2 Å, whereas macromolecular structure determination at lower resolution requires either molecular replacement using a homologous structure or experimental phases using a derivative such as covalent labeling (for example selenomethionine or mercury derivatization) or heavy-atom soaking (for example iodide ions). Here, a case is presented in which crystals were obtained from a 30.8 kDa protein sample and yielded a 1.6 Å resolution data set with a unit cell that could accommodate approximately 8 kDa of protein. Thus, it was unclear what had been crystallized. Molecular replacement with pieces of homologous proteins and attempts at iodide ion soaking failed to yield a solution. The crystals could not be reproduced. Sequence-independent molecular replacement using the structures available in the Protein Data Bank also failed to yield a solution. Ultimately, ab initio structure solution proved successful using the program ARCIMBOLDO, which identified two α-helical elements and yielded interpretable maps. The structure was the C-terminal dimerization domain of the intended target from Mycobacterium smegmatis. This structure is presented as a user-friendly test case in which an unknown protein fragment could be determined using ARCIMBOLDO.

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Section: Resultsmentioning

confidence: 99%

Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO

et al. 2018

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“…For particularly long helices, such as those present in coiled coils and at resolutions below 2 Å (Caballero et al, 2018), an alternative, more constrained helical extension is worth trying (Figs. 2b and 3b).…”

Section: Additional Constraints In Chain Tracingmentioning

confidence: 99%

“…This turns out to be a rather good indication as to whether the structure is correct; for a resolution of 2.5 Å or better, a CC value of 25% or higher makes it likely that the structure is solved. However, in the presence of translational NCS false positives with high CC values are not uncommon (Caballero et al, 2018), but the correct solution has a higher CC. The phases calculated from the trace are combined with the experimental phases to calculate the map to be traced in the next global cycle (if any).…”

Section: Preliminary Refinement Of the Tracementioning

confidence: 99%

An introduction to experimental phasing of macromolecules illustrated bySHELX; new autotracing features

Usón

Sheldrick

2018

Acta Cryst Sect D Struct Biol

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158

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For the purpose of this article, experimental phasing is understood to mean the determination of macromolecular structures by exploiting small intensity differences of Friedel opposites and possibly of reflections measured at different wavelengths or for heavy-atom derivatives, without the use of specific structural models. TheSHELXprograms provide a robust and efficient route for routine structure solution by the SAD, MAD and related methods, but involve a number of simplifying assumptions that may limit their applicability in borderline cases. The substructure atoms (i.e.those with significant anomalous scattering) are first located by direct methods, and the experimental data are then used to estimate phase shifts that are added to the substructure phases to obtain starting phases for the native reflections. These are then improved by density modification and, if the resolution of the data and the type of structure permit, polyalanine tracing. A number of extensions to the tracing algorithm are discussed; these are designed to improve its performance at low resolution. Given native data to 2.5 Å resolution or better, a correlation coefficient greater than 25% between the structure factors calculated from such a trace and the native data is usually a good indication that the structure has been solved.

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“…The use of this sophisticated approach enabled the solution of increasingly challenging structures with lower resolutions (up to 3 Å ) and larger numbers of residues in the asymmetric unit. Additionally, this approach proved to be successful in the solution of a variety of folds, including coiled coils (Caballero et al, 2018), which are notoriously difficult to solve through MR as they often suffer from different crystallographic data pathologies such as anisotropic diffraction and apparent translational noncrystallographic symmetry (Thomas et al, 2020). Targets containing as many as 600 residues have been solved in this way (Caballero et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Helical ensembles outperform ideal helices in molecular replacement

Rodríguez¹,

Simpkin²,

Davies³

et al. 2020

Acta Cryst Sect D Struct Biol

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The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the `helical ensembles' mode.

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ARCIMBOLDOon coiled coils

Cited by 44 publications

References 71 publications

Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO

Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO

An introduction to experimental phasing of macromolecules illustrated bySHELX; new autotracing features

Helical ensembles outperform ideal helices in molecular replacement

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