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Macromolecular ab initio phasing enforcing secondary and tertiary structure.

Millán C, Sammito M, Usón I - IUCrJ (2015)

Bottom Line: Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method.Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved.In the 2014 release, use of the program has been simplified.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Biology, Molecular Biology Institute of Barcelona , Baldiri Reixac 15, Barcelona, 08028, Spain.

ABSTRACT
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

No MeSH data available.


Related in: MedlinePlus

ARCIMBOLDO algorithm for ab initio phasing with model fragments at resolution up to 2 Å.
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fig3: ARCIMBOLDO algorithm for ab initio phasing with model fragments at resolution up to 2 Å.

Mentions: Building on the atomic resolution dual-space recycling experience, the central idea in our approach to overcome the resolution barrier and to extend the scope of ab initio phasing to resolutions up to 2 Å was to substitute atomicity constraints by the enforcement of a secondary structure. Rather than starting the phasing from a collection of atoms, secondary structure model fragments would be randomly placed and their starting position locally optimized or alternatively located with the program PHASER (McCoy et al., 2007 ▶). Instead of improving phases through the tangent formula and interpreting as atoms the maxima in the electron-density maps produced, maps would be improved by density modification techniques and the improved maps would be interpreted in terms of the main chain with the program SHELXE (Sheldrick, 2002 ▶). Main chain autotracing would in turn provide a reliable figure of merit at the proposed resolution (Sheldrick, 2010 ▶). The CC characterizing the trace is distinctly higher for correct rather than for wrong traces (Thorn & Sheldrick, 2013 ▶). Fig. 3 ▶ displays a scheme of this approach. We named the method after the 16th century painter Arcimboldo, who assembled portraits out of objects such as fruit and vegetables. Our starting hypothesis assembles partial structures out of secondary structure fragments and, if correct enough, density modification succeeds in revealing the portrait of our protein, expanding to a nearly complete structure. As most of our trials remain a ‘still life’, the method requires extensive computing. Fortunately, the calculations can be easily split into small tasks and distributed over a grid of computers or a supercomputer.


Macromolecular ab initio phasing enforcing secondary and tertiary structure.

Millán C, Sammito M, Usón I - IUCrJ (2015)

ARCIMBOLDO algorithm for ab initio phasing with model fragments at resolution up to 2 Å.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4285884&req=5

fig3: ARCIMBOLDO algorithm for ab initio phasing with model fragments at resolution up to 2 Å.
Mentions: Building on the atomic resolution dual-space recycling experience, the central idea in our approach to overcome the resolution barrier and to extend the scope of ab initio phasing to resolutions up to 2 Å was to substitute atomicity constraints by the enforcement of a secondary structure. Rather than starting the phasing from a collection of atoms, secondary structure model fragments would be randomly placed and their starting position locally optimized or alternatively located with the program PHASER (McCoy et al., 2007 ▶). Instead of improving phases through the tangent formula and interpreting as atoms the maxima in the electron-density maps produced, maps would be improved by density modification techniques and the improved maps would be interpreted in terms of the main chain with the program SHELXE (Sheldrick, 2002 ▶). Main chain autotracing would in turn provide a reliable figure of merit at the proposed resolution (Sheldrick, 2010 ▶). The CC characterizing the trace is distinctly higher for correct rather than for wrong traces (Thorn & Sheldrick, 2013 ▶). Fig. 3 ▶ displays a scheme of this approach. We named the method after the 16th century painter Arcimboldo, who assembled portraits out of objects such as fruit and vegetables. Our starting hypothesis assembles partial structures out of secondary structure fragments and, if correct enough, density modification succeeds in revealing the portrait of our protein, expanding to a nearly complete structure. As most of our trials remain a ‘still life’, the method requires extensive computing. Fortunately, the calculations can be easily split into small tasks and distributed over a grid of computers or a supercomputer.

Bottom Line: Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method.Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved.In the 2014 release, use of the program has been simplified.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Biology, Molecular Biology Institute of Barcelona , Baldiri Reixac 15, Barcelona, 08028, Spain.

ABSTRACT
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

No MeSH data available.


Related in: MedlinePlus