Carbohydrate structure:: the rocky road to automation

Jon Agirre; Gideon J. Davies; Keith S. Wilson; Kevin D. Cowtan

doi:10.1016/j.sbi.2016.10.010

Carbohydrate structure: the rocky road to automation

Jon Agirre, Gideon J. Davies, Keith S. Wilson, Kevin D. Cowtan

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to ‘protein standards’ will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.

Original language	English
Pages (from-to)	39-47
Number of pages	9
Journal	CURRENT OPINION IN STRUCTURAL BIOLOGY
Volume	44
Early online date	9 Dec 2016
DOIs	https://doi.org/10.1016/j.sbi.2016.10.010 https://doi.org/10.1016/j.sbi.2016.11.011
Publication status	Published - 2017

Bibliographical note

© 2016 Elsevier Ltd. All rights reserved. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.

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© 2016 Elsevier Ltd. All rights reserved. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.
Accepted author manuscript, 260 KBLicence: CC BY-NC-ND

Cite this

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title = "Carbohydrate structure:: the rocky road to automation",

abstract = "With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to {\textquoteleft}protein standards{\textquoteright} will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most.",

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Carbohydrate structure: the rocky road to automation

Abstract

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