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Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
Published on: October 2, 2017
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Tools to assist determination and validation of carbohydrate 3D structure data
Paul Emsley1, Axel T Brunger, Thomas Lütteke
1MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2015
Summary
Glycoprotein 3D structures are underrepresented in the Protein Data Bank due to software limitations. This work reviews tools for improving carbohydrate structure determination and validation in crystallography.
Area of Science:
- Structural Biology
- Biochemistry
- Computational Chemistry
Background:
- Glycoproteins are abundant in nature, yet their 3D structures are underrepresented in the Protein Data Bank (PDB).
- Existing glycan 3D structures in the PDB often contain significant errors.
- Limited software support for carbohydrates hinders accurate structure determination and validation.
Purpose of the Study:
- To highlight current software features aiding crystallographers in handling glycans.
- To improve the accuracy of glycoprotein 3D structure determination and validation.
- To address the underrepresentation of accurate glycan structures in structural databases.
Main Methods:
- Review of features within Coot for glycan handling during 3D structure determination.
- Examination of CNS capabilities for carbohydrate structure refinement.
- Analysis of validation tools for assessing glycan 3D structure quality.
Main Results:
- Coot and CNS offer specific functionalities to assist with glycan incorporation and refinement.
- Current validation tools can identify and help correct errors in glycan conformations.
- Improved software support can lead to more accurate and complete glycoprotein structures.
Conclusions:
- Enhanced software support in tools like Coot and CNS is crucial for accurate glycoprotein structure determination.
- Addressing software limitations will improve the quality and quantity of glycan 3D structures in the PDB.
- This work provides a guide for crystallographers to better handle and validate carbohydrate structures.
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