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Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed

Author(s):

Robbie P. Joosten, Robert A. Nicholls and Jon Agirre*   Pages 1 - 15 ( 15 )

Abstract:


Macromolecular restrained refinement is nowadays the most used method for improving the agreement between an atomic structural model and experimental data. Restraint dictionaries, a key tool behind the success of the method, allow fine-tuning geometric properties such as distances and angles between atoms beyond simplistic expectations. Dictionary generators can provide restraint target estimates derived from different sources, from fully theoretical to experimental and any combination in between. Carbohydrates are stereochemically complex biomolecules and, in their pyranose form, have clear conformational preferences. As such, they pose unique problems to dictionary generators and in the course of this study, require special attention from software developers. Functional differences between restraint generators will be discussed, as well as the process of achieving consistent results with different software designs. The study will conclude a set of practical considerations, as well as recommendations for the generation of new restraint dictionaries, using the improved software alternatives discussed.

Keywords:

Geometry restraints, ring conformation, pyranose, structural biology, dictionaries, refinement.

Affiliation:

Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD



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