Current Status of Carbohydrates Information in the Protein Data Bank

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Abstract
Carbohydrates are well known for their physico-chemical, biological, functional and therapeutic characteristics. Unfortunately, their chemical nature impose severe chal- lenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates, but also the development of new biotechno- logical and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has in- creased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available on the Protein Data Bank. From high quality structures, it is clear that most of the data is highly concentrated on a few set of residue types, on their monosaccharidic forms and connected by a small di- versity of glycosidic linkages. The geometries of these linkages can be mostly associated to the types of linkages instead of residues, while the level of puckering distortion was characterized, quantified and located in a pseudorotational equilibrium landscape - not only to local minima, but also to transitional states. These qualitative and quantitative analyses offer a global picture of carbohydrate structural content on PDB, potentially supporting the building of new models for carbohydrate related biological phenomena at the atomistic level, including new developments on force field parameters.
Funding Information
  • Fundaci?n S?neca (19948/IV/15)
  • Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico
  • Funda??o de Amparo ? Pesquisa do Estado do Rio Grande do Sul
  • Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (23038.007777/2014-87)

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