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chapman by n7fHPn0

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									                 An analysis of
pdb-care (PDB CArbohydrate REsidue check): a
  program to support annotation of complex
     carbohydrate structures in PDB files
               by Thomas Lütteke
            and Claus-W von der Lieth



               By David Chapman
Background
   Protein Data Bank includes 3-D data for
    carbohydrate structures as well as amino acid
    structures
   3-D data for protein / carbohydrate interactions is
    analyzed through X-Ray crytallography and
    Nuclear Magnetic Resonance
      The absence of 3-D glycan data in PDB does
       not necessarily mean a potential glycosolation
       site is unoccupied
Background
  The crytallography may have been done on
   plasmid replicated proteins, which may not
   have the same carbohydrates attached as the
   human form.
  Glycosylation usually occurs at asparagine
   residues in Asn-X-Ser/Thr sequons where X
   does not equal proline
  Approximately 30% of all 1663 PDB entries
   (Sep 2003) containing carbohydrates contain
   errors in glycan description
Biological Significance
   Protein / Carbohydrate interactions are
    important because they are involved in a
    variety of biological processes
      Fertilization

      Embryonic development

      Cellular differentiation
Background
   High error rate in PDB glycan description is mainly due to
    incorrect assignment of saccharide units
      Sequences for complex carbohydrates differ

       significantly from single letter amino acid sequences
      The number of naturally occurring residues is much

       larger for carbohydrates
      Each pair of monosaccharide residues can be linked in

       several ways
      A residue can be connected to three or four others
       (branching)
Background
 Unlike amino acids, carbohydrates use a
  three letter code which are defined the HET
  dictionary in PDB
 A new residue name is required for each
  stereochemically different sugar unit
 This makes the correct assignment
  complicated, tedious and error prone
Background
    Examples of Definitions of carbohydrate
     residues:
       AGC       alpha-D-Glucopyranose
       BGC       beta -D-Glucopyranose
       FCA       alpha-D-Fucose
       FCB       beta-D-Fucose

    There are more than 200 carbohydrate residues
     used in PDB
Implementation
   Pdb-care is based on the pdb2linucs carbohydrate detection
    program
      Pdb2linucs is able to identify and assign carbohydrate

        structures using only the reported atom types and their
        3D coordinates
      The program output is in LINUCS notation and is used
        to normalize complex carbohydrate structures
   Pdb-care uses a translation table built in XML in order to
    compare the LINUCS notation from pdb2linucs to the
    residue assignments in the PDB group dictionary
Implementation
 The translation table contains:
    141 monosaccharides

    31 oligosaccharides

    77 combined residues

 Pdb-care was written in the C language
 Front end is a web interface implemented in
  PHP
Implementation
 Pdb-care web interface can accommodate
  either direct input using copy/paste of a pdb
  file or locating a file on a local hard drive or
  using a PDB-ID
 The pdb-care protocol reports the type of
  problems, inconsistencies and errors
  detected
Program Example
   pdb-care examples
Conclusion
   The authors made relevant points regarding the
    biological significance of protein-carbohydrate
    interactions and the need for accurate glycan
    residue information in PDB.
   However, the authors did not go into detail
    regarding the actual implementation of the
    translation table used in pdb-care so it is difficult
    to judge the accuracy of their program.

								
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