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Updated: May 31, 2025

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Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures.

Lou Holland1, Phuong Thao Pham1, Haroldas Bagdonas1

  • 1York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.

Protein Science : a Publication of the Protein Society
|January 22, 2025
PubMed
Summary

This study introduces methods to detect and model tryptophan mannosylation, a rare protein modification. These techniques improve the accuracy of structural data for this post-translational modification (PTM) in protein databases.

Keywords:
C‐glycanscarbohydratesmodel buildingvalidation

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Glycobiology

Background:

  • Tryptophan mannosylation is a post-translational modification (PTM) involving the addition of mannose to tryptophan.
  • This modification, though uncommon, impacts protein stability, folding, and interactions.
  • Similar to N- and O-glycans, tryptophan mannosylation is susceptible to conformational anomalies and modeling errors in structural databases.

Purpose of the Study:

  • To develop and report methods for detecting, building, and refining mannose structures attached to tryptophans.
  • To identify instances of unmodeled tryptophan mannosylation in existing structural data.
  • To address and resolve conformational issues associated with this PTM.

Main Methods:

  • Development of novel computational methods for identifying and modeling mannose on tryptophan residues.
  • Mining of X-ray crystallography and cryo-electron microscopy (cryo-EM) data from the Protein Data Bank (PDB).
  • Creation of a structural template to recognize thrombospondin repeats (TSR) domains associated with tryptophan mannosylation.

Main Results:

  • Successful identification of several cases of high-confidence tryptophan mannosylation in PDB structural maps.
  • Resolution of common conformational problems encountered with this modification.
  • Establishment of a template enabling the prediction and modeling of mannosylation in protein structures, including those from AlphaFold.

Conclusions:

  • The developed methods enhance the accurate representation of tryptophan mannosylation in structural biology.
  • This work facilitates the discovery and correct modeling of this PTM in various protein contexts.
  • The findings contribute to a better understanding of protein structure and function influenced by glycosylation.