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

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.