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

TY - JOUR

T1 - Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures

AU - Holland, Lou

AU - Pham, Phuong Thao

AU - Bagdonas, Haroldas

AU - Dialpuri, Jordan S

AU - Schofield, Lucy C

AU - Agirre, Jon

N1 - © 2025 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

PY - 2025/1/22

Y1 - 2025/1/22

N2 - Tryptophan mannosylation, the covalent addition of an α-ᴅ-mannose sugar to a tryptophan side chain, is a post-translational modification (PTM) that can affect protein stability, folding, and interactions. Compared to other forms of protein glycosylation, it is relatively uncommon but is affected by conformational anomalies and modeling errors similar to those seen in N- and O-glycans in the Protein Data Bank (PDB). In this work, we report methods for detecting, building, and improving mannose structures linked to tryptophans. These methods have been used to mine X-ray crystallographic and cryo-electron microscopy maps in the PDB looking for unmodeled mannosylation, resulting in a number of cases where the modification can be placed in the map with high confidence. Additionally, we address most conformational issues affecting this modification. Finally, the development of a structural template to recognize thrombospondin repeats (TSR) domains where tryptophan mannosylation occurs will allow for the mannosylation of candidate-predicted models, for example, those predicted with AlphaFold.

AB - Tryptophan mannosylation, the covalent addition of an α-ᴅ-mannose sugar to a tryptophan side chain, is a post-translational modification (PTM) that can affect protein stability, folding, and interactions. Compared to other forms of protein glycosylation, it is relatively uncommon but is affected by conformational anomalies and modeling errors similar to those seen in N- and O-glycans in the Protein Data Bank (PDB). In this work, we report methods for detecting, building, and improving mannose structures linked to tryptophans. These methods have been used to mine X-ray crystallographic and cryo-electron microscopy maps in the PDB looking for unmodeled mannosylation, resulting in a number of cases where the modification can be placed in the map with high confidence. Additionally, we address most conformational issues affecting this modification. Finally, the development of a structural template to recognize thrombospondin repeats (TSR) domains where tryptophan mannosylation occurs will allow for the mannosylation of candidate-predicted models, for example, those predicted with AlphaFold.

KW - Tryptophan/chemistry

KW - Glycoproteins/chemistry

KW - Mannose/chemistry

KW - Models, Molecular

KW - Glycosylation

KW - Crystallography, X-Ray

KW - Protein Processing, Post-Translational

KW - Protein Conformation

KW - Databases, Protein

KW - Cryoelectron Microscopy

U2 - 10.1002/pro.70025

DO - 10.1002/pro.70025

M3 - Article

C2 - 39840780

SN - 0961-8368

VL - 34

JO - Protein science : a publication of the Protein Society

JF - Protein science : a publication of the Protein Society

IS - 2

M1 - e70025

ER -