Glycoengineering

---
name: glycoengineering
description: Analyze and engineer protein glycosylation. Scan sequences for canonical N-glycosylation sequons (N-X-S/T with X not proline, including overlapping sites), predict O-GalNAc hotspots, read glycan notation, and reach the curated external tooling (NetNGlyc, NetOGlyc, GlycoShield, GlycoWorkbench, GlyTouCan, GlyConnect). Use this skill for therapeutic antibody glycoengineering and afucosylation for ADCC, Fc glycan control, glycan shielding in vaccine immunogen design, sequon removal or insertion, and half-life engineering through sialylation. Also trigger on N-glycosylation, sequon, NXS/NXT, O-glycosylation, glycoform heterogeneity, afucosylation, high-mannose, GlyTouCan, or WURCS.
license: MIT
compatibility: Requires Python 3.10+. The bundled sequon and notation analysis is standard library only. Optional extras — pandas and requests for the database lookups, glycoshield for ensemble modelling. The external predictors (NetNGlyc, NetOGlyc) are DTU web services requiring manual submission and, for some, an academic licence; there is no public REST API.
allowed-tools: Read Write Edit Bash
metadata:
  version: "1.2"
  skill-author: Kuan-lin Huang
---

# Glycoengineering

## Overview

Glycosylation is the most common and complex post-translational modification (PTM) of proteins, affecting over 50% of all human proteins. Glycans regulate protein folding, stability, immune recognition, receptor interactions, and pharmacokinetics of therapeutic proteins. Glycoengineering involves rational modification of glycosylation patterns for improved therapeutic efficacy, stability, or immune evasion.

**Two major glycosylation types:**
- **N-glycosylation**: Attached to asparagine (N) in the sequon N-X-[S/T] where X ≠ Proline; occurs in the ER/Golgi
- **O-glycosylation**: Attached to serine (S) or threonine (T); no strict consensus motif; primarily GalNAc initiation

## When to Use This Skill

Use this skill when:

- **Antibody engineering**: Optimize Fc glycosylation for enhanced ADCC, CDC, or reduced immunogenicity
- **Therapeutic protein design**: Identify glycosylation sites that affect half-life, stability, or immunogenicity
- **Vaccine antigen design**: Engineer glycan shields to focus immune responses on conserved epitopes
- **Biosimilar characterization**: Compare glycan patterns between reference and biosimilar
- **Drug target analysis**: Does glycosylation affect target engagement for a receptor?
- **Protein stability**: N-glycans often stabilize proteins; identify sites for stabilizing mutations

## N-Glycosylation Sequon Analysis

### Scanning for N-Glycosylation Sites

N-glycosylation occurs at the sequon **N-X-[S/T]** where X ≠ Proline.

```python
import re
from typing import List, Tuple

def find_n_glycosylation_sequons(sequence: str) -> List[dict]:
    """
    Scan a protein sequence for canonical N-linked glycosylation sequons.
    Motif: N-X-[S/T], where X ≠ Proline.

    Args:
        sequence: Single-letter amino acid sequence

    Returns:
        List of dicts with position (1-based), motif, and context
    """
    seq = sequence.upper()
    results = []
    # Step by one, not by three. Sequons overlap: in NNTS both N1 (NNT) and
    # N2 (NTS) are glycosylation sites, and advancing past a match would
    # silently drop the second one -- a missed liability, reported as clean.
    for i in range(len(seq) - 2):
        triplet = seq[i:i+3]
        if triplet[0] == 'N' and triplet[1] != 'P' and triplet[2] in {'S', 'T'}:
            results.append({
                'position': i + 1,   # 1-based, the asparagine
                'motif': triplet,
                'context': seq[max(0, i-3):i+6],  # ±3 residue context
                'sequon_type': 'NXS' if triplet[2] == 'S' else 'NXT'
            })
    return results

def summarize_glycosylation_sites(sequence: str, protein_name: str = "") -> str:
    """Generate a research log summary of N-glycosylation sites."""
    sequons = find_n_glycosylation_sequons(sequence)

    lines = [f"# N-Glycosylation Sequon Analysis: {protein_name or 'Protein'}"]
    lines.append(f"Sequence length: {len(sequence)}")
    lines.append(f"Total N-glycosylation sequons: {len(sequons)}")

    if sequons:
        lines.append(f"\nN-X-S sites: {sum(1 for s in sequons if s['sequon_type'] == 'NXS')}")
        lines.append(f"N-X-T sites: {sum(1 for s in sequons if s['sequon_type'] == 'NXT')}")
        lines.append(f"\nSite details:")
        for s in sequons:
            lines.append(f"  Position {s['position']}: {s['motif']} (context: ...{s['context']}...)")
    else:
        lines.append("No canonical N-glycosylation sequons detected.")

    return "\n".join(lines)

# Example: IgG1 Fc region
fc_sequence = "APELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"
print(summarize_glycosylation_sites(fc_sequence, "IgG1 Fc"))
```

### Mutating N-Glycosylation Sites

```python
def eliminate_glycosite(sequence: str, position: int, replacement: str = "Q") -> str:
    """
    Eliminate an N-glycosylation site by substituting Asn → Gln (conservative).

    Args:
        sequence: Protein sequence
        position: 1-based position of the Asn to mutate
        replacement: Amino acid to substitute (default Q = Gln; similar size, not glycosylated)

    Returns:
        Mutated sequence
    """
    seq = list(sequence.upper())
    idx = position - 1
    assert seq[idx] == 'N', f"Position {position} is '{seq[idx]}', not 'N'"
    seq[idx] = replacement.upper()
    return ''.join(seq)

def add_glycosite(sequence: str, position: int, flanking_context: str = "S") -> str:
    """
    Introduce an N-glycosylation site by mutating a residue to Asn,
    and ensuring X ≠ Pro and +2 = S/T.

    Args:
        position: 1-based position to introduce Asn
        flanking_context: 'S' or 'T' at position+2 (if modification needed)
    """
    seq = list(sequence.upper())
    idx = position - 1

    # Mutate to Asn
    seq[idx] = 'N'

    # Ensure X+1 != Pro (mutate to Ala if needed)
    if idx + 1 < len(seq) and seq[idx + 1] == 'P':
        seq[idx + 1] = 'A'

    # Ensure X+2 = S or T
    if idx + 2 < len(seq) and seq[idx + 2] not in ('S', 'T'):
        seq[idx + 2] = flanking_context

    return ''.join(seq)
```

## O-Glycosylation Analysis

### Heuristic O-Glycosylation Hotspot Prediction

```python
def predict_o_glycosylation_hotspots(
    sequence: str,
    window: int = 7,
    min_st_fraction: float = 0.4,
    disallow_proline_next: bool = True
) -> List[dict]:
    """
    Heuristic O-glycosylation hotspot scoring based on local S/T density.
    Not a substitute for NetOGlyc; use as fast baseline.

    Rules:
    - O-GalNAc glycosylation clusters on Ser/Thr-rich segments
    - Flag Ser/Thr residues in windows enriched for S/T
    - Avoid S/T immediately followed by Pro (TP/SP motifs inhibit GalNAc-T)

    Args:
        window: Odd window size for local S/T density
        min_st_fraction: Minimum fraction of S/T in window to flag site
    """
    if window % 2 == 0:
        window = 7
    seq = sequence.upper()
    half = window // 2
    candidates = []

    for i, aa in enumerate(seq):
        if aa not in ('S', 'T'):
            continue
        if disallow_proline_next and i + 1 < len(seq) and seq[i+1] == 'P':
            continue

        start = max(0, i - half)
        end = min(len(seq), i + half + 1)
        segment = seq[start:end]
        st_count = sum(1 for c in segment if c in ('S', 'T'))
        frac = st_count / len(segment)

        if frac >= min_st_fraction:
            candidates.append({
                'position': i + 1,
                'residue': aa,
                'st_fraction': round(frac, 3),
                'window': f"{start+1}-{end}",
                'segment': segment
            })

    return candidates
```

## External Glycoengineering Tools

### 1. NetOGlyc 4.0 (O-glycosylation prediction)

Web service for high-accuracy O-GalNAc site prediction:
- **URL**: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/
- **Input**: FASTA protein sequence
- **Output**: Per-residue O-glycosylation probability scores
- **Method**: Neural network trained on experimentally verified O-GalNAc sites

```python
import requests

def submit_netoglycv4(fasta_sequence: str) -> str:
    """
    Submit sequence to NetOGlyc 4.0 web service.
    Returns the job URL for result retrieval.

    Note: This uses the DTU Health Tech web service. Results take ~1-5 min.
    """
    url = "https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi"
    # NetOGlyc submission (parameters may vary with web service version)
    # Recommend using the web interface directly for most use cases
    print("Submit sequence at: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/")
    return url

# Also: NetNGlyc for N-glycosylation prediction
# URL: https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/
```

### 2. GlycoShield-MD (Glycan Shielding Analysis)

GlycoShield-MD analyzes how glycans shield protein surfaces during MD simulations:
- **URL**: https://gitlab.mpcdf.mpg.de/dioscuri-biophysics/glycoshield-md/
- **Use**: Map glycan shielding on protein surface over MD trajectory
- **Output**: Per-residue shielding fraction, visualization

```bash
# Installation
uv pip install glycoshield

# Basic usage: analyze glycan shielding from glycosylated protein MD trajectory
glycoshield \
    --topology glycoprotein.pdb \
    --trajectory glycoprotein.xtc \
    --glycan_resnames BGLCNA FUC \
    --output shielding_analysis/
```

### 3. GlycoWorkbench (Glycan Structure Drawing/Analysis)

- **URL**: https://www.eurocarbdb.org/project/glycoworkbench
- **Use**: Draw glycan structures, calculate masses, annotate MS spectra
- **Format**: GlycoCT, IUPAC condensed glycan notation

### 4. GlyConnect (Glycan-Protein Database)

- **URL**: https://glyconnect.expasy.org/
- **Use**: Find experimentally verified glycoproteins and glycosylation sites
- **Query**: By protein (UniProt ID), glycan structure, or tissue

```python
import requests

def query_glyconnect(uniprot_id: str) -> dict:
    """Query GlyConnect for glycosylation data for a protein."""
    url = f"https://glyconnect.expasy.org/api/proteins/uniprot/{uniprot_id}"
    response = requests.get(url, headers={"Accept": "application/json"})
    if response.status_code == 200:
        return response.json()
    return {}

# Example: query EGFR glycosylation
egfr_glyco = query_glyconnect("P00533")
```

### 5. UniCarbKB (Glycan Structure Database)

- **URL**: https://unicarbkb.org/
- **Use**: Browse glycan structures, search by mass or composition
- **Format**: GlycoCT or IUPAC notation

## Key Glycoengineering Strategies

### For Therapeutic Antibodies

| Goal | Strategy | Notes |
|------|----------|-------|
| Enhance ADCC | Defucosylation at Fc Asn297 | Afucosylated IgG1 has ~50× better FcγRIIIa binding |
| Reduce immunogenicity | Remove non-human glycans | Eliminate α-Gal, NGNA epitopes |
| Improve PK half-life | Sialylation | Sialylated glycans extend half-life |
| Reduce inflammation | Hypersialylation | IVIG anti-inflammatory mechanism |
| Create glycan shield | Add N-glycosites to surface | Masks vulnerable epitopes (vaccine design) |

### Common Mutations Used

| Mutation | Effect |
|----------|--------|
| N297A/Q (IgG1) | Removes Fc glycosylation (aglycosyl) |
| N297D (IgG1) | Removes Fc glycosylation |
| S298A/E333A/K334A | Increases FcγRIIIa binding |
| F243L (IgG1) | Increases defucosylation |
| T299A | Removes Fc glycosylation |

## Glycan Notation

### IUPAC Condensed Notation (Monosaccharide abbreviations)

| Symbol | Full Name | Type |
|--------|-----------|------|
| Glc | Glucose | Hexose |
| GlcNAc | N-Acetylglucosamine | HexNAc |
| Man | Mannose | Hexose |
| Gal | Galactose | Hexose |
| Fuc | Fucose | Deoxyhexose |
| Neu5Ac | N-Acetylneuraminic acid (Sialic acid) | Sialic acid |
| GalNAc | N-Acetylgalactosamine | HexNAc |

### Complex N-Glycan Structure

```
Typical complex biantennary N-glycan:
Neu5Ac-Gal-GlcNAc-Man\
                       Man-GlcNAc-GlcNAc-[Asn]
Neu5Ac-Gal-GlcNAc-Man/
(±Core Fuc at innermost GlcNAc)
```

## Best Practices

- **Start with NetNGlyc/NetOGlyc** for computational prediction before experimental validation
- **Verify with mass spectrometry**: Glycoproteomics (Byonic, Mascot) for site-specific glycan profiling
- **Consider site context**: Not all predicted sequons are actually glycosylated (accessibility, cell type, protein conformation)
- **For antibodies**: Fc N297 glycan is critical — always characterize this site first
- **Use GlyConnect** to check if your protein of interest has experimentally verified glycosylation data

## Composing with the rest of the bundle

- `antibody-engineering` → before: **an N-glycosylation sequon inside a CDR is a developability
  liability, not a feature.** Its liability scanner flags them with region weighting; come here to
  decide whether to remove the sequon or keep it.
- `esm` / `protein-binder-design` → after: scan any designed or generated sequence. Design tools
  introduce sequons without noticing, and the glycan then blocks the interface you designed.
- `uniprot-rcsb` → before: the canonical sequence, plus UniProt's own CARBOHYD annotations, which
  tell you which sequons are actually occupied rather than merely present.
- `immunogenicity` → alongside: glycan shielding and T-cell epitope exposure are the same surface
  argued from two directions.
- `molecular-dynamics` → after: GlycoShield-style ensembles are what turn a sequon list into an
  actual picture of what the glycan covers.

**A sequon is necessary, not sufficient.** Occupancy depends on local structure and expression
system; roughly a third of predicted sequons are unoccupied. Report predicted sites as predicted.

## Resources

Read [references/glycan_databases.md](references/glycan_databases.md) when you need to look a
structure up rather than scan a sequence — GlyTouCan accessions, GlyConnect site-specific data,
UniCarbKB, the notation formats (GlycoCT, WURCS, IUPAC) and worked lookup code.

## Additional Resources

- **GlyTouCan** (glycan structure repository): https://glytoucan.org/
- **GlyConnect**: https://glyconnect.expasy.org/
- **CFG Functional Glycomics**: http://www.functionalglycomics.org/
- **DTU Health Tech servers** (NetNGlyc, NetOGlyc): https://services.healthtech.dtu.dk/
- **GlycoWorkbench**: https://www.eurocarbdb.org/project/glycoworkbench
- **Review**: Apweiler R, Hermjakob H, Sharon N (1999) *On the frequency of protein glycosylation,
  as deduced from analysis of the SWISS-PROT database*. Biochim Biophys Acta. PMID: 10580125
- **Therapeutic glycoengineering review**: Jefferis R (2009) *Glycosylation as a strategy to improve
  antibody-based therapeutics*. Nature Reviews Drug Discovery. PMID: 19247305