glycoengineering

Name: glycoengineering
Author: K-Dense-AI

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How to install glycoengineering?

k-dense-ai/scientific-agent-skills/glycoengineering

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering

Installs into the current project.

Summary

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization,

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SKILL.md

1	# Glycoengineering
2
3	## Overview
4
5	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.
6
7	Two major glycosylation types:
8	- N-glycosylation: Attached to asparagine (N) in the sequon N-X-[S/T] where X ≠ Proline; occurs in the ER/Golgi
9	- O-glycosylation: Attached to serine (S) or threonine (T); no strict consensus motif; primarily GalNAc initiation
10
11	## When to Use This Skill
12
13	Use this skill when:
14
15	- Antibody engineering: Optimize Fc glycosylation for enhanced ADCC, CDC, or reduced immunogenicity
16	- Therapeutic protein design: Identify glycosylation sites that affect half-life, stability, or immunogenicity
17	- Vaccine antigen design: Engineer glycan shields to focus immune responses on conserved epitopes
18	- Biosimilar characterization: Compare glycan patterns between reference and biosimilar
19	- Drug target analysis: Does glycosylation affect target engagement for a receptor?
20	- Protein stability: N-glycans often stabilize proteins; identify sites for stabilizing mutations
21
22	## N-Glycosylation Sequon Analysis
23
24	### Scanning for N-Glycosylation Sites
25
26	N-glycosylation occurs at the sequon N-X-[S/T] where X ≠ Proline.
27
28	```python
29	import re
30	from typing import List, Tuple
31
32	def find_n_glycosylation_sequons(sequence: str) -> List[dict]:
33	"""
34	Scan a protein sequence for canonical N-linked glycosylation sequons.
35	Motif: N-X-[S/T], where X ≠ Proline.
36
37	Args:
38	sequence: Single-letter amino acid sequence
39
40	Returns:
41	List of dicts with position (1-based), motif, and context
42	"""
43	seq = sequence.upper()
44	results = []
45	i = 0
46	while i <= len(seq) - 3:
47	triplet = seq[i:i+3]
48	if triplet[0] == 'N' and triplet[1] != 'P' and triplet[2] in {'S', 'T'}:
49	context = seq[max(0, i-3):i+6] # ±3 residue context
50	results.append({
51	'position': i + 1, # 1-based
52	'motif': triplet,
53	'context': context,
54	'sequon_type': 'NXS' if triplet[2] == 'S' else 'NXT'
55	})
56	i += 3
57	else:
58	i += 1
59	return results
60
61	def summarize_glycosylation_sites(sequence: str, protein_name: str = "") -> str:
62	"""Generate a research log summary of N-glycosylation sites."""
63	sequons = find_n_glycosylation_sequons(sequence)
64
65	lines = [f"# N-Glycosylation Sequon Analysis: {protein_name or 'Protein'}"]
66	lines.append(f"Sequence length: {len(sequence)}")
67	lines.append(f"Total N-glycosylation sequons: {len(sequons)}")
68
69	if sequons:
70	lines.append(f"\nN-X-S sites: {sum(1 for s in sequons if s['sequon_type'] == 'NXS')}")
71	lines.append(f"N-X-T sites: {sum(1 for s in sequons if s['sequon_type'] == 'NXT')}")
72	lines.append(f"\nSite details:")
73	for s in sequons:
74	lines.append(f" Position {s['position']}: {s['motif']} (context: ...{s['context']}...)")
75	else:
76	lines.append("No canonical N-glycosylation sequons detected.")
77
78	return "\n".join(lines)
79
80	# Example: IgG1 Fc region
81	fc_sequence = "APELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"
82	print(summarize_glycosylation_sites(fc_sequence, "IgG1 Fc"))
83	```
84
85	### Mutating N-Glycosylation Sites
86
87	```python
88	def eliminate_glycosite(sequence: str, position: int, replacement: str = "Q") -> str:
89	"""
90	Eliminate an N-glycosylation site by substituting Asn → Gln (conservative).
91
92	Args:
93	sequence: Protein sequence
94	position: 1-based position of the Asn to mutate
95	replacement: Amino acid to substitute (default Q = Gln; similar size, not glycosylated)
96
97	Returns:
98	Mutated sequence
99	"""
100	seq = list(sequence.upper())
101	idx = position - 1
102	assert seq[idx] == 'N', f"Position {position} is '{seq[idx]}', not 'N'"
103	seq[idx] = replacement.upper()
104	return ''.join(seq)
105
106	def add_glycosite(sequence: str, position: int, flanking_context: str = "S") -> str:
107	"""
108	Introduce an N-glycosylation site by mutating a residue to Asn,
109	and ensuring X ≠ Pro and +2 = S/T.
110
111	Args:
112	position: 1-based p

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glycoengineering

31kstars3.1kforks

View on GitHub

How to install glycoengineering?

k-dense-ai/scientific-agent-skills/glycoengineering

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill glycoengineering

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Glycoengineering
2
3	## Overview
4
5	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.
6
7	Two major glycosylation types:
8	- N-glycosylation: Attached to asparagine (N) in the sequon N-X-[S/T] where X ≠ Proline; occurs in the ER/Golgi
9	- O-glycosylation: Attached to serine (S) or threonine (T); no strict consensus motif; primarily GalNAc initiation
10
11	## When to Use This Skill
12
13	Use this skill when:
14
15	- Antibody engineering: Optimize Fc glycosylation for enhanced ADCC, CDC, or reduced immunogenicity
16	- Therapeutic protein design: Identify glycosylation sites that affect half-life, stability, or immunogenicity
17	- Vaccine antigen design: Engineer glycan shields to focus immune responses on conserved epitopes
18	- Biosimilar characterization: Compare glycan patterns between reference and biosimilar
19	- Drug target analysis: Does glycosylation affect target engagement for a receptor?
20	- Protein stability: N-glycans often stabilize proteins; identify sites for stabilizing mutations
21
22	## N-Glycosylation Sequon Analysis
23
24	### Scanning for N-Glycosylation Sites
25
26	N-glycosylation occurs at the sequon N-X-[S/T] where X ≠ Proline.
27
28	```python
29	import re
30	from typing import List, Tuple
31
32	def find_n_glycosylation_sequons(sequence: str) -> List[dict]:
33	"""
34	Scan a protein sequence for canonical N-linked glycosylation sequons.
35	Motif: N-X-[S/T], where X ≠ Proline.
36
37	Args:
38	sequence: Single-letter amino acid sequence
39
40	Returns:
41	List of dicts with position (1-based), motif, and context
42	"""
43	seq = sequence.upper()
44	results = []
45	i = 0
46	while i <= len(seq) - 3:
47	triplet = seq[i:i+3]
48	if triplet[0] == 'N' and triplet[1] != 'P' and triplet[2] in {'S', 'T'}:
49	context = seq[max(0, i-3):i+6] # ±3 residue context
50	results.append({
51	'position': i + 1, # 1-based
52	'motif': triplet,
53	'context': context,
54	'sequon_type': 'NXS' if triplet[2] == 'S' else 'NXT'
55	})
56	i += 3
57	else:
58	i += 1
59	return results
60
61	def summarize_glycosylation_sites(sequence: str, protein_name: str = "") -> str:
62	"""Generate a research log summary of N-glycosylation sites."""
63	sequons = find_n_glycosylation_sequons(sequence)
64
65	lines = [f"# N-Glycosylation Sequon Analysis: {protein_name or 'Protein'}"]
66	lines.append(f"Sequence length: {len(sequence)}")
67	lines.append(f"Total N-glycosylation sequons: {len(sequons)}")
68
69	if sequons:
70	lines.append(f"\nN-X-S sites: {sum(1 for s in sequons if s['sequon_type'] == 'NXS')}")
71	lines.append(f"N-X-T sites: {sum(1 for s in sequons if s['sequon_type'] == 'NXT')}")
72	lines.append(f"\nSite details:")
73	for s in sequons:
74	lines.append(f" Position {s['position']}: {s['motif']} (context: ...{s['context']}...)")
75	else:
76	lines.append("No canonical N-glycosylation sequons detected.")
77
78	return "\n".join(lines)
79
80	# Example: IgG1 Fc region
81	fc_sequence = "APELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"
82	print(summarize_glycosylation_sites(fc_sequence, "IgG1 Fc"))
83	```
84
85	### Mutating N-Glycosylation Sites
86
87	```python
88	def eliminate_glycosite(sequence: str, position: int, replacement: str = "Q") -> str:
89	"""
90	Eliminate an N-glycosylation site by substituting Asn → Gln (conservative).
91
92	Args:
93	sequence: Protein sequence
94	position: 1-based position of the Asn to mutate
95	replacement: Amino acid to substitute (default Q = Gln; similar size, not glycosylated)
96
97	Returns:
98	Mutated sequence
99	"""
100	seq = list(sequence.upper())
101	idx = position - 1
102	assert seq[idx] == 'N', f"Position {position} is '{seq[idx]}', not 'N'"
103	seq[idx] = replacement.upper()
104	return ''.join(seq)
105
106	def add_glycosite(sequence: str, position: int, flanking_context: str = "S") -> str:
107	"""
108	Introduce an N-glycosylation site by mutating a residue to Asn,
109	and ensuring X ≠ Pro and +2 = S/T.
110
111	Args:
112	position: 1-based p

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