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Match Residues Added by an Enzyme

match_enzyme.Rd

This function finds residues in glycans that match the product motifs of a glycosyltransferase and returns their node indices.

Usage

match_enzyme(glycans, enzyme, method = c("motif", "path"))

Arguments

glycans

A glyrepr::glycan_structure() vector.

enzyme

A glycosyltransferase enzyme() or a gene symbol for one. Glycoside hydrolases are not supported.

method

Method used to decide whether the enzyme is involved. "motif" matches product motifs directly in each glycan. "path" matches substrates and products from trace_biosynthesis() results back to each glycan, which is more accurate but slower.

Value

A list of integer vectors with the same length as glycans. Each integer vector contains node indices for residues added by enzyme in the corresponding glycan.

Important notes

Here are some important notes for all functions in the glyenzy package.

Applicability

All algorithms and enzyme information in glyenzy are applicable only to humans, and specifically to N-glycans and O-GalNAc glycans. Results may be inaccurate for other types of glycans (e.g., GAGs, glycolipids) or for glycans in other species (e.g., plants, insects).

Inclusiveness

The algorithm takes an intentionally inclusive approach, assuming that all possible isoenzymes capable of catalyzing a given reaction may be involved. Therefore, results should be interpreted with caution.

For example, in humans, detection of the motif "Neu5Ac(a2-3)Gal(b1-" will return both "ST3GAL3" and "ST3GAL4". In reality, only one of them might be active, depending on factors such as tissue specificity.

Only "concrete" glycans

The function only works for glycans containing concrete residues (e.g., "Glc", "GalNAc"), and not for glycans with generic residues (e.g., "Hex", "HexNAc").

Substituents

Substituents (e.g. sulfation, phosphorylation) are not supported yet, and the algorithms might fail for glycans with substituents. If your glycans contain substituents, use glyrepr::remove_substituents() to get clean glycans.

Incomplete glycan structures

If the glycan structure is incomplete or partially degraded, the result may be misleading.

Starting points

  • For N-glycans, the starting structure is assumed to be "Glc(3)Man(9)GlcNAc(2)", the N-glycan precursor transferred to Asn by OST.

  • For O-GalNAc glycans, the starting structure is assumed to be "GalNAc(a1-".

  • For O-GlcNAc glycans, the starting structure is assumed to be "GlcNAc(b1-".

  • For O-Man glycans, the starting structure is assumed to be "Man(a1-".

  • For O-Fuc glycans, the starting structure is assumed to be "Fuc(a1-".

  • For O-Glc glycans, the starting structure is assumed to be "Glc(b1-".

Examples

glycan <- glyrepr::as_glycan_structure("Neu5Ac(a2-3)Gal(b1-3)GlcNAc(b1-")
match_enzyme(glycan, "ST3GAL3")
#> [[1]]
#> [1] 1
#> 
match_enzyme(glycan, "ST3GAL3", method = "path")
#> [[1]]
#> [1] 1
#>