Diff for "Molecular_Interaction_Maps/AsymmetricBinding"

TableOfContents([2])

Summary

A user wants to describe the possibility that a protein binds to another and contributes a peptide that binds to a receptor site or pocket on another protein.

Step-by-Step User Action

1. User specifies a protein to be involved in the interaction as a contributor
2. User specifies another protein to be involved in the reaction as a receptor
3. User specifies that there is an asymmetric binding reaction between the two
4. User optionally specifies the evidence for this reaction

Visual Aides

The Kohn notation for this reaction is the following:

attachment:asymmetricbinding1_061115_dwk.png

An example using this notation follows:

attachment:asymmetricbinding2_061115_dwk.png

Requirements for Cytoscape

This would be modeled similarly to a SimpleBinding, i.e. with a group, but with a specific edge type. The barbed arrow would require custom rendering.

Importance

This notation is fairly rare and is not as important as the other use cases.

Variations

If the bound proteins are used in a subsequent reaction, a dot is placed on the line, and that is used to anchor the edges for the subsequent reactions. (See CompoundBinding)

attachment:asymmetricbinding3_061115_dwk.png

Other Examples

Comments

The BioPAX representation of this binding could be a Conversion Object, i.e. with Participants = A,B, AB, Left = A,B, Right=AB, where A and B are Proteins, but AB is a complex with components A and B). It is not clear how to differentiate simple binding from asymmetric binding in BioPAX. PageComment2