Molecular_Interaction_Maps/CovalentBinding

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Summary

A user wants to describe the possibility that a small molecule is covalently bound to large molecule or another small molecule.

Step-by-Step User Action

1. User specifies a protein to be involved in the interaction
2. User specifies the molecule to be bound
3. User specifies that protein to be covalently bound to the protein
4. User optionally specifies the evidence for this reaction

Visual Aides

The Kohn notation for this reaction is the following:

An example showing the binding of a phosphate to a protein follows:

The color in this example is convention, and is not an essential element in the notation.

Requirements for Cytoscape

A is a node (representing unmodified protein); central dot is a node (representing phosphorylated A) - every state is represented as a node. The PTM e.g. P is not a node, it is an annotation on the 'central' state node. The edge between A and its state is of type 'state of'. The set of all states is grouped to represent the set of all states of A. View: Constraint: the states always move together (would be like a template).

Binding two small molecules might have a different representation.

Importance

Binding of small molecules is a basic reaction that occurs in most maps using Kohn notation.

Variations

Common molecules that are used include:

• Ac: Acetyl
• Me: Methyl
• OH: Hydroxy
• P: Phosphate
• Ub: Ubiquitin

If the protein in the covalently bound state is 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)

Unlike proteins, which appear only once on a particular map, for small molecules a copy of the icon appears each time it is involved in a reaction.

In the past, a different notation for covalent binding was used. The current notation better communicates the notion that the bond is symmetrical. This legacy notation does not need to be supported:

Other Examples

Comments

Shared ../MimEditorUseCaseComments

The BioPAX representation of this reaction could be a Biochemical Reaction object (e.g. Biochemical Reaction object with Interaction-Type = "phosphorylation", Participants = AP,A,P, Left = A,P, and Right = AP, where A, AP and P are physicalEntities. Binding two small molecules might have a different representation.

AllanKuchinsky - 2007-01-27 14:22:11

From the 2006 Cytoscape Retreat notes: Model: In the cases above, A is a node (representing unmodified protein); central dot is a node (represented modified A) - every state is represented as a node. The PTM e.g. P is not a node, it is an annotation on the 'central' state node. The edge between A and its state is of type 'state of'. The set of all states is grouped to represent the set of all states of A. View: Constraint: the states always move together (would be like a template)