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If the protein is modeled with details about ProteinDomains, it is also possible to specify that the protein itself is cleaved. If the protein is modeled with details about ../ProteinDomains, it is also possible to specify that the protein itself is cleaved.
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Shared ../MimEditorUseCaseComments

Use Case Name : ../ShowCleavage

For Feature : MIM Editor

Editors: DavidKane

TableOfContents([2])

Summary

A user wants to describe the possibility that a covalent bond can be cleaved.

Step-by-Step User Action

  1. User specifies a covalent bond that is to be cleaved
  2. User specifies a species that acts to cleave the bond
  3. User specifies that there is a cleaving relationship between the two
  4. User optionally specifies the evidence for this relationship

Visual Aides

The Kohn notation for this binding is the following. The species that is cleaving the bond is on end of the edge. The other end of the edge goes across the bond that is being cleaved.

attachment:cleavage1_061115_dwk.png

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

Requirements for Cytoscape

This could be modeled as a hyperedge containing node1: Phtase (hyperedge attribute: enzyme), node2: phosphorylated A, node3: unphosphorylated A. The mapping might be different if it is a protein that is being cleaved. View: Use case for hyperedge view. Might require a new line type in Vizmapper.

Importance

This is important because it is a fairly common activity in the maps. In addition, it is an example of a reversal of another reaction.

Variations

If the protein is modeled with details about ../ProteinDomains, it is also possible to specify that the protein itself is cleaved.

attachment:cleavage2_061115_dwk.png

Other Examples

Comments

Shared ../MimEditorUseCaseComments

The BioPAX representation of this binding could be a Biochemical Reaction object (e.g. Biochemical Reaction object with Interaction-Type = "de-phosphorylation", Participants = AP,A,P, Left = AP, and Right = A,P, where A, AP and B are physicalEntities.)

PageComment2

Molecular_Interaction_Maps/ShowCleavage (last edited 2009-02-12 01:03:51 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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