(Logo) Domains in Proteins

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Ca-Ca distances between secondary structures are represented in the form of average values termed 'proximity indices' and the secondary structural organisation is indicated in the form of dendrograms. An example is shown for the case of calmodulin.

18Kb GIF

Download the calmodulin structure from your nearest PDB mirror: 3cln (111Kb) [Bbk|BNL|ExP|Waw|Hal]

Then use this script to render the structure as above, illustrating the domains. (If you require help with using these scripts, click here.)

Specific nodes in these dendrograms are identified as tertiary structural clusters of the protein; these include supersecondary structures and domains. A ratio of the average proximity indices (ignoring inter-clusteral distances) to the average of all proximity indices, weighted for the aggregation of small sub-clusters and termed the disjoint factor, is employed as a discriminatory parameter to identify automatically clusters representing individual domains. An example of domains identified in glutathione reducatase is shown below :

59Kb GIF

Download the glutathione reducatase structure from the PDB: 3grs (354Kb) [Bbk|BNL|ExP|Waw|Hal] ...SCRIPT

The domains identified by this clustering method may not correspond to the functional domains proposed.

The "disjoint factor" gives a measure of the extent of interaction between domains and has been used to classify domains into one of the three types, disjoint, interacting and conjoint. Domains are classified as those with sparse inter-domain interfaces (disjoint), intermediate interactions (interacting) and elaborate interfaces (conjoint) based on the magnitude of the disjoint factor. An example of the three types is shown below :

44Kb GIF

Download the three structures in the diagram above, and use the scripts to highlight the domains:

1pfk (461Kb) [Bbk|BNL|ExP|Waw|Hal] ...SCRIPT

2phh (285Kb) [Bbk|BNL|ExP|Waw|Hal] ...SCRIPT (domain boundaries for 1pbe in Protein Domain Database)

3rp2 (310Kb) [Bbk|BNL|ExP|Waw|Hal] ...SCRIPT (see Sowdhamini and Blundell, 1995 for domain boundaries)

R. Sowdhamini
RasMolized by J. Walshaw
IndexIndex to Course Material IndexIndex to Section 10 BackIdentification NextDomain Movements

Last updated 13th Jun '96