Illustrated Example Of How An Ensemble Of Structures Is Analysed - Application To Troponin C (1TNW)

The analysis is performed in 3 stages: (i) definition of the core atoms, (ii) definition of the rigid body(ies) (domains) in which these lie, and (iii) definition of conformationally-related sub-families.

Domain Definition

Firstly, the core atoms were identified. These are coloured magenta and green in the animation below. The two rigid bodies (domains) which comprise the core were then identified.

Selected Models of Troponin C, coloured according to domains identified by NMRCORE. This animation shows superposition on all atoms, followed by the N-terminal domain, followed by the C-terminal domain. ______ N-terminal Domain ______ C-terminal Domain ______ Flexible Linker

It can be seen above that Troponin C clearly consists of two distinct domains which are not simultaneously superposable. NMRCORE has determined the colouring shown above.

Clustering

Once NMRCORE had determined that the C-terminal domain was the largest, all structures were superposed on this domain, and the structures clustered into families by NMRCLUST. To the left, four clusters can be seen coloured as follows: ______ Largest Cluster ______ 2nd Cluster ______ 3rd Cluster ______ Smallest Cluster

Single Representative Structure

The structure closest to the centroid of the largest (red) cluster is then selected as the most representative model in the ensemble, in this case Model 13.