From: Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring
 | Results | Predictions for further research |
---|---|---|
1. | Attribute clusters can be grouped into a hierarchical cluster tree composed of branches, nodes, and modules | Cluster trees may reveal details of folding constraints and other functionality relationships |
2. | Within modules, two types of branches were found: (i) Type I; independent/non-interlacing with other branches and (ii) Type II; interlacing with other branches | The relationship between Types I and II branches may indicate constraints in the folding, tertiary structure and functionality of protein molecules |
3. | Attribute clusters with highest SR(mode) values were most commonly third- and fourth-order (3 to 4 associated sites) | Support for the next largest building block in proteins above single amino acids is typically a 3 to 4 amino acid structural unit |
4. | Three types of attribute clusters were found: (i) H-bonded clusters, (ii) Van der Waals clusters, and (iii) extended clusters | Identifying attribute clusters may support possibility of predicting protein tertiary structural relationships involving H-bonds, van der Waals interactions, or multiple site effects |
5. | Representative clusters found in ubiquitin confirm that the statistical criterion used can identify structural constraints such as bonding, binding and recognition sites (Table 2) | Can be used to locate key sub-molecular components of a protein, as well as components critical for the function of that protein |
6. | Ubiquitin molecule found to be composed of four major modules | Consistent with the four major areas of chemical shift perturbations between Ub1 and Ub2 |