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Table 3 Overview of experimental results and predictions

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