In addition, it facilitates the discovery of regions such as the C-terminal area that displays weak secondary structure propensities but no disorder propensity, and disordered flanks that have a propensity for alpha-helical conformation.
Panel F shows that there is very little conservation of secondary structure propensity, while Panel G shows there is a strong tendency to have very hydrophobic residues on the interior surface (cyan color).
SSP (secondary structure propensity) is a method developed by Forman-Kay and co-workers to determine the residue-specific secondary structure propensity of IDPs based on their measured chemical shifts (49).
Current knowledge of protein folding identifies properties of complexity, secondary structure propensity, hydrophobic hydrophilic patterning, core-packing potential, among others, as necessary elements of foldability.
The parameters considered in pcSM are a C-alpha Euclidean metric, secondary structural propensity, surface areas and an intramolecular energy function.
We support that the folded three-dimensional (3D) structure is the Aβ Aβ interacting species, that the whole sequence is involved in that 3D fold which has a low secondary structure propensity and a high susceptibility to mutations and thus should have a low stability.
Consensus secondary structure propensity was determined based on SSPro [34], Jpred [35], GOR IV, SOPMA and HNN [36].
For example, for the secondary structure propensity, each amino acid can be classified as: helix, strand or coil, as predicted by SSpro [35].
Our results suggest that KEGG enrichment scores, subcellular locations, polarity, amino acids composition, hydrophobicity, secondary structure propensity, and number of protein complexes, play irreplaceable roles for protein's metabolic stability.
With the feature selection approach based on the mRMR method and IFS procedure, we found that the following seven features would play the major roles in determining the stability of proteins: KEGG enrichment scores, subcellular locations, polarity, amino acids composition, hydrophobicity, secondary structure propensity, and the number of protein complexes.
