Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Prediction of protein function based on its surface properties
Prediction of functions by surface properties
Hydrophobic surface

One of the primary goals of structural Genomics projects is to expand the universe of known protein folds, specifically to determine the structures of Proteins with unknown Functions or those of significant medical importance. For proteins of unknown function, target Selection is often driven by the absence of significant Homology to proteins with established functions, as this approach holds the potential for discovering novel fold types. The main Structure-based Methods for protein function prediction involve comparing local sequence or Structural motifs. This topic is discussed in detail in Chapters 8 and 11. There are also similar approaches based solely on protein Surface Conservation rather than its entire structure; these are examined below in the same order as the Surface Properties described in Section 7.2.

Extensive patches of hydrophobic surface are inherently unstable and uncharacteristic of protein–protein interfaces in non-obligate complexes, whose individual components must be capable of stable independent existence in Water. Early methods for predicting protein interaction interfaces relied on identifying hydrophobic regions on the protein surface (Lijnzaad et al. 1996). However, these methods were typically applied to predict obligate interfaces, such as those found in oligomeric complexes. At the same time, this issue is somewhat artificial, since obligate interfaces form during the protein folding process, making their prediction inherently different from that of non-obligate interfaces. Furthermore, non-obligate interfaces exhibit greater Hydrophobicity compared to the overall protein surface, a feature frequently exploited in predicting the structures of protein–Protein Complexes from individual monomers (Berchanski et al. 2004).