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

Prediction of Protein Function from Surface Properties
Protein-Protein Interface
Hot Spots in Protein Interfaces

It has been shown that mutating specific interface residues to Alanine (a technique known as alanine-scanning mutagenesis) has a significantly greater impact on complex stability than mutating other protein interface residues (Clackson and Wells 1995). The most critical Amino Acids, referred to as “hot spot” residues, tend to cluster deep within pockets on the protein surface (Bogan and Thom 1998). The surrounding areas of these pockets are lined with amino acids of moderate importance. The majority of hot spots identified in this manner are cataloged in the ASEdb database (Thom and Bogan 2001). Analysis of these residues suggests that hot spots are most frequently large and aromatic (such as Tryptophan or Tyrosine) or positively charged arginines (though notably not lysines). Conversely, hot spots are much less likely to be small amphiphilic residues (Serine, Threonine) or hydrophobic ones (valine, leucine) (Bogan and Thom 1998).

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Fig. 7.6. The surface of DNase I (shown in white, PDB code 1ATN) in complex with Actin (not shown), displaying all pockets predicted by the Q-SiteFinder program (gray/black). Pockets shaded in black correspond to those occupied by actin atoms

Analysis of interface pockets suggests that The most significant distinction between these pockets and those found across the rest of the protein is that the former undergo desolvation much more readily (Burgoyne and Jackson 2006). The authors employed the Q-SiteFinder pocket detection software (Section 7.4.2.3, Fig. 7.6) to map all surface pockets, which were subsequently ranked based on various Surface Properties.

Ranking by desolvation energy proves to be the most successful method for clearly distinguishing interface pockets from other protein pockets. In terms of desolvation ease, aromatic and aliphatic surfaces outperform polar surfaces and, more importantly, charged surfaces, which are the least favorable for desolvation. This implies that hot spots likely serve to facilitate desolvation upon binding or to expel Water from the pockets. Although it might seem counterintuitive to include Arginine among hot spots—given that its charge should make it difficult to desolvate—its guanidino group is substantially easier to desolvate than the amino group of Lysine when a positively charged residue is required for interface recognition. It has also been suggested that a hydrophobic environment can lower the effective dielectric constant around critical Hydrogen Bonds, thereby strengthening the interaction (Bogan and Thom 1998). Furthermore, hot spots often represent some of the most evolutionarily conserved residues within a protein family (Ma et al. 2003); however, this conservation typically becomes apparent only through Multiple Sequence Alignments where the interacting Proteins are interlogs (interlogs being interacting proteins whose homologs in other species are also capable of interacting).