Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins.
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tend to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity, and we quantify this by analyzing the surface-exposure distributions of all amino acids. Lastly, we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding.
Moelbert
Susanne
S
NEC Laboratories America, Princeton, NJ 08540, USA.
Emberly
Eldon
E
Tang
Chao
C
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D040681:Structural Homology, Protein; D013499:Surface Properties
D000596:Amino Acids; D011506:Proteins