Breaking the Protein Amino Acid Code (aka the Code of Life)

Jim Phillips
Rutgers University

Monolayer water films mediate interactions between proteins that determine 
protein functionality.  Conventional molecular dynamics simulations view 
protein-water interactions in terms of "flickering" hydrogen bonds, 
parameterized by force fields with multiple adjustable parameters and 
simplistic interatomic force fields adjusted to fit dry crystallized 
protein structures.  Following Pauling (and his electronegativity scale) 
and myself (the dielectric ionicity scale for semiconductors), I examine 
several universal hydrophobicity scales, and identify the best one.  With 
this scale one can recognize phantom water-protein interactions that are 
invisible to conventional analysis, and analyze protein functionality, 
as illustrated by several examples of proteins containing 300+ amino acid 
side groups.