|Breaking the Protein Amino Acid Code (aka the Code of Life) |
Physics and Astronomy
|Jim Phillips, Rutgers University|
4:45 PM, Physics lecture Hall
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.