  Protein function depends on both protein structure and amino acid (aa)
sequence. Here we show that modular features of both structure and function can
be quantified from the aa sequence alone for the amyloid 770 aa precursor
protein A4. Both the new second order hydropathicity scale, based on
evolutionary optimization (self-organized criticality), and the standard first
order scale, based on complete protein (water-air) unfolding, yield
thermodynamically significant features of amyloid function related to spinodal
decomposition into modules. Spinodal crossings are marked by breaks in slope of
algebraic functions of aa sequences. The new scale is associated with a lower
effective temperature than the standard scale.
