title: Thermodynamic description of Beta amyloid formation using physicochemical scales and fractal bioinformatic scales.
abstract: 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 economically from the aa sequences alone for the small (40,42 aa) plaque-forming (aggregative) amyloid beta fragments. Some edge and center features of the fragments are predicted. Bioinformatic scales based on β strand formation propensities and the thermodynamically second order fractal hydropathicity scale based on evolutionary optimization (self-organized criticality) are contrasted with the standard first order physicochemical scale based on complete protein (water-air) unfolding. The results are consistent with previous studies of these physicochemical factors that show that aggregative properties, even of beta fragments, are driven primarily by near-equilibrium hydropathic forces.
authors.affiliation: Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, United States.
authors.forename: J C
authors.initials: JC
authors.lastname: Phillips
mesh_terms: D000595:Amino Acid Sequence; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D055598:Chemical Phenomena; D019295:Computational Biology; D017709:Fractals; D006801:Humans; D008958:Models, Molecular; D017433:Protein Structure, Secondary / Q000502:physiology*; D013816:Thermodynamics
chemical_list: D016229:Amyloid beta-Peptides
keywords: Protein; amino acid; criticality; evolutionary; function; self-organized; sequence