The programming and simulation of a topological model of protein folding begun last year has produced new insights into the role of hydrophobicity in the formation of protein secondary structure and the packing of the central core of the protein. In the topological model of a protein, hydrophilic interactions are represented as link between positive polarizable atoms (amide nitrogen and positive counter ions) and negative polarizable atoms (carbonyl oxygen, hydroxyl and negative counter ions). The hydrophobic interactions are represented as link between the non- polarizable atoms. An ordering of the hydro-phobicity of each amino acid is based on the number of free electrons and is represented as a discrete number of edges. The conjunction of one hydrophobic edge and two hydrophilic edges was used to catalyze the exchange and movement of the edges. Using this and similar exchange operators, the simulation of protein folding produced helices in the structure of the test protein TIM (Triose Phosphate Isomerase) but would not produce the beta sheets nor the correct packing of the hydrophobic core of the protein. Many produce the beta sheets nor the correct packing of the hydrophobic core of the protein. Many variations of this basic model as well as many parametric variations were tried but none produced significant results. A new computer graphic representation of a protein with the topology of a circle was developed and was then applied to structures from the simulations as well as the x-ray crystal structure. In TIM the number of hydrophobic edges outweigh the number of hydrophilic edges by 6 to 1. In making a series of the circle graphics for each length of the protein crystal structure as it would be synthesized by the ribosome, it became clear that the hydrophobic interactions totally dominate protein folding. The distribution of hydrophobic edges is modulated as a function of protein length thus providing a coherent pattern which directs folding. The circle graphic was applied to other classes of protein architectures producing different but similar coherent modulation of hydrophobicity. Using the hydrophobic and hydrophilic edges derived from the crystal structure as constraints, the distance geometry program DGEOM re- synthesized the 3-dimensional structure of TIM to within 2 angstroms. The simulation program is being modified in an attempt to generate the same pattern of hydrophobic edge position modulation.
