Tight-binding "dihedral orbitals" approach to the degree of folding of macromolecular chains.
We develop a tight-binding molecular approach to quantify the degree of folding of a macromolecular chain. This approach is based on the linear combination of "dihedral" orbitals to give molecular orbitals (LCDO-MO). The dihedral orbitals are a set of orbitals situated in each dihedral angle of the chain. The LCDO-MO approach remains basically topological, and we display its direct relation to known graph theoretical concepts. Using this approach, we define the dihedral electronic energy and the dihedral electronic partition function of a linear macromolecular chain. We show that the partition function per dihedral angle quantifies the degree of folding of the dihedral graph. We analyze the empirical relationship between these two functions by using a series of 100 proteins. We also study the relation between these two functions and the percentages of secondary structure for these proteins. Finally, we illustrate the use of the dihedral energy and the partition function in structure-property studies of proteins by analyzing the binding of steroids to DB3 antibody.
Estrada
Ernesto
E
Complex Systems Research Group, X-rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain. estrada66@yahoo.com
D008958:Models, Molecular; D008968:Molecular Conformation