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Ogan Gurel and Prof. Wayne A. Hendrickson
6 March 1996
One of the great unsolved problems in modern biology is the protein folding problem: namely, the
prediction of the threedimensional structure of proteins from their linear amino acid sequence. Most study
in this area has focussed on secondary and tertiary structure prediction with relatively little emphasis on
quaternary structure. In general biophysical terms, it is felt that secondary structural elements such as α
helices and βsheets largely depend upon the minimization of van der Waals steric contacts while for
tertiary structure the hydrophobic effect is a major
determining factor. This work proposes that electrostatic
interactions — in particular, the intermolecular alignment of
protein subunit dipole moments — accounts for (and can
predict) the symmetry elements that define a protein’s
quaternary structure.
In this study, we focus on protein homodimers — a common
quaternary structural motif. The Protein Data Bank (PDB)
was surveyed for protein dimers and for each individual
entry, monomeric dipoles were calculated and analyzed using
the program GRASP. A highly significant number of dimers
were characterized by monomeric dipole moments that were
oriented in opposite directions implying that the twofold