Determining the Structure of a Cytoplasmic Polyadenylation Element Binding Protein via AMBER9

The neurons of \textit{Aplysia californica }contain cytoplasmic polyadenylation element binding protein (CPEB). CPEB shows prion-like properties when expressed in yeast cells. Because prions have misfolded and normally folded forms, prions can code in neurons like binary codes in computers, with ``present'' and ``not present'' signals available. CPEB thus provides a candidate protein for the molecular basis of memory. I attempt to determine CPEB's structure, by first threading the known protein sequence around a $\beta $-helical structure. Threading is preformed by hand, and by a program written to minimize the energy cost of building the structure. I then analyze the stability of the thread using the molecular dynamics program AMBER9. I also analyze a protein of only glutamine (PolyQ) in a $\beta $-helical structure to substantiate my use of a $\beta $-helix with the glutamine-rich CPEB. I found PolyQ to be stable in a left-handed $\beta $-helical structure with eighteen residues per turn. A candidate structure for CPEB was located with the same $\beta $-helical structure.