Stranding and Looping
Objectives/Goals:
I will test the hypothesis that nature prefers strands and helices in building
biomolecules. I will also test if
strands and helices are more stable structures than extended conformations.
Methods/Materials:
I used a computer to make model peptides with repeating pentapeptide blocks of
the type of [AAAAA](n)
and [DAAAK](n), where n is the number of blocks; n=1-4. I modeled extended,
strand, and helical
structures. I measured and compared the stabilities of the peptides with and
without energy minimization.
I used the programs Insight II, IsisDraw, and DeepView.
Results:
Examination of the potential energies, showed that helix is in general the most
stable conformation,
followed by strand, whereas the least stable is the extended conformation. As
more amino acid blocks
were added the gaps in the stabilities of helices, strands, and extended
conformations become larger.
Conclusions/Discussion:
Analysis of the individual potential energy terms for bond, angle, torsion, van
der Waals, and electrostatic
contributions, showed that the van der Waals term contributed the most to the
increase in stability and to a
lesser extend the electrostatic term. The [DAAAK](n) peptides were more stable
than the [AAAAA](n)
peptides, because of the formation of favorable anion-cation interaction between
D, an acid, and K, a
base.
Summary Statement:
My project demonstrated that helices and strands are the preferred conformations
for arranging amino
acids in biomolecules.
