Published on Sep 28, 2024
The objective: 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.
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.
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.
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.
The project demonstrated that helices and strands are the preferred conformations for arranging amino acids in biomolecules.