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Stranding and Looping

CSEF · 2005 Chemistry

Vasilios A. Morikis · Polytechnic High School, Riverside

Overview

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.

Help received

Father suggested the project and introduced me in molecular mechanics. Part of this work was performed at the University of California, Riverside under the supervision of Dr. Dimitrios Morikis. Mother helped me in gluing the project.

Competition history

  • CSEF 2005 Chemistry · Entry S0599

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