The Structural Stability of Alpha-Helix Determined by the Preference of Amino Acids

To accomplish their functions, proteins have to achieve different conformations accompanied by conformational transitions. However, the relationship between the preference of amino acids and the stability of the secondary structure is still unclear. Here we perform molecular simulations on a series of helical structures. Our data show that the dissociation energy of the helical structure is related to the preference of amino acids, and the electrostatic repulsion of the residue $i$ and $i+3/4$ with the same sign of charge destabilizes the alpha helix.