Dynamics of the Neuropeptide Met-Enkephalin by Using Action-Derived Molecular Dynamics

The brain neuropeptide Met-enkephalin, well known for its pain inhibition activities in the brain, is one of the most important biomolecules. It is composed of five amino acids with the sequence Tyr-Gly-Gly-Phe-Met. The folding dynamics of Met-enkephalin is investigated with all-atom resolution by using action-derived molecular dynamics. The AMBER all-atom force field and the GB/SA solvation potential implemented in the TINKER molecular design package are used to represent the Met-enkephalin with all-atom resolution. With only the inputs of the initial (extended) and the final (ground-state) conformations, the unknown dynamic pathways between the two given conformations of Met-enkephalin have been successfully obtained by using action-derived molecular dynamics. Also, the method of principal component analysis is introduced to analyze the dynamic pathways of Met-enkephalin in detail.