Native monellin, an intensely sweet protein from a tropical plant, consists of two chains, A and B chains. The crystal structure of native monellin has been solved at low resolution. Single chain monellin, PS1 has been produced by genetic method. We have done 100 ps molecular dynamics studies of the two chain protein in order to obtain initial coordinates for the B-A fused monellin, PS1. Fifteen sets of coordinates from the dynamics trajectory were picked. Two chains were connected by a peptide bond and minimized each. One of fifteen minimized PS1 contains cis-peptide in the fusion loop. In addition, loop search to find the protein fragments from the well-defined structures which fit the C alpha atomic positions of nearby beta-strands results in several fragments containing cis-Pro. The informations from the present studies are useful in designing the fusion loop of monellin to increase the themostability.