One of the most interesting questions in biophysics is how protein sequences determine their unique three-dimensional structure. Previous studies reported that the residues at C-terminal can have effects on the protein folding behaviors. Since a large protein is highly complex, for simplicity, in this study we use MP-B (14 amino acids) and its analogues in 30% TFE-d3 aqueous solution as a model system. By using circular dichroism (CD) and NMR methods, we can get insight into how the C-terminal segment may influence the folding behavior of proteins. Spectra of CD indicated that our peptides may form α-helical conformations in 30%TFE. Oligomerization and thermal stability of peptides were investigated by performing diffusional experiments with variable temperatures. The antimicrobial activity of MP-B1-13, MP-B and MP-BL15, is ordered as MP-B > MP-BL15 > MP-B1-13. 100 of structures of different kind foldings were calculated with NMR data to investigate the effects of C-terminal segment on folding. Our results suggested that while the disordered residues at C-terminal can’t provide enough motional entropy, the helical N-terminal may be partially unfolded to increase the entropy. When peptides have more stable structure and oligomeric state, they may have greater antimicrobial activity. The results implied the disordered C-terminal residues may play a critical role for the structure and activity of a peptide. The knowledge is especially important while a peptide segment is designed or truncated for studies of structure and function.