Abstract: Zwitterionic polypeptides (ZIPPs) have demonstrated great protection to protein drugs owing for their anti-fouling or “stealth” properties. ZIPPs endow the target protein with better pharmacokinetics than non-zwitterionic counterparts, while the microscopic mechanism is still unclear due to the complicated conformation space. As an alternative, in the present work, we designed three pentapeptides, which share the ZIPP-repeat units VPX₁X₂G. Here, X₁ and X₂ are cationic and anionic amino acids, respectively. Glucagon-like peptide-1 (GLP-1), an important drug for type-II diabetes, was selected as a research subject, which is mixed with different types of pentapeptides. The interaction mode and conformation space were explored using molecular simulation with coarse-grained PACE (Protein in Atomistic details coupled with Coarse-grained Environment) forcefield. Our molecular simulations revealed that the initially constructed α-helix was quickly destroyed by thermal fluctuation for isolated GLP-1. Finally, only 30% of helix exited in the conformation of GLP-1 and the N- and C-terminus tended to contact each other to form short β-sheet. When mixed with pentapeptides, the percent of helical structure increased to about 60% for GLP-1, and the formations of one or two helical segment depended on the interaction mode between pentapeptide and GLP-1. Among them, the zwitterionic pentapeptide VPKEG with the strongest hydrophilicity preferred to be uniformly dispersed in solution, and thus producing a loose protective layer around GLP-1. Because of the arginine residue, the zwitterionic pentapeptide VPREG exerted the strongest electrostatic interaction to GLP-1, which is conducive to the highest helicity of GLP-1 but hardest to the diffusion process. In the control system, pentapeptide VPGAG with the strongest hydrophobicity formed the densest aggregate, but cannot fully enwrapped GLP-1 and provide sufficient protection yet. In short, the same content of lysine and glutamate endows zwitterionic pentapeptide VPKEG with proper hydrophobicity and electrostatic effects, which can not only maintain GLP-1 conformation but also avoid being recognized by immune protein, showing the "stealth" property. In contrast, the arginine residing in VPREG tended to form electrostatic interactions with other residues instead of water molecules, making it not so hydrophilic as VPKEG.