Analysis of the Differential Conformational Behavior of Two Antigens of the Hepatitis A Virus through Molecular Dynamics and Physicochemical Measurements

The surface activity of peptides with proven antigenic activity toward the hepatitis A virus (HAV), [Glu¹¹⁴]VP3(110-121) and [Lys¹¹³]VP3(110-121), analogues of the VP3(110-121) antigen of HAV with sequence FWRGDLVFDFQV, was deduced from compression isotherm experiments. The results showed that the lysine analogue exhibits a surface area about three times smaller than that of the glutamic acid analogue. To understand whether this observed differential conformational behavior of the two peptide analogues is a characteristic feature of the peptide sequences, we carried out 10 ns molecular dynamics simulations of the two analogues in water. The results of this study confirm a differential conformational behavior of the two peptides and provide support to the hypothesis of this observed behavior as the reason for the different surface areas obtained from compression isotherm experiments.