Rationalization of poor solubility of TGF-β3 using MD simulation

Despite sequence and structural similarity, TGF-β3 has low solubility among other isoforms of TGF-β. We used nanosecond of molecular dynamic simulations (MD) with explicit solvent, alone and in presence of urea, to investigate the intermediates resulting from the unfolding process of TGF-β3 and TGF-β1. MD simulations of the full-length proteins show a very early loss of α-helix in TGF-β3 compared to the one in the TGF-β1. MD simulation of a small fragment consisting of H3 α-helix of TGF-β3 shows conversion of this segment to β-sheet. Relative instability of H3 α-helix in TGF-β3 and its propensity to form β-sheet may explain the poor solubility of TGF-β3 compared to TGF-β1. The other reasons for poor solubility of TGF-β3 may be the hydrophobic patches on its surface and low charge over the entire range of pH.

Research highlights► TGF-β3 has hydrophobic patch which may be responsible for low solubility. ► TGF-β3 has low charge than TGF-β1 under all pH conditions. ► One of the α-helix in TGF-β3 is unstable. ► This α-helix segment changes to β-sheet after 10 ns MD simulation at 500 K.