Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins

Abstract

Group 3 late embryogenesis abundant (G3LEA) proteins, which act as a well-characterized desiccation protectant in anhydrobiotic organisms, are structurally disordered in solution, but they acquire a predominantly α-helical structure during drying. Thus, G3LEA proteins are now accepted as intrinsically disordered proteins (IDPs). Their functional regions involve characteristic 11-mer repeating motifs. In the present study, to elucidate the origin of the IDP property of G3LEA proteins, we applied replica exchange molecular dynamics (REMD) simulation to a model peptide composed of two tandem repeats of an 11-mer motif and its counterpart peptide whose amino acid sequence was randomized with the same amino acid composition as that of the 11-mer motif. REMD simulations were performed for a single α-helical chain of each peptide and its double-bundled strand in a wide water content ranging from 5 to 78.3 wt%. In the latter case, we tested different types of arrangement: 1) the dipole moments of the two helices were parallel or anti-parallel and 2) due to the amphiphilic nature of the α-helix of the 11-mer motif, two types of the side-to-side contact were tested: hydrophilic-hydrophilic facing or hydrophobic-hydrophobic facing. Here, we revealed that the single chain alone exhibits no IDP-like properties, even if it involves the 11-mer motif, and the hydrophilic interaction of the two chains leads to the formation of a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant.

Keywords: desiccation protectant; late embryogenesis abundant proteins; α-helical coiled coil.

Figure 1

The initial structures for the REMD simulations of PvLEA-22. (a) anti-parallel hydrophilic-facing model, (b) anti-parallel hydrophobic-facing model. In each figure, a side view (left) and a top view along the helix axis (right) are shown. The red, blue and green stick models represent the side chains of acidic (Asp and Glu), basic (Lys) and neutral (Ala and Thr) amino acid residues, respectively.

Figure 2

Water content dependence of the helix rates of PvLEA-22. (a) The anti-parallel hydrophilic-facing (blue) and hydrophobic-facing (red) models. The results for the single-chain model are represented in orange. (b) The antiparallel double helix model (green) and single-chain model (violet) for the scrambled peptide.

Figure 3

Free energy maps were obtained from the PCA analysis for the anti-parallel hydrophilic-facing model. (a), (b) and (c) represent the results for the water content levels of 78.3, 65.5 and 7.5 wt%, respectively. The energy values (kJ/mol) are indicated by the color code.

Figure 4

Representative structure of the anti-parallel hydrophilic-facing model in each water content level (given in wt%).

Figure 5

Water content dependence of the number of interchain hydrogen bonds (blue) and of the peptide-water hydrogen bonds (red) in the anti-parallel hydrophilic-facing model.

Figure 6

Representative structure of the anti-parallel hydrophilic-facing model at a water content level of 22.5 wt%. The red and blue stick models represent the side chains of acidic (Asp and Glu) and basic (Lys) amino acid residues, respectively.