Distributions of the number of contacts in each condition. The horizontal axis indicates the number of inter-residue contacts between two peptides. The vertical axis is the relative frequency in each ensemble. The upper row (A and B) and the lower row (C and D) show the host and GXXXG peptides, respectively. The left column (A and C) and right column (B and D) show the antiparallel and parallel directions of the dimer, respectively. The red and blue curves correspond to pure-POPC and cholesterol-mixed membrane, respectively. The bin width of the histogram is 1.

Contexts in source publication

Context 1

... the dimers with a parallel orientation, the average numbers (and the standard errors) of the inter-residue contacts between the GXXXG peptides were 23.5 (7.66) and 4.64 (2.53) for pure-POPC and cholesterol-mixed membranes, respectively, and for the host peptide, these values were 10.44 (3.96) and 8.30 (2.59), respectively (Table S1 in the Supporting Information). The GXXXG peptide was in tighter contact than the host peptides in the pure-POPC environment (Figure 2), reflecting the fact that the GXXXG motif facilitates the dimer formation. The host peptide in the pure-POPC membrane yielded a bimodal distribution ( Figure 2B, red). ...

Context 2

... GXXXG peptide was in tighter contact than the host peptides in the pure-POPC environment (Figure 2), reflecting the fact that the GXXXG motif facilitates the dimer formation. The host peptide in the pure-POPC membrane yielded a bimodal distribution ( Figure 2B, red). The first peak at zero number of contacts indicates that the dimer was dissociated. ...

Context 3

... first peak at zero number of contacts indicates that the dimer was dissociated. For the GXXXG peptide in the pure-POPC membrane, the dimer was not dissociated, and there were peaks around 11, 26, and 50 contacts ( Figure 2D, red). The snapshots of the third peak show tightly contacted dimer conformations that are not observed for the host peptides ( Figure 2D). ...

Context 4

... the GXXXG peptide in the pure-POPC membrane, the dimer was not dissociated, and there were peaks around 11, 26, and 50 contacts ( Figure 2D, red). The snapshots of the third peak show tightly contacted dimer conformations that are not observed for the host peptides ( Figure 2D). In addition, it was confirmed that adding cholesterols to the membrane clearly reduced the interactions of the GXXXG dimers. ...

Context 5

... contact distribution for the GXXXG peptide in the cholesterol-mixed membrane has a strong peak at zero contact. These results were qualitatively consistent with those of the single-pair FRET experiments reported by Yano et al. 17 In the antiparallel configuration, cholesterol facilitated interactions of the host peptide dimer (Figure 2A), in agreement with the findings of Yano et al. 16 In contrast, the results of the antiparallel GXXXG dimer disagreed with the experimental results. Although the experiment reported that the GXXXG helix dimerization was inhibited by addition of cholesterols in both parallel and antiparallel configurations, 17 our simulation with the antiparallel GXXXG dimer yielded more frequent contact in the cholesterol-mixed membrane than in the pure-POPC membrane. ...

Context 6

... the antiparallel configuration showed the opposite trend ( Figure 3A,B). This is consistent with the differences in the number of inter-residue contacts shown in Figure 2. Comparing the host and GXXXG peptides, a lower frequency of hydrogen bond formation was observed in the GXXXG peptide than in the host peptide, regardless of the frequency of inter-residue contacts. ...

Context 7

... theoretical study by Sengupta et al. 27 reported that shorter helices yield stronger helix macrodipole effects. Our simulations reproduced an increase in peptide−peptide interactions in the antiparallel dimers by introducing cholesterol (Figure 2A). Although a certain amount of interpeptide contacts were observed in the parallel dimers ( Figure 2B), they were clearly weaker than those of the antiparallel dimer in the cholesterol-mixed membrane. ...

Context 8

... simulations reproduced an increase in peptide−peptide interactions in the antiparallel dimers by introducing cholesterol (Figure 2A). Although a certain amount of interpeptide contacts were observed in the parallel dimers ( Figure 2B), they were clearly weaker than those of the antiparallel dimer in the cholesterol-mixed membrane. ...

Context 9

... contrast, the behavior of the GXXXG antiparallel dimer did not agree with the experimental results, which reported that cholesterols inhibit the dimer formation of the GXXXG peptides. Our simulations showed that the GXXXG helices had a certain amount of interpeptide contacts, even in the cholesterol-mixed membrane ( Figure 2C). The introduction of cholesterols increased the membrane thickness (Figure 4) and decreased the angles (Figure 3), but interactions were retained, in contrast to the parallel dimer. ...

Context 10

... evolution of helix content of each run ( Figure S1); examples of snapshots at the final steps ( Figure S2); RMSF and helix content of each residue ( Figure S3); backbone dihedral angles of the 9th and 13th residues ( Figure S4); residue-wise frequency for hydrogen bond formation ( Figure S5); distributions of helix tilt angles ( Figure S6); order parameters of POPC ( Figure S7); time evolution of the number of interpeptide contacts ( Figure S8); distribution of the number of interpeptide contacts in each replicate of simulations ( Figure S9); distribution of the number of interpeptide contacts in each 200 ns time window ( Figure S10); average and errors for the number of inter-residue contacts ( Figure S11); and summary of simulation systems (Table S1) (PDF) ...