Table 1.
Summary of various accelerated molecular dynamics parameters.
Fig 1.
Multiple sequence alignment of homologous RsAFP2 proteins from different species.
Red columns indicate conserved residues with in the alignment, and red stars indicate the 9th and 39th positions in the alignment. Abbreviations RAPSA: Raphanus sativus; ARATH: Arabidopsis thaliana; ARAHH: Arabidopsis halleri subsp. halleri; BRARP: Brassica rapa subsp. pekinensis; BRAS: Bradyrhizobium spp.; SINAL: Sinapis alba; BRAJU: Brassica juncea; ORYVI: Orychophragmus violaceus; BRAOL: Brassica oleracea.
Fig 2.
Molecular dynamics trajectory analysis.
(a) Root mean square deviation (b) Root mean square fluctuation (c) Radius of gyration (d) Number of hydrogen bond for 500 ns MD simulations run.
Table 2.
RMSD of RsAFP2 wild-type and mutant proteins at different time intervals.
Table 3.
RMSF of critical residues in wild-type and mutants at different time intervals.
Table 4.
Energy analysis for the RsAFP2 wild-type and mutants.
Table 5.
Variation in the secondary structure elements of RsAFP2 at different time intervals.
Fig 3.
The deuterium order parameter, SCD, calculated for the sn-1 and sn-2 lipid acyl chains from all five systems comprising a wild-type RsAFP2, its two mutants and two homologs embedded in fungal mimicking bilayer membrane.
Fig 4.
The 2D-deformation maps calculated from bilayer thickness for each protein-membrane system comprising a wild-type RsAFP2, its two mutants and two homologs.
The darkest blue regions define the thinnest regions of the membrane owing to leakage of water molecules across the trans-membrane region. The red areas are indicating thickest membrane regions.
Fig 5.
Snapshots at 100 and 200 ns of protein-membrane simulations for each system a wild-type RsAFP2, its two mutants and two homologs highlighting the extent of leakage of water molecules across the trans-membrane region.
The two mutants cause higher influx of water molecules owing to the charged Arg residue replacement.
Fig 6.
The area-per-lipid profiles of every constitutive lipid for each protein-membrane system comprising a wild-type RsAFP2, its two mutants and two homologs.
Increasing area-per-lipid profiles increased membrane deformation. The profile remains very stable for RsAFP2 in comparison to its mutants suggesting that the mutation bring higher deformity in the fungal membranes.