Figure 1.
Phylogenetic tree of EPF/EPFL genes.
Amino acid sequences for the mature peptide region were aligned using the ClustalW program. The phylogenetic tree was reconstructed by the ME method from the numbers of amino acid substitutions estimated by the JTT model. The numerals at the branch indicate bootstrap values calculated by the ME method with 1,000 replications. Bootstrap values >50% are shown.
Figure 2.
Structures of AtEPF1/EPF2-like peptides and AtEPFL9/Stomagen-like peptides.
(A) Primary structures of AtEPF1/EPF2-like peptides and AtEPFL9/Stomagen-like peptides in land plants. Sequence alignment was generated by the ClustalW program. Pairs of cysteine residues forming disulfide bonds predicted for A. thaliana EPF/EPFL genes are indicated by lines. (B) and (C) Ribbon models of EPF/EPFL peptides. Structural models shown here were generated by homology modeling. The structure of AtEPFL9/Stomagen determined by NMR was used as the template for the homology modeling. A model of the disulfide bonds is shown as a ball-and-stick representation.
Figure 3.
Results of MD simulation of AtEPF1/EPF2-like peptides and AtEPFL9/Stomagen-like peptides.
(A) RMSD values (in nm) during a 10 ns molecular dynamic simulation. (B) and (C) RMSF value (in nm) through the amino acid sequence of each peptide. RMSD indicates conformational changes from the initial structure and RMSF indicates fluctuating area in the molecule. Blue and red bars indicate the ß-strand and loop, respectively.