Ne residues; triangle: glycine residues; circle: all other residues. blue and

Ne residues; triangle: glycine residues; circle: all other residues. blue and purple: favorable regions; all else: unfavorable regions. doi:10.1371/journal.pone.0047611.gconditions in the presence of different concentrations of rhodojaponin III (0, 50, 100, 300, and 600 mM).S.litura and other insects (Fig. 2). The dendrogram showed that the CSPSlit had 25033180 closer ancestry from the same order insects.Results 3.1 cDNA Cloning and Sequence Analysis of CSPSlitTwo RACE fragments were amplified with four pairs of specific primers CB 5083 chemical information designed according to the nucleotide sequence of the fragment. By using rapid amplification of cDNA ends PCR (RACE-PCR), a full-length CSPSlit of 473 bp was obtained by overlapping the RACE fragments (GenBank Accession No: DQ007458). Sequence analysis showed that the full-length (ORF) of CSPSlit was 378 bp, encoding 126 amino acid residues, with a predicted MW of 14.67 kD. A 16-residue signal peptide in the CSPSlit was identified by SignalP, with a calculated molecular mass of a mature protein (110 amino acids) of 12.69 kD with an estimated pI of 6.66 by ExPASy [51] (Fig. 1). The phylogenetic tree was constructed based on the amino acid sequences CSP from3.2 Tissues-specificity Expession Analysis of CSPSlitTo determine whether CSPSlit is present in various tissues in the S. litura, we used northern blot to characterize the pattern of tissues-specificity expression of CSPSlit gene from different tissues (male female antennae, de-antennated heads, forelegs, mesopedes, metapedes, thoraces, wings and abdomens). Total RNA of each sample was isolated and separated, an approximately of 500 bps a-[32P]dCTP labeled CSPSlit antisense RNA probe gave strong hybridization signals to the antennae, legs and wings, lower trace was detected from de-antennated heads and thoraces, and it was expessed in female abdomen but absent in male (Fig. 3).3.3 3D Modelling of CSPSlit ProteinThe sequence of CSPSlit was compared to all known proteins in PDB and the results showed that chemosensory protein A6 fromFigure 6. Potential energy (A) and root-mean-square deviation (A) with respect to simulation time for 1000 ps free MD simulation on the CSPSlit model. doi:10.1371/journal.pone.0047611.gCharacterisation Binding Properties of CSPSlit?Figure 7. The complex (A) and detailed binding mode (B) of CSPSlit with rhodojaponin III. The residues within 6 A from ligand are shown. doi:10.1371/journal.pone.0047611.gMamestra brassicae (CSPMbraA6) (PDB code 1N8V) had the sequence identity (52 ) with CSPSlit, so CSPMbraA6 was chose as template to model the 3D structure of the CSPSlit. Following the homology modeling, the best model (Fig. 4) was chosen from 10 candidates, and its quality was further checked by Ramachardran plot and verify score (Fig. 5). Figure 6 shows the time series of potential energy and root-mean-square deviation (RMSD) of backbone for 700 ps MD simulation of CSPSlit structure. The potential energy of the model was stabilized at 200 ps production after 800 ps equilibration and the RMSD of backbone compared ?to the starting coordinate remained at 1.0 A up and down fluctuations. These 2 properties converged at production, in-dicating that the model is stable and can be used for subsequent docking calculation.3.4 Molecular Interaction Analysis between Rhodojaponin III and CSPSlitConsidering the sequence conservation of CSPSlit with CSPMbraA6, the binding site was Madrasin biological activity confirmed for its hydrophobicity. These binding poses were evaluated by score l.Ne residues; triangle: glycine residues; circle: all other residues. blue and purple: favorable regions; all else: unfavorable regions. doi:10.1371/journal.pone.0047611.gconditions in the presence of different concentrations of rhodojaponin III (0, 50, 100, 300, and 600 mM).S.litura and other insects (Fig. 2). The dendrogram showed that the CSPSlit had 25033180 closer ancestry from the same order insects.Results 3.1 cDNA Cloning and Sequence Analysis of CSPSlitTwo RACE fragments were amplified with four pairs of specific primers designed according to the nucleotide sequence of the fragment. By using rapid amplification of cDNA ends PCR (RACE-PCR), a full-length CSPSlit of 473 bp was obtained by overlapping the RACE fragments (GenBank Accession No: DQ007458). Sequence analysis showed that the full-length (ORF) of CSPSlit was 378 bp, encoding 126 amino acid residues, with a predicted MW of 14.67 kD. A 16-residue signal peptide in the CSPSlit was identified by SignalP, with a calculated molecular mass of a mature protein (110 amino acids) of 12.69 kD with an estimated pI of 6.66 by ExPASy [51] (Fig. 1). The phylogenetic tree was constructed based on the amino acid sequences CSP from3.2 Tissues-specificity Expession Analysis of CSPSlitTo determine whether CSPSlit is present in various tissues in the S. litura, we used northern blot to characterize the pattern of tissues-specificity expression of CSPSlit gene from different tissues (male female antennae, de-antennated heads, forelegs, mesopedes, metapedes, thoraces, wings and abdomens). Total RNA of each sample was isolated and separated, an approximately of 500 bps a-[32P]dCTP labeled CSPSlit antisense RNA probe gave strong hybridization signals to the antennae, legs and wings, lower trace was detected from de-antennated heads and thoraces, and it was expessed in female abdomen but absent in male (Fig. 3).3.3 3D Modelling of CSPSlit ProteinThe sequence of CSPSlit was compared to all known proteins in PDB and the results showed that chemosensory protein A6 fromFigure 6. Potential energy (A) and root-mean-square deviation (A) with respect to simulation time for 1000 ps free MD simulation on the CSPSlit model. doi:10.1371/journal.pone.0047611.gCharacterisation Binding Properties of CSPSlit?Figure 7. The complex (A) and detailed binding mode (B) of CSPSlit with rhodojaponin III. The residues within 6 A from ligand are shown. doi:10.1371/journal.pone.0047611.gMamestra brassicae (CSPMbraA6) (PDB code 1N8V) had the sequence identity (52 ) with CSPSlit, so CSPMbraA6 was chose as template to model the 3D structure of the CSPSlit. Following the homology modeling, the best model (Fig. 4) was chosen from 10 candidates, and its quality was further checked by Ramachardran plot and verify score (Fig. 5). Figure 6 shows the time series of potential energy and root-mean-square deviation (RMSD) of backbone for 700 ps MD simulation of CSPSlit structure. The potential energy of the model was stabilized at 200 ps production after 800 ps equilibration and the RMSD of backbone compared ?to the starting coordinate remained at 1.0 A up and down fluctuations. These 2 properties converged at production, in-dicating that the model is stable and can be used for subsequent docking calculation.3.4 Molecular Interaction Analysis between Rhodojaponin III and CSPSlitConsidering the sequence conservation of CSPSlit with CSPMbraA6, the binding site was confirmed for its hydrophobicity. These binding poses were evaluated by score l.