Acyl-coA binding domain alignment in <i>Bn</i>ACBPs.

<p>Alignment was generated using Vector NTI. Identical residues in all ACBPs are highlighted in yellow, identical residues in most of ACBPs are in blue. YKQA and KWDAW motifs correspond to the acyl-coA-binding site. The coenzyme-A head group-binding site are underlined. Capital letters indicate residues conserved in all ACBP of all species.</p

3D alignment between <i>Bn</i>ACBPs and their structure neighbors.

<p>The models were generated from Phyre2 with 100% of confidence. A part of each ACBP could be modeled: small ACBP (95%), ankyrin repeats ACBP (51%), large ACBP (23%), kelch motif ACBP(59%). Structure neighbors and 3D alignments were generated from VAST. Entire chains including only the aligned residues are shown. Red labels indicate amino acid residues that are identical in <i>Bn</i>ACBPs and their neighbors.</p

Predicted secondary structure of <i>Bn</i>ACBPs.

<p>Structures were predicted using GOR4 and PSIPRED. Pictures were reproduced from the server. Predicted structure of Small <i>Bn</i>ACBP is presented. Those of ankyrin repeats, large and kelch motif <i>Bn</i>ACBPs are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129650#pone.0129650.s001" target="_blank">S1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129650#pone.0129650.s002" target="_blank">S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129650#pone.0129650.s003" target="_blank">S3</a> Figs, respectively.</p

Computational Prediction of acyl-coA Binding Proteins Structure in <i>Brassica napus</i>

<div><p>Acyl-coA binding proteins could transport acyl-coA esters from plastid to endoplasmic reticulum, prior to fatty acid biosynthesis, leading to the formation of triacylglycerol. The structure and the subcellular localization of acyl-coA binding proteins (ACBP) in <i>Brassica napus</i> were computationally predicted in this study. Earlier, the structure analysis of ACBPs was limited to the small ACBPs, the current study focused on all four classes of ACBPs. Physicochemical parameters including the size and the length, the intron-exon structure, the isoelectric point, the hydrophobicity, and the amino acid composition were studied. Furthermore, identification of conserved residues and conserved domains were carried out. Secondary structure and tertiary structure of ACBPs were also studied. Finally, subcellular localization of ACBPs was predicted. The findings indicated that the physicochemical parameters and subcellular localizations of ACBPs in <i>Brassica napus</i> were identical to <i>Arabidopsis thaliana</i>. Conserved domain analysis indicated that ACBPs contain two or three kelch domains that belong to different families. Identical residues in acyl-coA binding domains corresponded to eight amino acid residues in all ACBPs of <i>B</i>. <i>napus</i>. However, conserved residues of common ACBPs in all species of animal, plant, bacteria and fungi were only inclusive in small ACBPs. Alpha-helixes were displayed and conserved in all the acyl-coA binding domains, representing almost the half of the protein structure. The findings confirm high similarities in ACBPs between <i>A</i>. <i>thaliana</i> and <i>B</i>. <i>napus</i>, they might share the same functions but loss or gain might be possible.</p></div

Predictive 3D domain structure of <i>Bn</i>ACBPs.

<p>The model were generated from Phyre2 with 100% of confidence. Conserved domain analysis were highlighted using VAST. Front view and top view are presented for each class of ACBP. Small ACBP: 95% of the protein are with presented ACBD highlighted in pink. Ankyrin repeats ACBP: 51% of the protein are shown with ACBD in pink and the ankyrin domain in blue. Large ACBP: 23% of the protein are shown, with ACBD in pink. Kelch motif ACBP: 59% of the protein are shown, ACBD are highlighted in pink, kelch domains are in blue, brown and green.</p

Domain architecture of <i>Bn</i>ACBPs.

<p>Domains were analyzed using SMART and annotated from Pfam. The numbers indicate residues position. The length of each ACBP are indicated at the end of each structure. The ACBD are labeled in red (PF00887). The ankyrin repeats are labeled in yellow (PF00023). Transmembrane domains are labeled in purple. Kelch motif domains are in green (PF13854), pink (PF13964), blue (PF13418) and grey (not found on Pfam).</p