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Computational Prediction of acyl-coA Binding Proteins Structure in Brassica napus.

Raboanatahiry NH, Lu G, Li M - PLoS ONE (2015)

Bottom Line: 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 A. thaliana and B. napus, they might share the same functions but loss or gain might be possible.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China; Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, 435599, China.

ABSTRACT
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 Brassica napus 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 Brassica napus were identical to Arabidopsis thaliana. 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 B. napus. 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 A. thaliana and B. napus, they might share the same functions but loss or gain might be possible.

No MeSH data available.


Domain architecture of BnACBPs.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).
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pone.0129650.g001: Domain architecture of BnACBPs.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).

Mentions: Conserved domains of BnACBPs were analyzed with SMART, focusing on their location and their taxonomy. Domain architecture is shown in Fig 1. The location of domains in each BnACBP differed from one to another even within the same class. In all ACBPs, the acyl-coA binding domain (ACBD) belonged to PF00887, but their location differed greatly. In small ACBPs, they were placed between amino acid residues 3 to 87, which were largely extended in the proteins. In large ACBPs, these ACBD were located near the C-terminal of the proteins, they were placed between residues 236 to 335. The ACBD in ankyrin repeats and kelch motif BnACBPs were localized near the N-terminal of the proteins. Ankyrin repeats ACBD were located between residues 90 to 182 in BnACBP1 (BnaA02g10270D and BnaC02g44810D) and between 101 to 190 in BnACBP2 (BnaA01g16660D and BnaC01g20440D). In kelch motif BnACBPs, they were located between residues 14 to 104 or 21 to 105 in BnACBP4 (Ais76194, Ais76195, Ais76196, Ais76199, Ais76200 and Ais76201) and between residues 26 to 104 in BnACBP5 (Ais76197 and Ais76198). N-terminal transmembrane domains could be found in ankyrin repeats and large BnACBPs as indicated in Fig 1. These structures were extended from amino acids 10 to 32 in BnACBP1 and 7 to 29 in BnACBP2 of ankyrin repeats BnACBPs. In large BnACBPs, the N-terminal transmembrane domains were found in residues 7 to 29 in two BnACBPs (BnaA01g13710D and BnaC01g16110D) but no transmembrane domain was detected in the two other BnACBPs (BnaA03g46540D and BnaC07g38820D). The additional conserved domains in ankyrin repeats and kelch motif BnACBPs made them different from the other classes. In fact, two ankyrin repeats domains were detected and they were extended between residues 251 to 283 and 284 to 316 in BnACBP1, and between residues 275 to 304 and 308 to 337 in BnACBP2. They belonged to PF00023. Furthermore, the kelch motif domains were placed in different positions. Three kelch motif domains were detected in three BnACBP4 (Ais76194, Ais76199, Ais76201) and in BnACBP5 (Ais76197 and Ais76198). Kelch domains were placed between residues 179 to 219, 292 to 345 and 344 to 394. They respectively belonged to PF13854, PF13964 and PF13418. However, three other BnACBP4 (Ais76196, Ais76195, Ais76200) contained only two kelch motif domains. The first domains were located between residues 183 to 239 and they belonged to PF13418, the second domains were located between residues 305 to 355 but their affiliation on the Pfam database was not found. These results indicated the difference of location and family of domains conserved in ACBPs, especially in kelch motif BnACBPs.


Computational Prediction of acyl-coA Binding Proteins Structure in Brassica napus.

Raboanatahiry NH, Lu G, Li M - PLoS ONE (2015)

Domain architecture of BnACBPs.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).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4465970&req=5

pone.0129650.g001: Domain architecture of BnACBPs.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).
Mentions: Conserved domains of BnACBPs were analyzed with SMART, focusing on their location and their taxonomy. Domain architecture is shown in Fig 1. The location of domains in each BnACBP differed from one to another even within the same class. In all ACBPs, the acyl-coA binding domain (ACBD) belonged to PF00887, but their location differed greatly. In small ACBPs, they were placed between amino acid residues 3 to 87, which were largely extended in the proteins. In large ACBPs, these ACBD were located near the C-terminal of the proteins, they were placed between residues 236 to 335. The ACBD in ankyrin repeats and kelch motif BnACBPs were localized near the N-terminal of the proteins. Ankyrin repeats ACBD were located between residues 90 to 182 in BnACBP1 (BnaA02g10270D and BnaC02g44810D) and between 101 to 190 in BnACBP2 (BnaA01g16660D and BnaC01g20440D). In kelch motif BnACBPs, they were located between residues 14 to 104 or 21 to 105 in BnACBP4 (Ais76194, Ais76195, Ais76196, Ais76199, Ais76200 and Ais76201) and between residues 26 to 104 in BnACBP5 (Ais76197 and Ais76198). N-terminal transmembrane domains could be found in ankyrin repeats and large BnACBPs as indicated in Fig 1. These structures were extended from amino acids 10 to 32 in BnACBP1 and 7 to 29 in BnACBP2 of ankyrin repeats BnACBPs. In large BnACBPs, the N-terminal transmembrane domains were found in residues 7 to 29 in two BnACBPs (BnaA01g13710D and BnaC01g16110D) but no transmembrane domain was detected in the two other BnACBPs (BnaA03g46540D and BnaC07g38820D). The additional conserved domains in ankyrin repeats and kelch motif BnACBPs made them different from the other classes. In fact, two ankyrin repeats domains were detected and they were extended between residues 251 to 283 and 284 to 316 in BnACBP1, and between residues 275 to 304 and 308 to 337 in BnACBP2. They belonged to PF00023. Furthermore, the kelch motif domains were placed in different positions. Three kelch motif domains were detected in three BnACBP4 (Ais76194, Ais76199, Ais76201) and in BnACBP5 (Ais76197 and Ais76198). Kelch domains were placed between residues 179 to 219, 292 to 345 and 344 to 394. They respectively belonged to PF13854, PF13964 and PF13418. However, three other BnACBP4 (Ais76196, Ais76195, Ais76200) contained only two kelch motif domains. The first domains were located between residues 183 to 239 and they belonged to PF13418, the second domains were located between residues 305 to 355 but their affiliation on the Pfam database was not found. These results indicated the difference of location and family of domains conserved in ACBPs, especially in kelch motif BnACBPs.

Bottom Line: 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 A. thaliana and B. napus, they might share the same functions but loss or gain might be possible.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China; Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, 435599, China.

ABSTRACT
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 Brassica napus 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 Brassica napus were identical to Arabidopsis thaliana. 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 B. napus. 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 A. thaliana and B. napus, they might share the same functions but loss or gain might be possible.

No MeSH data available.