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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.


Acyl-coA binding domain alignment in BnACBPs.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.
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pone.0129650.g002: Acyl-coA binding domain alignment in BnACBPs.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.

Mentions: Conserved amino acid residues of ACBD in all four classes of BnACBPs were analyzed through alignment of all ACBPs (Fig 2). Identical residues in all four classes of BnACBPs corresponded to residues Leu-32, Thr-37, Gly-39, Pro-46, Lys-56, Trp-57, Trp-60, Ala-71 in small BnACBPs, Leu-135, Thr-140, Gly-142, Pro-149, Lys-159, Trp-160, Trp-163, Ala-174 in ankyrin repeats BnACBPs, Leu-267, Thr-272, Gly-274, Pro-281, Lys-291, Trp-292, Trp-295, Ala-306 in large BnACBPs and Leu-50, Thr-55, Gly-57, Pro-64, Lys-74, Trp-75, Trp-78, Ala-89 in kelch motif BnACBPs. In addition, some residues were conserved in almost all of the BnACBPs. These findings suggested eight amino acid residues conserved in all ACBD of BnACBPs.


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

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

Acyl-coA binding domain alignment in BnACBPs.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.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0129650.g002: Acyl-coA binding domain alignment in BnACBPs.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.
Mentions: Conserved amino acid residues of ACBD in all four classes of BnACBPs were analyzed through alignment of all ACBPs (Fig 2). Identical residues in all four classes of BnACBPs corresponded to residues Leu-32, Thr-37, Gly-39, Pro-46, Lys-56, Trp-57, Trp-60, Ala-71 in small BnACBPs, Leu-135, Thr-140, Gly-142, Pro-149, Lys-159, Trp-160, Trp-163, Ala-174 in ankyrin repeats BnACBPs, Leu-267, Thr-272, Gly-274, Pro-281, Lys-291, Trp-292, Trp-295, Ala-306 in large BnACBPs and Leu-50, Thr-55, Gly-57, Pro-64, Lys-74, Trp-75, Trp-78, Ala-89 in kelch motif BnACBPs. In addition, some residues were conserved in almost all of the BnACBPs. These findings suggested eight amino acid residues conserved in all ACBD of 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.