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Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp

Notulae Scientia Biologicae, 01 June 2017, Vol.9(2), pp.204-208 [Peer Reviewed Journal]

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  • Title:
    Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp
  • Author: Emre Sevindik
  • Found In: Notulae Scientia Biologicae, 01 June 2017, Vol.9(2), pp.204-208 [Peer Reviewed Journal]
  • Subjects: Ribulose-Bisphosphate Carboxylase ; Amino Acids ; Phylogenetics ; Ph ; Amino Acids ; Phosphorylation ; Molecular Structure ; Bioinformatics ; Atmosphere ; Amino Acids ; Carbon Dioxide ; Carbon Dioxide ; Dimensional Analysis ; Phylogeny ; Bioinformatics ; Proteins ; Proteins ; Amino Acids ; Bioinformatics ; Carbon Dioxide ; Phosphorylation ; Gravy ; Residues ; Stability ; Residues ; Proteins ; Atmosphere ; Oxygenase ; Plants (Botany)
  • Language: English
  • Description: RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.
  • Identifier: ISSN: 2067-3205 ; E-ISSN: 2067-3264 ; DOI: 10.15835/nsb9210053

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