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In silico analyses of Rubisco Enzymes from different classes of Algae

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Author Affiliations

  • 1The Virtual Institute of Bioinformatics, Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, INDIA

Int. Res. J. Biological Sci., Volume 3, Issue (4), Pages 11-17, April,10 (2014)

Abstract

Rubisco (Ribulose 1, 5 Bisphosphate Carboxylase Oxygenase) is the most predominant enzyme of one of the few carbon assimilatory processes in nature i.e. Photosynthesis. The rbcL and rbcS genes code for the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) respectively. In this study the rbcL protein sequences selected from various classes of algae were phylogenetically analyzed. Expasy’s Prot-param server and Cys_rec tool were used for physico-chemical and functional characterization of these proteins. For comparative structural analysis, experimental structures (X-ray and NMR) of rubisco proteins of representative species of Rhodophyta (Galderia sp. PDBID 1IWA) and Chlorophyta (Chlamydomonas sp. 1GK8) were used. Also, as no experimental structure of rubisco from any member of phaeophyta group is available, homology modeling approach was employed in order to derive structure of the same from Lessonia vadosa, a representative species of phaeophyta group. The validity of the modeled protein was further checked by RAMPAGE, Procheck, WHATIF, Errat, and Verify-3d servers. Studies of secondary structure of these proteins were carried out by the SSCP server. The in silico analysis, confirmed the close correlation between the rhodophyte and the phaeophyte rubico proteins at the functional level due to similarity in adaptability of the enzyme.

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