Modeling and structural comparison of betaine aldehyde dehydrogenase 2 of fragrant and non-fragrant soybean (Glycine max) and rice (Oryza sativa L.)

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dc.contributor.advisorSudhir Kumar
dc.contributor.authorShilpi
dc.date.accessioned2016-09-08T13:47:03Z
dc.date.available2016-09-08T13:47:03Z
dc.date.issued2013
dc.description.abstractBetaine aldehyde dehydrogenase2 (BADH2) is an important protein involved in presence of the fragrance in soybean and rice. It was predicted that loss of function of BADH2 leads to the fragrance. In rice 8bp deletion leads to the premature stop codon and hence non-functioning truncated BADH2 protein but in soybean a change in amino acid glycine 334 with aspartate334 leads to the fragrance without any shortening of protein. In this study, homology modeling of the BADH2 protein of fragrant and non-fragrant soybean (Glycine max) and rice (Oryza sativa) was done using Swiss Model Server and Modeller. The crystal structure of BADH2 of Pisum sativum and of Zea mays were taken as the template for soybean and rice, respectively. On verification by Anolea, QMEAN and GROMOS, the models generated by Swiss Model Server were selected. The selected models were evaluated using PROCHECK, VERIFY3D and ERRAT from SAVES. On comparison of fragrant and non-fragrant soybean BADH2, no structural differences were observed (RMSD 0.016). However, nonfragrant soybean BADH2 differed from non-fragrant rice only at three places viz. E260, G472 and E473 (RMSD 0.588). The BADH2 variant of fragrant rice superimposed on non-fragrant rice BADH2from 1-266 position only (RMSD 0.318). The surface topologies of the proteins were analyzed using CASTp server. A total of 65 pockets were observed in soybean and 66 and 35 in non-fragrant and fragrant riceBADH2 protein, respectively. Two binding pockets (7 and 32) were in contact with each other in non-fragrant soybean BADH2 while in fragrant soybean a single pocket was present at the corresponding position with no matching increase in area and volume.P335, however was a part of non-fragrant soybean (pocket 7) but not of fragrant soybean BADH2.Further, the refinement of results was done by active site prediction tool of SCFBio and interestingly K319 near the conserved region EGCRLD/GPIVS showed conformation change in fragrant soybean. Apart from this S255, L256, L258, S262of another highly conserved region also showed conformation change in two soybean BADH2 variants. Position variation of R296, K460 and R461 in a nearby side chains were also observed.en_US
dc.identifier.urihttp://krishikosh.egranth.ac.in/handle/1/76063
dc.language.isoenen_US
dc.publisherCCSHAUen_US
dc.subBioinformatics
dc.subjectBetaine aldehyde dehydrogenase 2, Homology modeling, Surface topology, Active site, Cavitiesen_US
dc.these.typeM.Sc
dc.titleModeling and structural comparison of betaine aldehyde dehydrogenase 2 of fragrant and non-fragrant soybean (Glycine max) and rice (Oryza sativa L.)en_US
dc.typeThesisen_US
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