Structural And Functional Prediction Of Hypothetical Proteins From Klebsiella Pneumoniae MGH78578 : Molecular Modelling Studies

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dc.contributor.authorChoi, Sy Bing
dc.date.accessioned2018-12-12T06:51:02Z
dc.date.available2018-12-12T06:51:02Z
dc.date.issued2011-10
dc.description.abstractTwenty percent of the genes from Klebsiella pneumonaie MGH78578 coded for hypothetical protein. Two particular hypothetical proteins KPN00728 and KPN00729 were identified using bioinformatics approaches. Both open reading frames showed high sequence homology to succinate dehydrogenase Chain C (SdhC) and D (SdhD) from Escherichia coli KPN00729 was annotated as SdhD in May 2008. Thus, investigation on KPN00728 remained as no annotation for SdhC gene in the complete genome sequence of Klebsiella pneumoniae MGH78578. In this study, KPN00728 has a missing region with conserved residues which is important for ubiquinone (UQ) and heme group binding. Structure and function prediction of KPN00728 coupled with secondary structure analysis and transmembrane topology showed KPN00728 adopts SDH-(subunit C)-like structure. To further probe its functionality, UQ was docked on the built model (consisting KPN00728 and KPN00729) and formation of hydrogen bonds between UQ and Ser27, Arg31 (KPN00728) and Tyr83 (KPN00729) further reinforced and supported that KPN00728 is indeed succinate dehydrogenase (SDH). However, limitation in docking simulation failed to provide in depth understanding of the SDH interaction that occurs in the trans-membrane of mitochondria. For more insight into its molecular role as SDH, molecular dynamics (MD) simulation of KPN00728 and Chain D in a membrane was performed. Structural stability was demonstrated in the calculation in area per lipid, tail order parameter, thickness of lipid and secondary structural properties. Interestingly, water molecules were found to be highly possible for the deviation of interaction of UQ with SDH in Ser27 and Arg31 as compared with earlier docking study. Polar residues such as Asp95 and Glu101 (SDH chain C), Asp15 and Glu78 (SDH chain D) might have contributed in the creation of a polar environment which is essential for the electron transport chain in Krebs cycle. Despite the structural stability comparability, the dynamics of the interaction had further proved that the interaction of KPN00728 as SDH is preserved and well agreed with our postulation earlier.en_US
dc.identifier.urihttp://hdl.handle.net/123456789/7273
dc.language.isoenen_US
dc.publisherUniversiti Sains Malaysiaen_US
dc.subjectStructural and functional prediction ofen_US
dc.subjecthypothetical proteins from Klebsiella pneumoniaeen_US
dc.titleStructural And Functional Prediction Of Hypothetical Proteins From Klebsiella Pneumoniae MGH78578 : Molecular Modelling Studiesen_US
dc.typeThesisen_US
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