title: Revealing the functionality of hypothetical protein KPN00728 from Klebsiella pneumoniae MGH78578: molecular dynamics simulation approaches.
abstract: BACKGROUND
  Previously, the hypothetical protein, KPN00728 from Klebsiella pneumoniae MGH78578 was the Succinate dehydrogenase (SDH) chain C subunit via structural prediction and molecular docking simulation studies. However, due to limitation in docking simulation, an in-depth understanding of how SDH interaction occurs across the transmembrane of mitochondria could not be provided.
  
  
  RESULTS
  In this present study, molecular dynamics (MD) simulation of KPN00728 and SDH chain D in a membrane was performed in order to gain a deeper insight into its molecular role as SDH. Structural stability was successfully obtained in the calculation for area per lipid, tail order parameter, thickness of lipid and secondary structural properties. Interestingly, water molecules were found to be highly possible in mediating the interaction between Ubiquinone (UQ) and SDH chain C via interaction with Ser27 and Arg31 residues as compared with earlier docking study. Polar residues such as Asp95 and Glu101 (KPN00728), Asp15 and Glu78 (SDH chain D) might have contributed in the creation of a polar environment which is essential for electron transport chain in Krebs cycle.
  
  
  CONCLUSIONS
  As a conclusion, a part from the structural stability comparability, the dynamic of the interacting residues and hydrogen bonding analysis had further proved that the interaction of KPN00728 as SDH is preserved and well agreed with our postulation earlier.
authors.affiliation: Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia.
authors.forename: Sy Bing
authors.initials: SB
authors.lastname: Choi
authors.forename: Yahaya M
authors.initials: YM
authors.lastname: Normi
authors.forename: Habibah A
authors.initials: HA
authors.lastname: Wahab
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D006860:Hydrogen Bonding; D007711:Klebsiella pneumoniae / Q000201:enzymology* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D013385:Succinate Dehydrogenase / Q000737:chemistry / Q000378:metabolism*; D014451:Ubiquinone / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D014451:Ubiquinone; D013385:Succinate Dehydrogenase