title: Isolation of thylakoid membrane complexes from rice by a new double-strips BN/SDS-PAGE and bioinformatics prediction of stromal ridge subunits interaction.
abstract: Thylakoid membrane complexes of rice (Oryza sativa L.) play crucial roles in growth and crop production. Understanding of protein interactions within the complex would provide new insights into photosynthesis. Here, a new "Double-Strips BN/SDS-PAGE" method was employed to separate thylakoid membrane complexes in order to increase the protein abundance on 2D-gels and to facilitate the identification of hydrophobic transmembrane proteins. A total of 58 protein spots could be observed and subunit constitution of these complexes exhibited on 2D-gels. The generality of this new approach was confirmed using thylakoid membrane from spinach (Spinacia oleracea) and pumpkin (Cucurita spp). Furthermore, the proteins separated from rice thylakoid membrane were identified by the mass spectrometry (MS). The stromal ridge proteins PsaD and PsaE were identified both in the holo- and core- PSI complexes of rice. Using molecular dynamics simulation to explore the recognition mechanism of these subunits, we showed that salt bridge interactions between residues R19 of PsaC and E168 of PasD as well as R75 of PsaC and E91 of PsaD played important roles in the stability of the complex. This stromal ridge subunits interaction was also supported by the subsequent analysis of the binding free energy, the intramolecular distances and the intramolecular energy.
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, China.
authors.forename: Jinzhen
authors.initials: J
authors.lastname: Shao
authors.forename: Yubo
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jianlan
authors.initials: J
authors.lastname: Yu
authors.forename: Lin
authors.initials: L
authors.lastname: Guo
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
mesh_terms: D019295:Computational Biology / Q000379:methods*; D028464:Cucurbita / Q000378:metabolism; D003902:Detergents / Q000494:pharmacology; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D056004:Molecular Dynamics Simulation; D008970:Molecular Weight; D046912:Multiprotein Complexes / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism; D012275:Oryza / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry / Q000302:isolation & purification* / Q000378:metabolism; D011485:Protein Binding / Q000187:drug effects; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism*; D012995:Solubility / Q000187:drug effects; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D018724:Spinacia oleracea / Q000378:metabolism; D020524:Thylakoids / Q000187:drug effects / Q000378:metabolism*
chemical_list: D003902:Detergents; D046912:Multiprotein Complexes; D010940:Plant Proteins; D021122:Protein Subunits