title: Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.).
abstract: BACKGROUND
  Rice (Oryza sativa L.) is one of the most important cereal crops in the world and its yield is closely related to the photosynthesis efficiency. The chloroplast stromal ridge complex consisting of PsaC-PsaD-PsaE plays an important role in plant photosynthesis, which has been a subject of many studies. Till now, the recognition mechanism between PsaC and PsaD in rice is still not fully understood.
  
  
  RESULTS
  Here, we present the interaction features of OsPsaC and OsPsaD by molecular dynamics simulations and bioinformatics. Firstly, we identified interacting residues in the OsPsaC-OsPsaD complex during simulations. Significantly, important hydrogen bonds were observed in residue pairs R19-E103, D47-K62, R53-E63, Y81-R20, Y81-R61 and L26-V105. Free energy calculations suggested two salt bridges R19-E103 and D47-K62 were essential to maintain the OsPsaC-OsPsaD interaction. Supportively, electrostatic potentials surfaces of OsPsaD exhibited electrostatic attraction helped to stabilize the residue pairs R19-E103 and D47-K62. In particular, the importance of R19 was further verified by two 500 ns CG-MD simulations. Secondly, this study compared the stromal ridge complex in rice with that in other organisms. Notably, alignments of amino acids showed these two salt bridges R19-E103 and D47-K62 also existed in other organisms. Electrostatic potentials surfaces and X-ray structural analysis strongly suggested the stromal ridge complex in other organisms adopted a similar and general recognition mechanism.
  
  
  CONCLUSIONS
  These results together provided structure basis and dynamics behavior to understand recognition and assembly of the stromal ridge complex in rice.
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China. zhyubo7@gmail.com.
authors.forename: Yubo
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China. yiding@whu.edu.cn.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
mesh_terms: D000595:Amino Acid Sequence; D002736:Chloroplasts / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D012275:Oryza / Q000737:chemistry* / Q000378:metabolism; D045322:Photosynthetic Reaction Center Complex Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment; D013816:Thermodynamics
chemical_list: D045322:Photosynthetic Reaction Center Complex Proteins