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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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here, we present the interaction features of <jats:italic>Os<\/jats:italic>PsaC and <jats:italic>Os<\/jats:italic>PsaD by molecular dynamics simulations and bioinformatics. Firstly, we identified interacting residues in the <jats:italic>Os<\/jats:italic>PsaC-<jats:italic>Os<\/jats:italic>PsaD 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 <jats:italic>Os<\/jats:italic>PsaC-<jats:italic>Os<\/jats:italic>PsaD interaction. Supportively, electrostatic potentials surfaces of <jats:italic>Os<\/jats:italic>PsaD 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\u00a0ns 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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>These results together provided structure basis and dynamics behavior to understand recognition and assembly of the stromal ridge complex in rice.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-0877-0","type":"journal-article","created":{"date-parts":[[2016,1,12]],"date-time":"2016-01-12T00:13:27Z","timestamp":1452557607000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.)"],"prefix":"10.1186","volume":"17","author":[{"given":"Yubo","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,1,12]]},"reference":[{"issue":"3","key":"877_CR1","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/S0022-2836(03)00145-1","volume":"327","author":"ML Antonkine","year":"2003","unstructured":"Antonkine ML, Jordan P, Fromme P, Krauss N, Golbeck JH, Stehlik D. 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