{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T15:24:29Z","timestamp":1778685869370,"version":"3.51.4"},"reference-count":53,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2022,8,5]],"date-time":"2022-08-05T00:00:00Z","timestamp":1659657600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2022,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The type III secretion system (T3SS) is an important molecular machinery in gram\u2010negative bacteria\n                    <jats:italic>Shigella flexneri<\/jats:italic>\n                    as it provides ways for translocating virulence factors from the bacteria into host cells, eventually leading to severe disease symptoms such as bacillary dysentery. Due to the rising concerns of antibiotics resistance in bactericidal strategy, the anti\u2010virulence strategy that primarily targets the T3SS components becomes an attractive alternative. MxiM, the secretin pilot protein of\n                    <jats:italic>Shigella flexneri<\/jats:italic>\n                    , binds the secretin MxiD and facilitates the formation of the secretin ring in outer membrane in T3SS assembly. MxiM harbors a large hydrophobic pocket that has been shown to be important in MxiM\u2010MxiD interaction. In this work, I examined the ligand binding property of MxiM by performing molecular dynamics (MD) simulations of the association between MxiM and a series of hydrophobic ligands, with simulation time amounted to 30\u2009\u03bcs. MD simulations successfully captured spontaneous ligand binding events in 153 of the 300 trajectories. The ligand binding can be categorized into two types: a fast type, in which the ligand binds quickly into the hydrophobic pocket and a slow type, in which the ligand forms an encounter complex with the protein before binding into the hydrophobic pocket. Using the MxiM\u2010ligand binding poses captured in MD simulations, I additionally performed umbrella\u2010sampling MD simulations with total simulation time amounted to 63\u2009\u03bcs to obtain protein\u2013ligand binding free energies. The relationship between the ligand binding free energy and ligand size appears to be nonlinear and exhibits an exponential decay pattern. In summary, I performed computational characterization of MxiM\u2010hydrophobic ligand binding capabilities and properties, which may provide valuable insights into designing anti\u2010bacterial medicine against antibiotics resistance in\n                    <jats:italic>Shigella flexneri<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1002\/prot.26402","type":"journal-article","created":{"date-parts":[[2022,7,24]],"date-time":"2022-07-24T07:14:20Z","timestamp":1658646860000},"page":"2116-2123","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Computational characterization of homologous ligands binding to a deep hydrophobic pocket in\n                    <i>Shigella flexneri<\/i>\n                    pilot protein MxiM"],"prefix":"10.1002","volume":"90","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4399-0687","authenticated-orcid":false,"given":"Shun","family":"Zhu","sequence":"first","affiliation":[{"name":"Department of Cellular and Genetic Medicine, School of Basic Medical Sciences Fudan University  Shanghai People's Republic of China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2022,8,5]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1995.tb02301.x"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.68.4.771-795.2004"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2008.08.006"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04162"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1021\/jo800527n"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm100112j"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1021\/cb500129t"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2006.12.017"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2008.04.002"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/anie.200502655"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2009.09.001"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-042910-155245"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7600610"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00255"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp8001614"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20290"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1080\/00268978800101881"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360320508"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.1332996"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22488"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct300418h"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23398"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00405"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00275"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.2978177"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2010.04.009"},{"key":"e_1_2_7_35_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-070816-033639"},{"key":"e_1_2_7_36_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.103.187801"},{"key":"e_1_2_7_37_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja1050082"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct1003077"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1516652112"},{"key":"e_1_2_7_40_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.4959969"},{"key":"e_1_2_7_41_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1221231110"},{"key":"e_1_2_7_42_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1312529110"},{"key":"e_1_2_7_43_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.5025118"},{"key":"e_1_2_7_44_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.2221683"},{"key":"e_1_2_7_45_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2009.09.049"},{"key":"e_1_2_7_46_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b00532"},{"key":"e_1_2_7_47_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm0608356"},{"key":"e_1_2_7_48_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-070816-033654"},{"key":"e_1_2_7_49_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi00869a013"},{"key":"e_1_2_7_50_1","doi-asserted-by":"publisher","DOI":"10.1021\/jz1014899"},{"key":"e_1_2_7_51_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja208909n"},{"key":"e_1_2_7_52_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1500806112"},{"key":"e_1_2_7_53_1","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.7b05028"},{"key":"e_1_2_7_54_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.18.9997"}],"container-title":["Proteins: 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