{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:05:58Z","timestamp":1761512758869},"reference-count":43,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2009,12,22]],"date-time":"2009-12-22T00:00:00Z","timestamp":1261440000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J of Molecular Recognition"],"published-print":{"date-parts":[[2010,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A molecular dynamics (MD) simulation has been performed for two sets of aminoglycoside antibiotics bound with an RNA duplex corresponding to the aminoacyl\u2010tRNA decoding site of the 16S rRNA to characterize the energetics and dynamics of binding for several aminoglycosides. The binding free energy, essential dynamics and hydration analysis have been conducted to characterize the dynamics' properties associated with the binding recognition between each set of antibiotics and the RNA duplex. We have built several dynamic models with reasonable binding free energies showing good correlation with the experimental data. We have also conducted a hydration analysis on some long residency water molecules detected as W8 and W49 sites around the U1406\u2009\u00b7\u2009U1495 pair and which are found to be important in binding recognition and in causing some apparent stretch variations of this pair during the dynamic studies. In addition, we also find that the hydration sites with long residence time identified between the ring III of two 4,6\u2010linked antibiotics (tobramycin and kanamycin) and phosphate oxygen atoms of G1405\/U1406 may be worthy of further exploration for rational drug design. Copyright \u00a9 2009 John Wiley &amp; Sons, Ltd.<\/jats:p>","DOI":"10.1002\/jmr.1008","type":"journal-article","created":{"date-parts":[[2009,12,22]],"date-time":"2009-12-22T10:56:18Z","timestamp":1261479378000},"page":"423-434","source":"Crossref","is-referenced-by-count":11,"title":["A molecular dynamics study on binding recognition between several 4,5 and 4,6\u2010linked aminoglycosides with A\u2010site RNA"],"prefix":"10.1002","volume":"23","author":[{"given":"Shih\u2010Yuan","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thy\u2010Hou","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2009,12,22]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340170408"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.physchem.51.1.129"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1021\/j100142a004"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0959\u2010440X(00)00061\u20100"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/0010\u20104655(95)00042\u2010E"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/35030019"},{"key":"e_1_2_6_8_1","volume-title":"AMBER8","author":"Case DA","year":"2004"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.8.1.147"},{"key":"e_1_2_6_10_1","first-page":"764","volume-title":"Basic and Clinical Pharmacology","author":"Chambers HF","year":"2004"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097\u20100134(19980501)31:2< 116::AID.\u2010PROT2>3.0.CO;2\u2010K"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.274.5291.1367"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1997.1551"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki862"},{"key":"e_1_2_6_16_1","unstructured":"FrischMJ TrucksGW SchlegelHB ScuseriaGE RobbMA CheesemanJR ZakrzewskiVG MontgomeryJAJr StratmannRE BurantJC DapprichS MillamJM DanielsAD KudinKN StrainMC FarkasO TomasiJ BaroneV CossiM CammiR MennucciB PomelliC AdamoC CliffordS OchterskiJ PeterssonGA AyalaPY CuiQ MorokumaK SalvadorP DannenbergJJ MalickDK RabuckAD RaghavachariK ForesmanJB CioslowskiJ OrtizJV BaboulAG StefanovBB LiuG LiashenkoA PiskorzP KomaromiI GompertsR MartinRL FoxDJ KeithT Al\u2010LahamMA PengCY NanayakkaraA ChallacombeM GillPMW JohnsonB ChenW WongMW AndresJL GonzalezC Head\u2010GordonM ReplogleES PopleJA.1998.Gaussian 98. 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