{"id":15943,"date":"2022-06-30T15:07:05","date_gmt":"2022-06-30T08:07:05","guid":{"rendered":"https:\/\/bgrssb.icgbio.ru\/2022\/?p=15943"},"modified":"2022-09-20T10:32:15","modified_gmt":"2022-09-20T03:32:15","slug":"developing-an-accurate-force-field-for-simulating-modified-rna","status":"publish","type":"post","link":"https:\/\/bgrssb.icgbio.ru\/2022\/2022\/06\/30\/developing-an-accurate-force-field-for-simulating-modified-rna\/","title":{"rendered":"Developing an accurate force field for simulating modified RNA"},"content":{"rendered":"<p><em>by Ansuman Lahiri | University of Calcutta<\/em><\/p>\n<p>Post-transcriptional modifications occur extensively in RNA and provide an additional layer<br \/>\nof chemical coding that presumably alters the chemistry, structure and dynamics of the<br \/>\nmolecules. Molecular dynamics simulations offer a convenient tool to elucidate the<br \/>\nmechanisms underlying the roles played by such modifications. However, since the<br \/>\nreliability of the simulation results depend on the accuracy of the force field employed, we<br \/>\ntested some of the available force field parameters for modified RNA residues for the<br \/>\nAMBER molecular modeling suite of programs. The results from our work revealed that the<br \/>\navailable parameters from the AMBER distribution were inadequate in reproducing the<br \/>\nexperimentally observed conformational distributions<br \/>\nWe earlier adopted a procedure for reoptimizing the dihedral parameters of a few modified<br \/>\nuridines using high-level ab initio calculations. We earlier adopted a procedure for<br \/>\nreoptimizing the dihedral parameters of a few modified uridines using high-level ab initio<br \/>\ncalculations.<br \/>\nThe reoptimized parameter set has been validated against experimentally observed<br \/>\nconformational distributions for a considerable number of modified residues. We have also<br \/>\nshown that for some of the modifications, like 2-thiolation of uridines and pseudouridylation,<br \/>\nthe modifications stabilize the RNA structure. A major role in such stabilization is played by<br \/>\nthe enhancement in stacking interaction.<br \/>\nThe results obtained suggest that the combination of AMBER force field for RNA with our<br \/>\nreoptimized set of dihedral parameters and the recalculated partial charges provide a better<br \/>\nagreement with experimental data and as such should be more useful in producing a more<br \/>\naccurate model of the structure and function of modified RNA.<\/p>\n<a href=\"https:\/\/bgrssb.icgbio.ru\/2022\/wp-content\/uploads\/sites\/3\/2022\/06\/2022BGRSslides.pdf\" class=\"pdfemb-viewer\" style=\"\" data-width=\"max\" data-height=\"max\"  data-toolbar=\"bottom\" data-toolbar-fixed=\"off\">2022BGRSslides<br\/><\/a>\n","protected":false},"excerpt":{"rendered":"<p>by Ansuman Lahiri | University of Calcutta Post-transcriptional modifications occur extensively in RNA and provide an additional layer of chemical coding that presumably alters the chemistry, structure and dynamics of the molecules. Molecular dynamics simulations offer a convenient tool to elucidate the mechanisms underlying the roles played by such modifications. However, since the reliability of [&hellip;]<\/p>\n","protected":false},"author":3967,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[7],"tags":[292,282,291],"_links":{"self":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts\/15943"}],"collection":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/users\/3967"}],"replies":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/comments?post=15943"}],"version-history":[{"count":2,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts\/15943\/revisions"}],"predecessor-version":[{"id":18077,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts\/15943\/revisions\/18077"}],"wp:attachment":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/media?parent=15943"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/categories?post=15943"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/tags?post=15943"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}