{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T11:02:55Z","timestamp":1791198175970,"version":"4.1.0"},"reference-count":35,"publisher":"AIP Publishing","issue":"13","funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32171246"],"award-info":[{"award-number":["32171246"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32671647"],"award-info":[{"award-number":["32671647"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Government Science Innovation Grant","award":["21JC1403700"],"award-info":[{"award-number":["21JC1403700"]}]}],"content-domain":{"domain":["pubs.aip.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:p>The CRISPR-Cas9 system\u2019s gene-editing fidelity relies on the HNH nuclease domain\u2019s ability to hydrolyze DNA via metal-ion catalysis. While IscB-\u03c9RNA variants offer advantages for viral delivery due to their small size, their editing efficiency is much lower than that of Cas9. The understanding of how HNH-domain dynamics and metal-ion selection jointly control catalysis is essential for its rational improvement. Here, we employ molecular dynamics (MD) simulations, quantum mechanics\/molecular mechanics (QM\/MM) simulations, and free energy perturbations (FEP) to study the conformation dynamics of the IscB\u2013\u03c9RNA\u2013target DNA complex and cation binding energy in the core HNH(IscB)\u2013DNA region. Our MD simulations revealed that the IscB\u2013\u03c9RNA\u2013DNA complex is overall stable. However, the core HNH(IscB)\u2013DNA region shifts to a larger separation, consistent with recent findings of coupling between HNH motion and activation in IscB\u2013\u03c9RNA\u2013DNA. However, the HNH domain motion may be decreased by Cas9-like H246D\/H270N mutations. QM\/MM and FEP studies found that three Cas9 activating ions, Mg2+, Mn2+, and Co2+, also have higher binding energy in the mutated HNH(IscB)\u2013DNA region, suggesting that the catalytic efficiencies of IscB\u2013\u03c9RNA could be subjected to the balance between stabilizing ion binding and domain motions.<\/jats:p>","DOI":"10.1063\/5.0350765","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T10:39:48Z","timestamp":1791196788000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Molecular dynamics simulation and QM\/MM study of IscB-\u03c9RNA complex"],"prefix":"10.1063","volume":"165","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-2688-4703","authenticated-orcid":false,"given":"Amina","family":"Abula","sequence":"first","affiliation":[{"name":"Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University , Shanghai 200240,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8885-4796","authenticated-orcid":false,"given":"Ganggang","family":"Bai","sequence":"additional","affiliation":[{"name":"Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University , Shanghai 200240,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0661-5642","authenticated-orcid":false,"given":"Jingjing","family":"Li","sequence":"additional","affiliation":[{"name":"Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University , Shanghai 200240,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7383-719X","authenticated-orcid":false,"given":"Buyong","family":"Ma","sequence":"additional","affiliation":[{"name":"Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University , Shanghai 200240,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"317","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"key":"2026100506394493600_c1","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1126\/science.1225829","article-title":"A programmable dual-RNA\u2013guided DNA endonuclease in adaptive bacterial immunity","volume":"337","year":"2012","journal-title":"Science"},{"key":"2026100506394493600_c2","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1016\/j.cell.2014.02.001","article-title":"Crystal structure of Cas9 in complex with guide RNA and target DNA","volume":"156","year":"2014","journal-title":"Cell"},{"key":"2026100506394493600_c3","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1126\/science.aad8282","article-title":"Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage","volume":"351","year":"2016","journal-title":"Science"},{"key":"2026100506394493600_c4","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1038\/nature15544","article-title":"Conformational control of DNA target cleavage by CRISPR\u2013Cas9","volume":"527","year":"2015","journal-title":"Nature"},{"key":"2026100506394493600_c5","doi-asserted-by":"publisher","first-page":"eaao0027","DOI":"10.1126\/sciadv.aao0027","article-title":"A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9","volume":"3","year":"2017","journal-title":"Sci. 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