{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:43:34Z","timestamp":1792784614444,"version":"4.5.0"},"reference-count":97,"publisher":"American Chemical Society (ACS)","issue":"19","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"National Natural Science Foundation of China (NSFC)","award":["22273033"],"award-info":[{"award-number":["22273033"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Zinc (Zn), the second most abundant transition metal in biological systems, plays essential roles in numerous metalloproteins present in diverse organisms including humans, plants, and bacteria. Currently, Zn-based proteins have attracted research interest owing to their involvement in a series of vital physiological processes, such as enzymatic reactions, deoxyribonucleic acid and ribonucleic acid binding, and the stability of biological structures. Although experimental methods can reveal macroscopic processes, they cannot efficiently capture the detailed behavior of these compounds. Therefore, theoretical exploration of Zn-binding conformations is significant. Herein, a fluctuating charge force field for Zn-containing metalloproteins is reported based on the atom-bond electronegativity equalization method (ABEEM). We designed our model molecules based on the Protein Data Bank (PDB) database, focusing primarily on tetracoordinated Zn proteins. The ABEEM polarizable force field parameters were determined and optimized using the quantum mechanical method, which were in good agreement with computed charge distributions, potential energy surfaces, and geometric structures. Molecular dynamics simulations were subsequently performed on 10 different protein segments. The developed ABEEM model reproduces the first Zn\u2013Ow peak position and maintains the structural stability of the systems throughout the simulations. Compared with the crystal structures from the PDB database, the ABEEM model shows lower root mean square deviation values for heavy atoms in these domains. All protein domains can dynamically capture the change in charge distributions. This process can be further applied to simulate the detailed behavior of the molecules and investigate their properties. The identified force field for Zn metalloproteins by the ABEEM provides a promising approach for simulating Zn-related biological systems while simplifying several complex and time-consuming processes.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c01082","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T04:02:06Z","timestamp":1789444926000},"page":"10244-10262","source":"Crossref","is-referenced-by-count":0,"title":["Developing the\nAtom-Bond Electronegativity Equalization\nMethod Polarizable Force Field for Zinc Metalloproteins and Their\nSimulations"],"prefix":"10.1021","volume":"22","author":[{"given":"Zhan-Qing","family":"Yu","sequence":"first","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuo-Peng","family":"Liang","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wan-Qing","family":"Wang","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing-Yan","family":"Sun","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Huang","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2979-2040","authenticated-orcid":true,"given":"Cui","family":"Liu","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3635-0606","authenticated-orcid":true,"given":"Dong-Xia","family":"Zhao","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6767-2915","authenticated-orcid":true,"given":"Zhong-Zhi","family":"Yang","sequence":"additional","affiliation":[{"name":"Liaoning Normal University , , ,","place":["Dalian, The People\u2019s Republic of China, 116029"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"2026101310065254600_cit1","doi-asserted-by":"publisher","first-page":"9937","DOI":"10.1021\/bi200619w","article-title":"Zn(II) Binding to Escherichia coli\n70S ribosomes","volume":"50","author":"Hensley","year":"2011","journal-title":"Biochemistry"},{"key":"2026101310065254600_cit2","doi-asserted-by":"publisher","first-page":"1221519","DOI":"10.3389\/fpls.2023.1221519","article-title":"The zinc finger\nprotein 3 of Arabidopsis\nthaliana regulates vegetative growth and root hair development","volume":"14","author":"Benyo\u0301","year":"2023","journal-title":"Front. 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Theory Comput."},{"issue":"9","key":"2026101310065254600_cit46","doi-asserted-by":"publisher","first-page":"3803","DOI":"10.1021\/acs.jcim.9b00407","article-title":"upgrading\nand validation of the AMBER force field for histidine and cysteine\nzinc(ii)-binding residues in sites with four protein ligands","volume":"59","author":"Macchiagodena","year":"2019","journal-title":"J. Chem. Inf. Model."},{"issue":"9","key":"2026101310065254600_cit47","doi-asserted-by":"publisher","first-page":"4983","DOI":"10.1021\/acs.chemrev.5b00505","article-title":"An empirical\npolarizable force field based on the classical drude oscillator model:\ndevelopment history and recent applications","volume":"116","author":"Lemkul","year":"2016","journal-title":"Chem. Rev."},{"issue":"1","key":"2026101310065254600_cit48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jcc.10355","article-title":"CHARMM fluctuating charge force field\nfor proteins: I parameterization\nand application to bulk organic liquid simulations","volume":"25","author":"Patel","year":"2004","journal-title":"J. Comput. Chem."},{"issue":"3","key":"2026101310065254600_cit49","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1007\/s00214-012-1098-x","article-title":"Mg2+\/Ca2+ binding\nto DNA bases: a quantum chemical method and ABEEM\u03c3\u03c0\/MM fluctuating charge model study","volume":"131","author":"Yu","year":"2012","journal-title":"Theor.\nChem. 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