{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T09:35:59Z","timestamp":1767864959414,"version":"3.49.0"},"reference-count":36,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2022,4,11]],"date-time":"2022-04-11T00:00:00Z","timestamp":1649635200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81902059"],"award-info":[{"award-number":["81902059"]}],"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":["32071448"],"award-info":[{"award-number":["32071448"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Major Projects of Guangdong Education Department for Foundation Research and Applied Re-search","award":["2020A1515011170"],"award-info":[{"award-number":["2020A1515011170"]}]},{"DOI":"10.13039\/501100002402","name":"Sun Yat-sen University","doi-asserted-by":"publisher","award":["19ykzd28"],"award-info":[{"award-number":["19ykzd28"]}],"id":[{"id":"10.13039\/501100002402","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Dengue virus (DENV) has four serotypes that complicate vaccine development. Envelope protein domain III (EDIII) of DENV is a promising target for therapeutic antibody development. One EDIII-specific antibody, dubbed 1A1D-2, cross-reacts with DENV 1, 2, and 3 but not 4. To improve the affinity of 1A1D-2, in this study, we analyzed the previously solved structure of 1A1D-2-DENV2 EDIII complex. Mutations were designed, including A54E and Y105R in the heavy chain, with charges complementary to the epitope. Molecular dynamics simulation was then used to validate the formation of predicted salt bridges. Interestingly, a surface plasmon resonance experiment showed that both mutations increased affinities of 1A1D-2 toward EDIII of DENV1, 2, and 3 regardless of their sequence variation. Results also revealed that A54E improved affinities through both a faster association and slower dissociation, whereas Y105R improved affinities through a slower dissociation. Further simulation suggested that the same mutants interacted with different residues in different serotypes. Remarkably, combination of the two mutations additively improved 1A1D-2 affinity by 8, 36, and 13-fold toward DENV1, 2, and 3, respectively. In summary, this study demonstrated the utility of tweaking antibody-antigen charge complementarity for affinity maturation and emphasized the complexity of improving antibody affinity toward multiple antigens.<\/jats:p>","DOI":"10.3390\/ijms23084197","type":"journal-article","created":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T00:23:11Z","timestamp":1649722991000},"page":"4197","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Charged Residue Implantation Improves the Affinity of a Cross-Reactive Dengue Virus Antibody"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5854-6100","authenticated-orcid":false,"given":"Huiling","family":"Wei","sequence":"first","affiliation":[{"name":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Tan","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bingjie","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaotong","family":"Guan","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiaoxian","family":"Zhong","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8399-188X","authenticated-orcid":false,"given":"Jiaqi","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,4,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1038\/s41564-019-0476-8","article-title":"The current and future global distribution and population at risk of dengue","volume":"4","author":"Messina","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.virol.2010.12.020","article-title":"Antibody-mediated neutralization of flaviviruses: A reductionist view","volume":"411","author":"Dowd","year":"2011","journal-title":"Virology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.cell.2017.09.002","article-title":"A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential","volume":"171","author":"Wang","year":"2017","journal-title":"Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1080\/19420862.2016.1148850","article-title":"A bispecific antibody effectively neutralizes all four serotypes of dengue virus by simultaneous blocking virus attachment and fusion","volume":"8","author":"Shi","year":"2016","journal-title":"mAbs"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1126\/science.1185181","article-title":"Cross-Reacting Antibodies Enhance Dengue Virus Infection in Humans","volume":"328","author":"Dejnirattisai","year":"2010","journal-title":"Science"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"7439","DOI":"10.1073\/pnas.1200566109","article-title":"Identification of human neutralizing antibodies that bind to complex epitopes on dengue virions","volume":"109","author":"Smith","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"139ra83","DOI":"10.1126\/scitranslmed.3003888","article-title":"The Structural Basis for Serotype-Specific Neutralization of Dengue Virus by a Human Antibody","volume":"4","author":"Teoh","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1126\/science.aaa8651","article-title":"Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers","volume":"349","author":"Fibriansah","year":"2015","journal-title":"Science"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/ni.3058","article-title":"A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus","volume":"16","author":"Dejnirattisai","year":"2014","journal-title":"Nat. Immunol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.chom.2010.08.007","article-title":"The Human Immune Response to Dengue Virus Is Dominated by Highly Cross-Reactive Antibodies Endowed with Neutralizing and Enhancing Activity","volume":"8","author":"Beltramello","year":"2010","journal-title":"Cell Host Microbe"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Edeling, M.A., Austin, S.K., Shrestha, B., Dowd, K.A., Mukherjee, S., Nelson, C.A., Johnson, S., Mabila, M.N., Christian, E., and Rucker, J. (2014). Potent Dengue Virus Neutralization by a Therapeutic Antibody with Low Monovalent Affinity Requires Bivalent Engagement. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1004072"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"4971","DOI":"10.4049\/jimmunol.1200227","article-title":"Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity","volume":"188","author":"Midgley","year":"2012","journal-title":"J. Immunol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/nsmb.1382","article-title":"Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins","volume":"15","author":"Lok","year":"2008","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"E1555","DOI":"10.1073\/pnas.1303645110","article-title":"Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency","volume":"110","author":"Tharakaraman","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1021\/acs.biochem.0c00912","article-title":"Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design","volume":"60","author":"Schoeder","year":"2021","journal-title":"Biochemistry"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"10037","DOI":"10.1073\/pnas.181342398","article-title":"Electrostatics of nanosystems: Application to microtubules and the ribosome","volume":"98","author":"Baker","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","first-page":"U1371","article-title":"PyMOL: A communications tool for computational models","volume":"Volume 230","author":"DeLano","year":"2005","journal-title":"Abstracts of Papers of the American Chemical Society"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","article-title":"gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS","volume":"17","author":"Valiente","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1073\/pnas.1218256109","article-title":"Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody","volume":"110","author":"Schmidt","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2523","DOI":"10.1172\/JCI80693","article-title":"Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth","volume":"125","author":"Willis","year":"2015","journal-title":"J. Clin. Investig."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Warszawski, S., Katz, A.B., Lipsh, R., Khmelnitsky, L., Ben Nissan, G., Javitt, G., Dym, O., Unger, T., Knop, O., and Albeck, S. (2019). Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLoS Comput. Biol., 15.","DOI":"10.2210\/pdb6gc2\/pdb"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1038\/nbt1336","article-title":"Computational design of antibody-affinity improvement beyond in vivo maturation","volume":"25","author":"Lippow","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.cell.2015.06.057","article-title":"Structure-Guided Design of an Anti-dengue Antibody Directed to a Non-immunodominant Epitope","volume":"162","author":"Robinson","year":"2015","journal-title":"Cell"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1126\/science.1079731","article-title":"Antibody Multispecificity Mediated by Conformational Diversity","volume":"299","author":"James","year":"2003","journal-title":"Science"},{"key":"ref_25","first-page":"537","article-title":"Rational design of faster associating and tighter binding protein complexes","volume":"7","author":"Selzer","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.virol.2009.06.037","article-title":"Dengue virus neutralization by human immune sera: Role of envelope protein domain III-reactive antibody","volume":"392","author":"Wahala","year":"2009","journal-title":"Virology"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/j.str.2012.01.001","article-title":"Mechanism of Dengue Virus Broad Cross-Neutralization by a Monoclonal Antibody","volume":"20","author":"Cockburn","year":"2012","journal-title":"Structure"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1099\/vir.0.055178-0","article-title":"Dengue virus envelope domain III immunization elicits predominantly cross-reactive, poorly neutralizing an-tibodies localized to the AB loop: Implications for dengue vaccine design","volume":"94","author":"Li","year":"2013","journal-title":"J. Gen. Virol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.str.2017.11.017","article-title":"Structural and Functional Characterization of a Cross-Reactive Dengue Virus Neutralizing Antibody that Recog-nizes a Cryptic Epitope","volume":"26","author":"Li","year":"2018","journal-title":"Structure"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Lim, X.-N., Shan, C., Marzinek, J., Dong, H., Ng, T.S., Ooi, J., Fibriansah, G., Wang, J., Verma, C.S., and Bond, P.J. (2019). Molecular basis of dengue virus serotype 2 morphological switch from 29 \u00b0C to 37 \u00b0C. PLoS Pathog., 15.","DOI":"10.1371\/journal.ppat.1007996"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"7585","DOI":"10.1128\/JVI.00757-13","article-title":"Structural Changes in Dengue Virus When Exposed to a Temperature of 37 \u00b0C","volume":"87","author":"Fibriansah","year":"2013","journal-title":"J. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Hu, D., Zhu, Z., Li, S., Deng, Y., Wu, Y., Zhang, N., Puri, V., Wang, C., Zou, P., and Lei, C. (2019). A broadly neutralizing germline-like human monoclonal antibody against dengue virus envelope domain III. PLoS Pathog., 15.","DOI":"10.1371\/journal.ppat.1007836"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.jchromb.2007.06.013","article-title":"A simplified purification procedure for recombinant human granulocyte macrophage-colony stimulating factor from periplasmic space of Escherichia coli","volume":"856","author":"Jazii","year":"2007","journal-title":"J. Chromatogr. B"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1002\/prot.22711","article-title":"Improved side-chain torsion potentials for the Amber ff99SB protein force field","volume":"78","author":"Piana","year":"2010","journal-title":"Proteins"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1002\/prot.20033","article-title":"Exploring protein native states and large-scale conformational changes with a modified generalized born model","volume":"55","author":"Onufriev","year":"2004","journal-title":"Proteins Struct. Funct. Bioinform."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/8\/4197\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:51:30Z","timestamp":1760136690000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/8\/4197"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,11]]},"references-count":36,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,4]]}},"alternative-id":["ijms23084197"],"URL":"https:\/\/doi.org\/10.3390\/ijms23084197","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,11]]}}}