{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T14:14:09Z","timestamp":1788358449874,"version":"build-2803163510"},"reference-count":90,"publisher":"American Chemical Society (ACS)","issue":"11","license":[{"start":{"date-parts":[[2018,11,13]],"date-time":"2018-11-13T00:00:00Z","timestamp":1542067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The scaffold nature of Xeroderma pigmentosum complementation group A (XPA) protein makes it an important member of nucleotide excision repair (NER) that removes bulky DNA lesions with the help of various protein\u2013protein interactions (PPI) and DNA\u2013protein interactions. However, many structural insights of XPA\u2019s interaction and the binding patterns with other NER proteins are yet to be understood. Here, we have studied one such crucial PPI of XPA with another NER protein, Xeroderma pigmentosum complementation group A (XPE), by using the previously identified binding site of XPA (residues 185\u2013226) in the Assisted Model Building With Energy Refinement force-field-mediated dynamic system. We studied the relationship between XPA185\u2013226\u2013XPE complex using three different docked models. The major residues observed in all of the models that were responsible for the PPI of this complex were Arg20, Arg47, Asp51, and Leu57 from XPE and the residues Leu191, Gln192, Val193, Trp194, Glu198, Glu202, Glu205, Arg207, Glu209, Gln216, and Phe219 from XPE185\u2013226. During the simulation study, the orientation of XPA was also noted to be changed by almost 180\u00b0 in models 1 and 3, which remain unchanged in model 2, indicating that XPA interacts with XPE with its N-terminal end facing downward and C-terminal end facing upward. The same was concurrent with the binding of DNA-binding domain region of XPA (aa98\u2013239) with XPE. The N-terminal of XPE was stretched for accommodating XPA. Using the per-residue energy decomposition analysis for the interface residues of all models, the binding affinity between these proteins were found to be dependent on R20, R47, and L57 of XPE and the residues L191, V193, W194, E198, E202, E205, R207, and F219 of XPA. The net binding free energy of the XPA185\u2013226\u2013XPE protein complex was found to be \u221248.3718 kcal mol\u20131 for model 1, \u221249.09 kcal mol\u20131 for model 2, and \u221256.51 kcal mol\u20131 for model 3.<\/jats:p>","DOI":"10.1021\/acsomega.8b01793","type":"journal-article","created":{"date-parts":[[2018,11,13]],"date-time":"2018-11-13T13:43:36Z","timestamp":1542116616000},"page":"15442-15454","source":"Crossref","is-referenced-by-count":4,"title":["Characterizing the Binding Interactions between DNA-Binding Proteins, XPA\nand XPE: A Molecular Dynamics Approach"],"prefix":"10.1021","volume":"3","author":[{"given":"Sushmita","family":"Pradhan","sequence":"first","affiliation":[{"name":"Tezpur University , , , ,","place":["Tezpur, Assam, India, 784 028"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pundarikaksha","family":"Das","sequence":"additional","affiliation":[{"name":"Tezpur University , , , ,","place":["Tezpur, Assam, India, 784 028"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5238-753X","authenticated-orcid":true,"given":"Venkata Satish Kumar","family":"Mattaparthi","sequence":"additional","affiliation":[{"name":"Tezpur University , , , ,","place":["Tezpur, Assam, India, 784 028"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2018,11,13]]},"reference":[{"key":"2026090209282481600_cit1","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1080\/07391102.1996.10508930","article-title":"NMR solution\nstructure of a DNA decamer containing an interstrand cross-link of\nthe antitumor drug cis-diamminedichloroplatinum (II)","volume":"14","author":"Paquet","year":"1996","journal-title":"J. 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Invest. Dermatol."},{"key":"2026090209282481600_cit19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2013\/854745","article-title":"Structural and sequence similarities\nof hydra Xeroderma pigmentosum a protein to human\nhomolog suggest early evolution and conservation","author":"Barve","year":"2013","journal-title":"Biomed. Res. Int."},{"key":"2026090209282481600_cit20","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1016\/0168-9525(93)90121-W","article-title":"Nucleotide\nexcision repair II: from yeast to mammals","volume":"9","author":"Hoeijmakers","year":"1993","journal-title":"Trends\nGenet."},{"key":"2026090209282481600_cit21","doi-asserted-by":"publisher","first-page":"22452","DOI":"10.1074\/jbc.270.38.22452","article-title":"Expression and functional\nanalyses\nof the Dxpa gene, the Drosophila homolog of the human excision repair\ngene XPA","volume":"270","author":"Shimamoto","year":"1995","journal-title":"J. Biol. 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Biochem."},{"key":"2026090209282481600_cit26","doi-asserted-by":"publisher","first-page":"2635","DOI":"10.1093\/nar\/29.12.2635","article-title":"DNA\u2013XPA interactions:\na 31P NMR and molecular\nmodeling study of dCCAATAACC association with the minimal DNA-binding\ndomain (M98\u2013F219) of the nucleotide excision repair protein\nXPA","volume":"29","author":"Buchko","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2026090209282481600_cit27","doi-asserted-by":"publisher","first-page":"3554","DOI":"10.1093\/emboj\/20.13.3554","article-title":"Double-check\nprobing of DNA bending and unwinding by XPA\u2013RPA: an architectural\nfunction in DNA repair","volume":"20","author":"Missura","year":"2001","journal-title":"EMBO J."},{"key":"2026090209282481600_cit28","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1042\/BSR20140158","article-title":"A new structural insight into XPA\u2013DNA\ninteractions","volume":"34","author":"Hilton","year":"2014","journal-title":"Biosci. 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Chem."},{"key":"2026090209282481600_cit31","doi-asserted-by":"publisher","first-page":"1025","DOI":"10.1016\/j.molcel.2015.08.012","article-title":"Tripartite\nDNA lesion recognition and verification by XPC, TFIIH,\nand XPA in nucleotide excision repair","volume":"59","author":"Li","year":"2015","journal-title":"Mol.\nCell"},{"key":"2026090209282481600_cit32","doi-asserted-by":"publisher","first-page":"14965","DOI":"10.1021\/bi061370o","article-title":"Biochemical\nand structural domain analysis of Xeroderma pigmentosum complementation group C protein","volume":"45","author":"Bunick","year":"2006","journal-title":"Biochemistry"},{"key":"2026090209282481600_cit33","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/S1097-2765(01)00281-7","article-title":"Sequential\nassembly of the nucleotide excision repair factors in vivo","volume":"8","author":"Volker","year":"2001","journal-title":"Mol. 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U.S.A."},{"key":"2026090209282481600_cit36","doi-asserted-by":"publisher","first-page":"9990","DOI":"10.1093\/nar\/gks818","article-title":"DNA repair endonuclease ERCC1\u2013XPF as a novel\ntherapeutic target to overcome chemoresistance in cancer therapy","volume":"40","author":"McNeil","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2026090209282481600_cit37","doi-asserted-by":"publisher","first-page":"4768","DOI":"10.1038\/sj.emboj.7601894","article-title":"Structural\nbasis for the recruitment\nof ERCC1-XPF to nucleotide excision repair complexes by XPA","volume":"26","author":"Tsodikov","year":"2007","journal-title":"EMBO J."},{"key":"2026090209282481600_cit38","doi-asserted-by":"publisher","first-page":"16096","DOI":"10.1074\/jbc.M200816200","article-title":"Xeroderma pigmentosum\ncomplementation group A protein\n(XPA) modulates RPA-DNA interactions via enhanced complex stability\nand inhibition of strand separation activity","volume":"277","author":"Patrick","year":"2002","journal-title":"J. Biol. Chem."},{"key":"2026090209282481600_cit39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001183","article-title":"Regulation\nof nucleotide excision repair by UV-DDB:\nprioritization of damage recognition to internucleosomal DNA","volume":"9","author":"Fei","year":"2011","journal-title":"PLoS Biol."},{"key":"2026090209282481600_cit40","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1016\/S1568-7864(02)00052-6","article-title":"Xeroderma pigmentosum complementation group E and UV-damaged DNA-binding\nprotein","volume":"1","author":"Tang","year":"2002","journal-title":"DNA Repair"},{"key":"2026090209282481600_cit41","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1016\/S1568-7864(03)00113-7","article-title":"DDB complexities","volume":"2","author":"Wittschieben","year":"2003","journal-title":"DNA Repair"},{"key":"2026090209282481600_cit42","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1093\/nar\/gkn964","article-title":"Physical and\nfunctional interaction between DDB and XPA in nucleotide excision\nrepair","volume":"37","author":"Wakasugi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2026090209282481600_cit43","doi-asserted-by":"publisher","first-page":"W96","DOI":"10.1093\/nar\/gkh354","article-title":"ClusPro: a fully\nautomated algorithm for protein\u2013protein docking","volume":"32","author":"Comeau","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2026090209282481600_cit44","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.1002\/prot.24403","article-title":"How good is\nautomated protein docking?","volume":"81","author":"Kozakov","year":"2013","journal-title":"Proteins"},{"key":"2026090209282481600_cit45","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server\nfor protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc."},{"key":"2026090209282481600_cit46","unstructured":"Case, D. A.; Babin, V.; Berryman, J. T.; Betz, R. M.; Cai, Q.; Cerutti, D. S.; Cheatham, T. E.; Darden, T. A.; Duke, R. E.; Gohlke, H.; Goetz, A. W.; Gusarov, S.; Homeyer, N.; Janowski, P.; Kaus, J.; Kolossva\u0301ry, I.; Kovalenko, A.; Lee, T. S.; LeGrand, S.; Luchko, T.; Luo, R.; Madej, B.; Merz, K. M.; Paesani, F.; Roe, D. R.; Roitberg, A.; Sagui, C.; Salomon-Ferrer, R.; Seabra, G.; Simmerling, C. L.; Smith, W.; Swails, J.; Walker, R. C.; Wang, J.; Wolf, R. M.; Wu, X.; Kollman, P. A.\n          AMBER 14; University of California: San Francisco, 2014."},{"key":"2026090209282481600_cit47","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1021\/ci100275a","article-title":"Assessing the performance\nof the MM\/PBSA and MM\/GBSA methods. 1. The accuracy of binding free\nenergy calculations based on molecular dynamics simulations","volume":"51","author":"Hou","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"2026090209282481600_cit48","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1021\/ar000033j","article-title":"Calculating\nstructures\nand free energies of complex molecules: combining molecular mechanics\nand continuum models","volume":"33","author":"Kollman","year":"2000","journal-title":"Acc. Chem. Res."},{"key":"2026090209282481600_cit49","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1023\/A:1008763014207","article-title":"Combined molecular mechanical and continuum solvent\napproach (MM-PBSA\/GBSA) to predict ligand binding","volume":"18","author":"Massova","year":"2000","journal-title":"Perspect. Drug Discovery Des."},{"key":"2026090209282481600_cit50","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1146\/annurev.biophys.30.1.211","article-title":"Biomolecular simulations:\nrecent developments in force fields, simulations of enzyme catalysis,\nprotein-ligand, protein\u2013protein, and protein-nucleic acid noncovalent\ninteractions","volume":"30","author":"Wang","year":"2001","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"2026090209282481600_cit51","doi-asserted-by":"publisher","first-page":"287","DOI":"10.2174\/157340906778226454","article-title":"Recent advances\nin free energy calculations with a\ncombination of molecular mechanics and continuum models","volume":"2","author":"Wang","year":"2006","journal-title":"Curr. 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