{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,8]],"date-time":"2023-09-08T09:41:31Z","timestamp":1694166091734},"reference-count":70,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2020,1,7]],"date-time":"2020-01-07T00:00:00Z","timestamp":1578355200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"Centre R\u00e9gional Informatique et d'Applications Num\u00e9riques de Haute Normandie","award":["1998053"]},{"name":"Grand Equipement National de Calcul Intensif (GENCI), Institut du D\u00e9veloppement et des Ressources en Informatique Scientifique (IDRIS), Centre Informatique de l'Enseignement Sup\u00e9rieur","award":["x2009-075009"]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2020,3,30]]},"abstract":"We calibrate and validate the parameters necessary to represent the dianionic phosphate group (DPG) in molecular mechanics. DPG is an essential fragment of signaling biological molecules and protein\u2010binding ligands. It is a constitutive fragment of biosensors, which bind to the dimer interface of phosphoglucose isomerase (PGI), an intracellular enzyme involved in sugar metabolism, as well as an extracellular protein known as autocrine motility factor (AMF) closely related to metastasis formation. Our long\u2010term objective is to design DPG\u2010based biosensors with enhanced affinities for AMF\/PGI cancer biomarker in blood. Molecular dynamics with polarizable potentials could be used toward this aim. This requires to first evaluate the accuracy of such potentials upon representing the interactions of DPG with its PGI ligands and tightly bound water molecules. Such evaluations are done by comparisons with high\u2010level ab initio quantum chemistry (QC) calculations. We focus on the Sum of Interactions Between Fragments Ab initio computed (SIBFA) polarizable molecular mechanics procedure. We present first the results of the DPG calibration. This is followed by comparisons between \u0394E(SIBFA) and \u0394E(QC) regarding bi\u2010molecular complexes of DPG with the main\u2010chain and side\u2010chain PGI residues, which bind to it in the recognition site. We then consider DPG complexes with an increasing number of PGI residues. The largest QC complexes encompass the entirety of the recognition site, with six structural water molecules totaling up to 211 atoms. A persistent and satisfactory agreement could be shown between \u0394E(SIBFA) and \u0394E(QC). These validations constitute an essential first step toward large\u2010scale molecular dynamics simulations of DPG\u2010based biosensors bound at the PGI dimer interface. \u00a9 2020 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.26134","type":"journal-article","created":{"date-parts":[[2020,1,7]],"date-time":"2020-01-07T16:47:26Z","timestamp":1578415646000},"page":"839-854","update-policy":"http:\/\/dx.doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase"],"prefix":"10.1002","volume":"41","author":[{"given":"Marion","family":"Devillers","sequence":"first","affiliation":[{"name":"Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Mol\u00e9culaire et des Mat\u00e9riaux d'Orsay (ICMMO), Univ Paris\u2010Saclay, Univ Paris\u2010Sud, UMR 8182 CNRS, rue du Doyen Georges Poitou F\u201091405 Orsay France"}]},{"given":"Jean\u2010Philip","family":"Piquemal","sequence":"additional","affiliation":[{"name":"Laboratoire de Chimie Th\u00e9orique, Sorbonne Universit\u00e9, UMR 7616 CNRS Paris France"},{"name":"Department of Biomolecular Engineering The University of Texas at Austin Texas 78712"}]},{"given":"Laurent","family":"Salmon","sequence":"additional","affiliation":[{"name":"Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Mol\u00e9culaire et des Mat\u00e9riaux d'Orsay (ICMMO), Univ Paris\u2010Saclay, Univ Paris\u2010Sud, UMR 8182 CNRS, rue du Doyen Georges Poitou F\u201091405 Orsay France"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-7174-2907","authenticated-orcid":false,"given":"Nohad","family":"Gresh","sequence":"additional","affiliation":[{"name":"Laboratoire de Chimie Th\u00e9orique, Sorbonne Universit\u00e9, UMR 7616 CNRS Paris France"}]}],"member":"311","published-online":{"date-parts":[[2020,1,7]]},"reference":[{"key":"e_1_2_6_1_1","doi-asserted-by":"publisher","DOI":"10.1038\/348125a0"},{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/iub.1997"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioorg.2014.08.002"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2019.00004"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tem.2015.09.013"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.2337\/db15-0640"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/emm.2015.122"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/brv.12140"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.28228"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01890460"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0596-470"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/1873-3468.13059"},{"key":"e_1_2_6_13_1","first-page":"2960","volume":"56","author":"Watanabe H.","year":"1996","journal-title":"Cancer Res."},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.3109\/07357909009012053"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bios.2017.04.031"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi991604m"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M002017200"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi0018483"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi002916o"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.052131799"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00186-9"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1107\/S0907444903007352"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct200133y"},{"key":"e_1_2_6_24_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct100578z"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh381"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00190"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20586"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22873"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp2024654"},{"key":"e_1_2_6_30_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24503"},{"key":"e_1_2_6_31_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct700134r"},{"key":"e_1_2_6_32_1","doi-asserted-by":"publisher","DOI":"10.1039\/C7SC04531J"},{"key":"e_1_2_6_33_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.10312"},{"key":"e_1_2_6_34_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp907629k"},{"key":"e_1_2_6_35_1","doi-asserted-by":"publisher","DOI":"10.1021\/cr00031a008"},{"key":"e_1_2_6_36_1","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.91.033201"},{"key":"e_1_2_6_37_1","doi-asserted-by":"publisher","DOI":"10.1016\/0009-2614(87)80143-4"},{"key":"e_1_2_6_38_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199910)20:13<1379::AID-JCC5>3.0.CO;2-0"},{"key":"e_1_2_6_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/1096-987X(200009)21:12<1011::AID-JCC1>3.0.CO;2-B"},{"key":"e_1_2_6_40_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.24830"},{"key":"e_1_2_6_41_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.456153"},{"key":"e_1_2_6_42_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199610)17:13<1571::AID-JCC9>3.0.CO;2-P"},{"key":"e_1_2_6_43_1","volume-title":"Gaussian 09, Revision A.1","author":"Frisch M. J.","year":"2009"},{"key":"e_1_2_6_44_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540141112"},{"key":"e_1_2_6_45_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00174"},{"key":"e_1_2_6_46_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.1558473"},{"key":"e_1_2_6_47_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.2358353"},{"key":"e_1_2_6_48_1","doi-asserted-by":"publisher","DOI":"10.1039\/c0cp02984j"},{"key":"e_1_2_6_49_1","doi-asserted-by":"publisher","DOI":"10.1080\/00268977000101561"},{"key":"e_1_2_6_50_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp112251z"},{"key":"e_1_2_6_51_1","doi-asserted-by":"publisher","DOI":"10.1021\/j100362a023"},{"key":"e_1_2_6_52_1","unstructured":"The HSL. Mathematical Software Library; Science and Technology Facilities Council.http:\/\/www.hsl.rl.ac.uk\/."},{"key":"e_1_2_6_53_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp035748t"},{"key":"e_1_2_6_54_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.540160705"},{"key":"e_1_2_6_55_1","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4655(87)90094-4"},{"key":"e_1_2_6_56_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B"},{"key":"e_1_2_6_57_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct500175m"},{"key":"e_1_2_6_58_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.7b00875"},{"key":"e_1_2_6_59_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12551-017-0311-5"},{"key":"e_1_2_6_60_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.9b00202"},{"key":"e_1_2_6_61_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23661"},{"key":"e_1_2_6_62_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.436518"},{"key":"e_1_2_6_63_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199609)17:12<1481::AID-JCC7>3.0.CO;2-G"},{"key":"e_1_2_6_64_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20012"},{"key":"e_1_2_6_65_1","doi-asserted-by":"publisher","DOI":"10.1093\/acprof:oso\/9780199672394.001.0001"},{"key":"e_1_2_6_66_1","doi-asserted-by":"publisher","DOI":"10.1051\/jcp\/1991882399"},{"key":"e_1_2_6_67_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.7b01053"},{"key":"e_1_2_6_68_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.5b01695"},{"key":"e_1_2_6_69_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpcb.7b01836"},{"key":"e_1_2_6_70_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja9059156"}],"container-title":["Journal of Computational Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fjcc.26134","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26134","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jcc.26134","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcc.26134","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,7]],"date-time":"2023-09-07T22:24:32Z","timestamp":1694125472000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.26134"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,7]]},"references-count":70,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2020,3,30]]}},"alternative-id":["10.1002\/jcc.26134"],"URL":"https:\/\/doi.org\/10.1002\/jcc.26134","archive":["Portico"],"relation":{},"ISSN":["0192-8651","1096-987X"],"issn-type":[{"value":"0192-8651","type":"print"},{"value":"1096-987X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,7]]},"assertion":[{"value":"2019-08-23","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-12-05","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-01-07","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}