{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T10:27:43Z","timestamp":1787048863728,"version":"build-2736575974"},"reference-count":61,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T00:00:00Z","timestamp":1680048000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T00:00:00Z","timestamp":1680048000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T00:00:00Z","timestamp":1680048000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","award":["AWD11297"],"award-info":[{"award-number":["AWD11297"]}],"id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000048","name":"American Cancer Society","doi-asserted-by":"publisher","award":["GM01432"],"award-info":[{"award-number":["GM01432"]}],"id":[{"id":"10.13039\/100000048","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM120574"],"award-info":[{"award-number":["R01 GM120574"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM122518"],"award-info":[{"award-number":["R35 GM122518"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM141818"],"award-info":[{"award-number":["R35 GM141818"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Intrinsically disordered regions of proteins often mediate important protein\u2013protein interactions. However, the folding-upon-binding nature of many polypeptide\u2013protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide\u2013protein complexes. Here, we use the MELD (Modeling Employing Limited Data) technique applied to polypeptide complexes formed with the extraterminal domain (ET) of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can adopt different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only protein receptor backbone chemical shift data, in excellent agreement with experimentally determined structures for moderately tight (Kd \u223c100 nM) binders. The hybrid MELD + NMR approach required additional peptide ligand chemical shift data for weaker (Kd \u223c250 \u03bcM) peptide binding partners. AlphaFold also successfully predicts the structures of some of these peptide\u2013protein complexes. However, whereas AlphaFold can provide qualitative peptide rankings, MELD can directly estimate relative binding affinities. The hybrid MELD + NMR approach offers a powerful new tool for structural analysis of protein\u2013polypeptide complexes involving disorder-to-order transitions upon complex formation, which are not successfully modeled with most other complex prediction methods, providing both the 3D structures of peptide\u2013protein complexes and their relative binding affinities.<\/jats:p>","DOI":"10.1021\/acs.jcim.2c01595","type":"journal-article","created":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T15:11:10Z","timestamp":1680102670000},"page":"2058-2072","source":"Crossref","is-referenced-by-count":29,"title":["Structure Determination\nof Challenging Protein\u2013Peptide\nComplexes Combining NMR Chemical Shift Data and Molecular Dynamics\nSimulations"],"prefix":"10.1021","volume":"63","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8970-3380","authenticated-orcid":true,"given":"Arup","family":"Mondal","sequence":"first","affiliation":[{"name":"University of Florida , , , ,","place":["Gainesville, Florida, United States, 32611"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G.V.T.","family":"Swapna","sequence":"additional","affiliation":[{"name":"The State University of New Jersey , , , ,","place":["Piscataway, New Jersey, United States, 08854"]},{"name":"Rensselaer Polytechnic Institute , , , ,","place":["Troy, New York, United States, 12180"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria M.","family":"Lopez","sequence":"additional","affiliation":[{"name":"Rensselaer Polytechnic Institute , , , ,","place":["Troy, New York, United States, 12180"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Klang","sequence":"additional","affiliation":[{"name":"Rensselaer Polytechnic Institute , , , ,","place":["Troy, New York, United States, 12180"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingzhou","family":"Hao","sequence":"additional","affiliation":[{"name":"Rensselaer Polytechnic Institute , , , ,","place":["Troy, New York, United States, 12180"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"LiChung","family":"Ma","sequence":"additional","affiliation":[{"name":"The State University of New Jersey , , , ,","place":["Piscataway, New Jersey, United States, 08854"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica J.","family":"Roth","sequence":"additional","affiliation":[{"name":"The State University of New Jersey , , , ,","place":["Piscataway, New Jersey, United States, 08854"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9440-3059","authenticated-orcid":true,"given":"Gaetano T.","family":"Montelione","sequence":"additional","affiliation":[{"name":"Rensselaer Polytechnic Institute , , , ,","place":["Troy, New York, United States, 12180"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5054-5338","authenticated-orcid":true,"given":"Alberto","family":"Perez","sequence":"additional","affiliation":[{"name":"University of Florida , , , ,","place":["Gainesville, Florida, United States, 32611"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2023,3,29]]},"reference":[{"key":"2026081804435828000_cit1","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1039\/c7md00184c","article-title":"Assessing the Performance of Docking\nScoring Function, FEP, MM-GBSA, and QM\/MM-GBSA Approaches on a Series\nof PLK1 Inhibitors","volume":"8","author":"Pu","year":"2017","journal-title":"Medchemcomm"},{"key":"2026081804435828000_cit2","doi-asserted-by":"publisher","first-page":"3959","DOI":"10.1021\/acs.jctc.9b01208","article-title":"Comprehensive Evaluation of Fourteen Docking Programs\non Protein\u2013Peptide Complexes","volume":"16","author":"Weng","year":"2020","journal-title":"J. Chem.\nTheory Comput."},{"key":"2026081804435828000_cit3","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1186\/s12859-018-2449-y","article-title":"Benchmarking\nof Different Molecular Docking Methods\nfor Protein-Peptide Docking","volume":"19","author":"Agrawal","year":"2019","journal-title":"Bmc Bioinformatics"},{"key":"2026081804435828000_cit4","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly Accurate Protein\nStructure Prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2026081804435828000_cit5","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate Prediction\nof Protein Structures and Interactions Using a Three-Track Neural\nNetwork","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2026081804435828000_cit6","doi-asserted-by":"publisher","first-page":"04.463034","DOI":"10.1101\/2021.10.04.463034","article-title":"Protein Complex Prediction with AlphaFold-Multimer","volume":"2021","author":"Evans","year":"2021","journal-title":"Biorxiv"},{"key":"2026081804435828000_cit7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.str.2021.01.010","article-title":"A Common Binding Motif in the ET Domain of BRD3 Forms\nPolymorphic Structural Interfaces with Host and Viral Proteins","volume":"29","author":"Aiyer","year":"2021","journal-title":"Structure"},{"key":"2026081804435828000_cit8","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1002\/jcc.23973","article-title":"Accurately\nModeling Nanosecond Protein Dynamics Requires at Least Microseconds\nof Simulation","volume":"37","author":"Bowman","year":"2016","journal-title":"J. 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Chem."},{"key":"2026081804435828000_cit22","doi-asserted-by":"publisher","first-page":"2086","DOI":"10.1073\/pnas.1516813113","article-title":"Structure of the\nBrd4 ET Domain Bound to a C-Terminal\nMotif from \u03b3-Retroviral Integrases Reveals a Conserved Mechanism\nof Interaction","volume":"113","author":"Crowe","year":"2016","journal-title":"Proc. Natl. Acad. Sci. (USA)"},{"key":"2026081804435828000_cit23","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1007\/978-1-4939-2239-0_2","article-title":"Protein Structural Information Derived\nfrom NMR Chemical Shift with\nthe Neural Network Program TALOS-N","volume":"1260","author":"Shen","year":"2015","journal-title":"Artif. 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Biol."},{"key":"2026081804435828000_cit30","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/s0009-2614(99)01123-9","article-title":"Replica-Exchange Molecular\nDynamics Method for Protein\nFolding","volume":"314","author":"Sugita","year":"1999","journal-title":"Chem. Phys. Lett."},{"key":"2026081804435828000_cit31","doi-asserted-by":"publisher","first-page":"2020","DOI":"10.1021\/ct3010485","article-title":"Improved Generalized\nBorn Solvent\nModel Parameters for Protein Simulations","volume":"9","author":"Nguyen","year":"2013","journal-title":"J.\nChem. Theory Comput."},{"key":"2026081804435828000_cit32","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"Ff14SB: Improving\nthe Accuracy of\nProtein Side Chain and Backbone Parameters from Ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. 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Theory Comput."},{"key":"2026081804435828000_cit46","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1007\/s10858-009-9310-6","article-title":"CPMG Relaxation\nDispersion NMR Experiments Measuring Glycine 1H\u03b1 and 13C\u03b1\nChemical Shifts in the \u2018Invisible\u2019 Excited States of\nProteins","volume":"45","author":"Vallurupalli","year":"2009","journal-title":"J. Biomol. NMR"},{"key":"2026081804435828000_cit47","doi-asserted-by":"publisher","first-page":"8148","DOI":"10.1021\/ja3001419","article-title":"Studying \u201cInvisible\u201d\nExcited Protein States in Slow Exchange with a Major State Conformation","volume":"134","author":"Vallurupalli","year":"2012","journal-title":"J. Am. Chem. 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Theory Comput."},{"key":"2026081804435828000_cit51","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1002\/prot.25857","article-title":"Docking Proteins\nand Peptides under Evolutionary Constraints in Critical Assessment\nof PRediction of Interactions Rounds 38 to 45","volume":"88","author":"Nadaradjane","year":"2020","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"2026081804435828000_cit52","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1002\/prot.10381","article-title":"CAPRI: A Critical\nAssessment of PRedicted Interactions","volume":"52","author":"Janin","year":"2003","journal-title":"Proteins\nStruct. Funct. 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