{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1050870219650930176.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"HDL","@value":"https://hdl.handle.net/2324/7400580"}},{"identifier":{"@type":"DOI","@value":"10.1016/j.jbc.2024.107989"}},{"identifier":{"@type":"URI","@value":"https://api.elsevier.com/content/article/PII:S0021925824024918?httpAccept=text/xml"}},{"identifier":{"@type":"URI","@value":"https://api.elsevier.com/content/article/PII:S0021925824024918?httpAccept=text/plain"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@language":"en","@value":"Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies"}],"dc:language":"en","description":[{"type":"Abstract","notation":[{"@language":"en","@value":"Protein phosphorylation is a crucial process in various cellular functions, and its irregularities have been implicated in several diseases, including cancer. Antibodies are commonly employed to detect protein phosphorylation in research. However, unlike the extensive studies on recognition mechanisms of the phosphate group by proteins such as kinases and phosphatases, only a few studies have explored antibody mechanisms. In this study, we produced and characterized two rabbit monoclonal antibodies that recognize a monophosphorylated Akt peptide. Through crystallography, thermodynamic mutational analyses, and molecular dynamics simulations, we investigated the unique recognition mechanism that enables higher binding affinity and selectivity of the antibodies compared to other generic proteins with lower binding affinity to phosphorylated epitopes. Our results demonstrate that molecular dynamics simulations provide novel insights into the dynamic aspects of molecular recognition of posttranslational modifications by proteins beyond static crystal structures, highlighting how specific atomic level interactions drive the exceptional affinity and selectivity of antibodies."}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1030859912489190144","@type":"Researcher","personIdentifier":[{"@type":"ORCID","@value":"0000-0003-2272-6999"}],"foaf:name":[{"@language":"en","@value":"Kasahara, Keisuke"},{"@language":"ja","@value":"笠原, 慶亮"},{"@language":"ja-Kana","@value":"カサハラ, ケイスケ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Department of Bioengineering, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学大学院工学系研究科バイオエンジニアリング専攻"}]},{"@id":"https://cir.nii.ac.jp/crid/1070870219650930181","@type":"Researcher","foaf:name":[{"@language":"en","@value":"Kawade, Raiji"},{"@language":"ja","@value":"河出, 来時"},{"@language":"ja-Kana","@value":"カワデ, ライジ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Department of Bioengineering, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学大学院工学系研究科バイオエンジニアリング専攻"}]},{"@id":"https://cir.nii.ac.jp/crid/1420564276167804544","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"80784511"},{"@type":"NRID","@value":"1000080784511"},{"@type":"ORCID","@value":"0000-0003-0328-9914"},{"@type":"NRID","@value":"9000006630631"},{"@type":"NRID","@value":"9000263039167"},{"@type":"NRID","@value":"9000375911930"},{"@type":"NRID","@value":"9000397851163"},{"@type":"NRID","@value":"9000002039561"},{"@type":"NRID","@value":"9000278498417"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/mnakakido"}],"foaf:name":[{"@language":"en","@value":"Nakakido, Makoto"},{"@language":"ja","@value":"中木戸, 誠"},{"@language":"ja-Kana","@value":"ナカキド, マコト"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Department of Bioengineering, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学大学院工学系研究科バイオエンジニアリング専攻"},{"@language":"en","@value":"Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学工学部化学生命工学科"}]},{"@id":"https://cir.nii.ac.jp/crid/1070307269697507971","@type":"Researcher","personIdentifier":[{"@type":"ORCID","@value":"0000-0001-7702-9176"}],"foaf:name":[{"@language":"en","@value":"Matsunaga, Ryo"},{"@language":"ja","@value":"松長, 遼"},{"@language":"ja-Kana","@value":"マツナガ, リョウ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Department of Bioengineering, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学大学院工学系研究科バイオエンジニアリング専攻"},{"@language":"en","@value":"Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学工学部化学生命工学科"}]},{"@id":"https://cir.nii.ac.jp/crid/1420845751143275776","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"70739945"},{"@type":"NRID","@value":"1000070739945"},{"@type":"ORCID","@value":"0000-0002-1450-5873"},{"@type":"NRID","@value":"9000410514728"},{"@type":"NRID","@value":"9000299513622"},{"@type":"NRID","@value":"9000410306878"},{"@type":"NRID","@value":"9000406061939"},{"@type":"NRID","@value":"9000375911928"},{"@type":"NRID","@value":"9000397851161"},{"@type":"NRID","@value":"9000367825852"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/HirokiAkiba"}],"foaf:name":[{"@language":"en","@value":"Akiba, Hiroki"},{"@language":"ja","@value":"秋葉, 宏樹"},{"@language":"ja-Kana","@value":"アキバ, ヒロキ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition"},{"@language":"ja","@value":"医薬基盤・健康・栄養研究所創薬デザイン研究センター"},{"@language":"en","@value":"Graduate School of Pharmaceutical Sciences, Kyoto University"},{"@language":"ja","@value":"京都大学大学院薬学研究科"}]},{"@id":"https://cir.nii.ac.jp/crid/1070870219650930183","@type":"Researcher","foaf:name":[{"@language":"en","@value":"Entzminger, Kevin C."}],"jpcoar:affiliationName":[{"@language":"en","@value":"Abwiz Bio Inc."}]},{"@id":"https://cir.nii.ac.jp/crid/1070870219650930178","@type":"Researcher","foaf:name":[{"@language":"en","@value":"Maruyama, Toshiaki"},{"@language":"ja","@value":"マルヤマ, トシアキ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Abwiz Bio Inc."}]},{"@id":"https://cir.nii.ac.jp/crid/1070870219650930184","@type":"Researcher","foaf:name":[{"@language":"en","@value":"Okumura, Shigeru C.J."},{"@language":"ja","@value":"オクムラ, シゲル"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Abwiz Bio Inc."}]},{"@id":"https://cir.nii.ac.jp/crid/1070303932803187462","@type":"Researcher","personIdentifier":[{"@type":"ORCID","@value":"0000-0001-5568-2369"}],"foaf:name":[{"@language":"en","@value":"Caaveiro, Jose M.M."},{"@language":"ja","@value":"カアベイロ, ホセ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University"},{"@language":"ja","@value":"九州大学大学院薬学研究院臨床薬学部門蛋白質創薬学分野"}]},{"@id":"https://cir.nii.ac.jp/crid/1420564276187709952","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"60756732"},{"@type":"NRID","@value":"1000060756732"},{"@type":"ORCID","@value":"0000-0003-2390-4785"},{"@type":"CINII_AUTHOR_ID","@value":"DB00029815"},{"@type":"URI","@value":"https://ci.nii.ac.jp/author/DB00029815#entity"},{"@type":"URI","@value":"https://viaf.org/viaf/NII%7CDB00029815"},{"@type":"NRID","@value":"9000397851162"},{"@type":"NRID","@value":"9000413753017"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/dkuroda1905"}],"foaf:name":[{"@language":"en","@value":"Kuroda, Daisuke"},{"@language":"ja","@value":"黒田, 大祐"},{"@language":"ja-Kana","@value":"クロダ, ダイスケ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Department of Bioengineering, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学大学院工学系研究科バイオエンジニアリング専攻"},{"@language":"en","@value":"Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学工学部化学生命工学科"},{"@language":"en","@value":"Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases"},{"@language":"ja","@value":"国立感染症研究所ワクチン開発研究センター"}]},{"@id":"https://cir.nii.ac.jp/crid/1420564276179260800","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"90271866"},{"@type":"NRID","@value":"1000090271866"},{"@type":"ORCID","@value":"0000-0001-7643-5164"},{"@type":"CINII_AUTHOR_ID","@value":"DA18425859"},{"@type":"URI","@value":"https://ci.nii.ac.jp/author/DA18425859#entity"},{"@type":"URI","@value":"https://viaf.org/viaf/NII%7CDA18425859"},{"@type":"NRID","@value":"9000287293734"},{"@type":"NRID","@value":"9000254841636"},{"@type":"NRID","@value":"9000401960688"},{"@type":"NRID","@value":"9000410514729"},{"@type":"NRID","@value":"9000258667981"},{"@type":"NRID","@value":"9000258663379"},{"@type":"NRID","@value":"9000414258437"},{"@type":"NRID","@value":"9000397938818"},{"@type":"NRID","@value":"9000398169843"},{"@type":"NRID","@value":"9000395376935"},{"@type":"NRID","@value":"9000361706500"},{"@type":"NRID","@value":"9000252814370"},{"@type":"NRID","@value":"9000299513623"},{"@type":"NRID","@value":"9000006032080"},{"@type":"NRID","@value":"9000006865882"},{"@type":"NRID","@value":"9000238280716"},{"@type":"NRID","@value":"9000238280282"},{"@type":"NRID","@value":"9000253181402"},{"@type":"NRID","@value":"9000010518414"},{"@type":"NRID","@value":"9000409194432"},{"@type":"NRID","@value":"9000004229569"},{"@type":"NRID","@value":"9000363282863"},{"@type":"NRID","@value":"9000361706495"},{"@type":"NRID","@value":"9000361706505"},{"@type":"NRID","@value":"9000363285697"},{"@type":"NRID","@value":"9000303639094"},{"@type":"NRID","@value":"9000253179505"},{"@type":"NRID","@value":"9000342450308"},{"@type":"NRID","@value":"9000383699955"},{"@type":"NRID","@value":"9000401543675"},{"@type":"NRID","@value":"9000406061940"},{"@type":"NRID","@value":"9000340455103"},{"@type":"NRID","@value":"9000402600022"},{"@type":"NRID","@value":"9000411982854"},{"@type":"NRID","@value":"9000303638876"},{"@type":"NRID","@value":"9000356570403"},{"@type":"NRID","@value":"9000303640122"},{"@type":"NRID","@value":"9000253169444"},{"@type":"NRID","@value":"9000412545817"},{"@type":"NRID","@value":"9000375911932"},{"@type":"NRID","@value":"9000408682197"},{"@type":"NRID","@value":"9000411982859"},{"@type":"NRID","@value":"9000259306817"},{"@type":"NRID","@value":"9000397851168"},{"@type":"NRID","@value":"9000002039567"},{"@type":"NRID","@value":"9000253182673"},{"@type":"NRID","@value":"9000367825857"},{"@type":"NRID","@value":"9000309558325"},{"@type":"NRID","@value":"9000238282127"},{"@type":"NRID","@value":"9000397846256"},{"@type":"NRID","@value":"9000375849953"},{"@type":"NRID","@value":"9000363291078"},{"@type":"NRID","@value":"9000278498426"},{"@type":"NRID","@value":"9000411952180"},{"@type":"NRID","@value":"9000019195517"},{"@type":"NRID","@value":"9000303640289"},{"@type":"NRID","@value":"9000413753018"},{"@type":"NRID","@value":"9000253180821"},{"@type":"NRID","@value":"9000006867665"},{"@type":"NRID","@value":"9000391605349"},{"@type":"NRID","@value":"9000411203037"},{"@type":"NRID","@value":"9000356605773"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/read0123465"}],"foaf:name":[{"@language":"en","@value":"Tsumoto, Kouhei"},{"@language":"ja","@value":"津本, 浩平"},{"@language":"ja-Kana","@value":"ツモト, コウヘイ"}],"jpcoar:affiliationName":[{"@language":"en","@value":"Department of Bioengineering, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学大学院工学系研究科バイオエンジニアリング専攻"},{"@language":"en","@value":"Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo"},{"@language":"ja","@value":"東京大学工学部化学生命工学科"},{"@language":"en","@value":"Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition"},{"@language":"ja","@value":"医薬基盤・健康・栄養研究所創薬デザイン研究センター"},{"@language":"en","@value":"Abwiz Bio Inc."},{"@language":"en","@value":"Medical Proteomics Laboratory, Institute of Medical Sciences, The University of Tokyo"},{"@language":"ja","@value":"東京大学医科学研究所疾患プロテオミクスラボラトリー"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"00219258"},{"@type":"EISSN","@value":"1083351X"},{"@type":"NCID","@value":"AA00251083"}],"prism:publicationName":[{"@language":"en","@value":"Journal of Biological Chemistry"}],"dc:publisher":[{"@value":"Elsevier"}],"prism:publicationDate":"2024-12","prism:volume":"300","prism:number":"12","prism:startingPage":"107989"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","dc:rights":["Creative Commons Attribution 4.0 International","© 2024 THE AUTHORS."],"url":[{"@id":"https://api.elsevier.com/content/article/PII:S0021925824024918?httpAccept=text/xml"},{"@id":"https://api.elsevier.com/content/article/PII:S0021925824024918?httpAccept=text/plain"}],"foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=antibody","dc:title":"antibody"},{"@id":"https://cir.nii.ac.jp/all?q=antigen","dc:title":"antigen"},{"@id":"https://cir.nii.ac.jp/all?q=posttranslational%20modification","dc:title":"posttranslational modification"},{"@id":"https://cir.nii.ac.jp/all?q=protein%20structure","dc:title":"protein structure"},{"@id":"https://cir.nii.ac.jp/all?q=peptide%20interaction","dc:title":"peptide interaction"},{"@id":"https://cir.nii.ac.jp/all?q=molecular%20dynamics","dc:title":"molecular dynamics"}],"dcterms:subject":[{"subjectScheme":"Other","notation":[{"@language":"en","@value":"antibody"}]},{"subjectScheme":"Other","notation":[{"@language":"en","@value":"antigen"}]},{"subjectScheme":"Other","notation":[{"@language":"en","@value":"posttranslational modification"}]},{"subjectScheme":"Other","notation":[{"@language":"en","@value":"protein structure"}]},{"subjectScheme":"Other","notation":[{"@language":"en","@value":"peptide interaction"}]},{"subjectScheme":"Other","notation":[{"@language":"en","@value":"molecular dynamics"}]}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040000781896226560","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"16H02420"},{"@type":"JGN","@value":"JP16H02420"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16H02420/"}],"notation":[{"@language":"ja","@value":"物理化学的理解に基づく蛋白質間相互作用プロセス制御剤の探索と設計"},{"@language":"en","@value":"Screening and design of ligands regulating the process of protein-protein interactions based on biophysical approaches"}]},{"@id":"https://cir.nii.ac.jp/crid/1040003825718910464","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"20H02531"},{"@type":"JGN","@value":"JP20H02531"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20H02531/"}],"notation":[{"@language":"ja","@value":"蛋白質エンジニアリングにおけるローカルフラクチュエーションの解明とその制御"},{"@language":"en","@value":"Elucidation and Control of Local Fractions in Protein Engineering"}]},{"@id":"https://cir.nii.ac.jp/crid/1040007282461122432","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"21K18310"},{"@type":"JGN","@value":"JP21K18310"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K18310/"}],"notation":[{"@language":"ja","@value":"計算・情報科学で挑む医薬品の合理的な脳内輸送"},{"@language":"en","@value":"Transporting drugs across the blood-brain barrier through information technology"}]},{"@id":"https://cir.nii.ac.jp/crid/1040014481289332096","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"23KJ0394"},{"@type":"JGN","@value":"JP23KJ0394"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23KJ0394/"}],"notation":[{"@language":"ja","@value":"スーパーチャージ抗体の物性・機能制御メカニズム解明とその応用展開"},{"@language":"en","@value":"Elucidation of the mechanisms controlling the physicochemical properties and functions of supercharged antibodies and development of their applications"}]},{"@id":"https://cir.nii.ac.jp/crid/1040282256991738752","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"19H04202"},{"@type":"JGN","@value":"JP19H04202"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19H04202/"}],"notation":[{"@language":"ja","@value":"バーチャル空間における機能性分子創製法の確立とその実験的検証"},{"@language":"en","@value":"Molecular design of real proteins in virtual space"}]},{"@id":"https://cir.nii.ac.jp/crid/1040285300650064000","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"19H05766"},{"@type":"JGN","@value":"JP19H05766"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PLANNED-19H05766/"}],"notation":[{"@language":"ja","@value":"生命金属動態の理解と制御のための分子認識素子の開発"},{"@language":"en","@value":"Development of molecular recognition elements for understanding and regulation of biometal dynamics"}]},{"@id":"https://cir.nii.ac.jp/crid/1040848250649373568","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"20H03228"},{"@type":"JGN","@value":"JP20H03228"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20H03228/"}],"notation":[{"@language":"ja","@value":"Understanding the efficacy of therapeutic antibodies through their interaction with cellular receptors."},{"@language":"en","@value":"Understanding the efficacy of therapeutic antibodies through their interaction with cellular receptors."}]},{"@id":"https://cir.nii.ac.jp/crid/1860019204192481413","@type":"Project","projectIdentifier":[{"@type":"JGN","@value":"JPMJCR20H8"}],"notation":[{"@language":"ja","@value":"Antibody-Based Molecular Designに基づくウイルスの機能制御技術およびセンシング技術の開発"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050307269697507968","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Unveiling the affinity–stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction"}]},{"@id":"https://cir.nii.ac.jp/crid/1360009142705881088","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structural basis for antigen recognition by methylated lysine–specific antibodies"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011142937242880","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"PROCHECK: a program to check the stereochemical quality of protein structures"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011146514564992","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review)"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292617910148608","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"UCSF Chimera—A visualization system for exploratory research and analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360302868278544768","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Enhancement of therapeutic potential of a naturally occurring human antibody targeting a phosphorylated Ser422 containing epitope on pathological tau"}]},{"@id":"https://cir.nii.ac.jp/crid/1360306913389145600","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies"}]},{"@id":"https://cir.nii.ac.jp/crid/1360306913488930816","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structural characterization of monoclonal antibodies targeting C-terminal Ser<sup>404</sup> region of phosphorylated tau protein"}]},{"@id":"https://cir.nii.ac.jp/crid/1360568464321845248","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574093835775744","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"An Ultra-specific Avian Antibody to Phosphorylated Tau Protein Reveals a Unique Mechanism for Phosphoepitope Recognition"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574094495175168","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Scaling and assessment of data quality"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574095131601408","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"CHARMM‐GUI: A web‐based graphical user interface for CHARMM"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574095881055488","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Refinement of Macromolecular Structures by the Maximum-Likelihood Method"}]},{"@id":"https://cir.nii.ac.jp/crid/1360588385276921728","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Tau Antibody Structure Reveals a Molecular Switch Defining a Pathological Conformation of the Tau Protein"}]},{"@id":"https://cir.nii.ac.jp/crid/1360848659673749888","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Roles of the disulfide bond between the variable and the constant domains of rabbit immunoglobulin kappa chains in thermal stability and affinity"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567870331904","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570869274624","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"LINCS: A linear constraint solver for molecular simulations"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855571464206080","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"CHARMM36m: an improved force field for folded and intrinsically disordered proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1360857593701572224","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Single-chain variable fragment (scFv) targeting streptolysin O controls group A Streptococcus infection"}]},{"@id":"https://cir.nii.ac.jp/crid/1360861292724346496","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The Different Interactions of Lysine and Arginine Side Chains with Lipid Membranes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360869862381106688","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structural Basis for Recognition of a Unique Epitope by a Human Anti-tau Antibody"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137045811908480","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers"}]},{"@id":"https://cir.nii.ac.jp/crid/1361418519924957696","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"SAbDab: the structural antibody database"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262945802017920","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Considering Protonation as a Posttranslational Modification Regulating Protein Structure and Function"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419363080064","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The activation of Akt/PKB signaling pathway and cell survival"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419885318016","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Comparison of simple potential functions for simulating liquid water"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544420680576768","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"<i>Phaser</i>crystallographic software"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825893734049024","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Strengths of Hydrogen Bonds Involving Phosphorylated Amino Acid Side Chains"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825894493145856","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Structure of the BRCT Repeats of BRCA1 Bound to a BACH1 Phosphopeptide"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825894992482048","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The Structural Basis for 14-3-3:Phosphopeptide Binding Specificity"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107369322798464","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Nature-inspired design of motif-specific antibody scaffolds"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107370089014528","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Features and development of <i>Coot</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388843513143552","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Phosphorylation by aurora kinase A induces Mdm2-mediated destabilization and inhibition of p53"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388846178626176","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670320209810304","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Overview of the<i>CCP</i>4 suite and current developments"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670320332134912","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Epitope mapping and structural basis for the recognition of phosphorylated tau by the anti‐tau antibody AT8"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951795062605440","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Tau protein isoforms, phosphorylation and role in neurodegenerative disorders11These authors contributed equally to this work."}]},{"@id":"https://cir.nii.ac.jp/crid/1364233268869231616","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269407432960","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Tumor-directed lymphocyte-activating cytokines: refolding-based preparation of recombinant human interleukin-12 and an antibody variable domain-fused protein by additive-introduced stepwise dialysis"}]}],"dataSourceIdentifier":[{"@type":"IRDB","@value":"oai:irdb.nii.ac.jp:01211:0007255120"},{"@type":"CROSSREF","@value":"10.1016/j.jbc.2024.107989"},{"@type":"KAKEN","@value":"PRODUCT-25577248"}]}