{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T10:09:26Z","timestamp":1748426966838},"reference-count":35,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T00:00:00Z","timestamp":1719792000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Bioorganic &amp; Medicinal Chemistry"],"published-print":{"date-parts":[[2024,7]]},"DOI":"10.1016\/j.bmc.2024.117795","type":"journal-article","created":{"date-parts":[[2024,6,11]],"date-time":"2024-06-11T06:28:58Z","timestamp":1718087338000},"page":"117795","update-policy":"http:\/\/dx.doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["How kelch domain-containing protein 3 distinguishes between the C-end degron of herpesviral protein UL49.5 and its mutants \u2013 Insights from molecular dynamics"],"prefix":"10.1016","volume":"109","author":[{"given":"Magdalena J.","family":"\u015alusarz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.bmc.2024.117795_b0005","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1099\/0022-1317-73-8-2167","article-title":"A novel herpes simplex virus gene (UL49A) encodes a putative membrane protein with counterparts in other herpesviruses","volume":"73","author":"Barnett","year":"1992","journal-title":"J Gen Virol"},{"key":"10.1016\/j.bmc.2024.117795_b0010","first-page":"199","article-title":"Herpesviruses: a brief overview","volume":"256","author":"Ackermann","year":"2004","journal-title":"Methods Mol Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0015","doi-asserted-by":"crossref","first-page":"2351","DOI":"10.1128\/JVI.01621-10","article-title":"The capacity of UL49.5 proteins to inhibit TAP is widely distributed among members of the genus Varicellovirus","volume":"85","author":"Verweij","year":"2011","journal-title":"J Virol"},{"key":"10.1016\/j.bmc.2024.117795_b0020","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004743","article-title":"Viral inhibition of the transporter associated with antigen processing (TAP): a striking example of functional convergent evolution","volume":"11","author":"Verweij","year":"2015","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.bmc.2024.117795_b0025","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2023.167964","article-title":"The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function","volume":"435","author":"Graul","year":"2023","journal-title":"J Mol Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0030","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2309841121","article-title":"The herpesvirus UL49.5 protein hijacks a cellular C-degron pathway to drive TAP transporter degradation","volume":"121","author":"W\u0105chalska","year":"2024","journal-title":"PNAS"},{"key":"10.1016\/j.bmc.2024.117795_b0035","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1073\/pnas.1816596116","article-title":"N-degron and C-degron pathways of protein degradation","volume":"116","author":"Varshavsky","year":"2019","journal-title":"PNAS"},{"key":"10.1016\/j.bmc.2024.117795_b0040","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/s41418-021-00890-0","article-title":"CRL2-KLHDC3 E3 ubiquitin ligase complex suppresses ferroptosis through promoting p14ARF degradation","volume":"29","author":"Zhang","year":"2022","journal-title":"Cell Death Differ"},{"key":"10.1016\/j.bmc.2024.117795_b0045","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0962-8924(99)01673-6","article-title":"The kelch repeat superfamily of proteins: propellers of cell function","volume":"10","author":"Adams","year":"2000","journal-title":"Trends Cell Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0050","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/1471-2105-4-42","article-title":"Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB\/kelch proteins in animals","volume":"4","author":"Prag","year":"2003","journal-title":"BMC Bioinf"},{"key":"10.1016\/j.bmc.2024.117795_b0055","doi-asserted-by":"crossref","DOI":"10.1038\/s41580-024-00729-9","article-title":"Targeted protein degradation: from mechanisms to clinic","author":"Tsai","year":"2024","journal-title":"Nat Rev Mol Cell Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0060","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/s41589-019-0362-y","article-title":"Development of targeted protein degradation therapeutics","volume":"15","author":"Chamberlain","year":"2019","journal-title":"Nat Chem Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0065","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.bmc.2024.117795_b0070","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.bmc.2024.117795_b0075","unstructured":"Case DA, Belfon K, Ben-Shalom LY et al. AMBER 2020, University of California, San Francisco."},{"key":"10.1016\/j.bmc.2024.117795_b0080","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"},{"key":"10.1016\/j.bmc.2024.117795_b0085","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J Comput Chem"},{"key":"10.1016\/j.bmc.2024.117795_b0090","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.molcel.2018.10.021","article-title":"Recognition of the Diglycine C-End Degron by CRL2KLHDC2 Ubiquitin Ligase","volume":"72","author":"Rusnac","year":"2018","journal-title":"Mol Cell"},{"key":"10.1016\/j.bmc.2024.117795_b0095","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1287\/moor.6.1.19","article-title":"Minimization by Random Search Techniques","volume":"6","author":"Solis","year":"1981","journal-title":"Math Operat Res"},{"key":"10.1016\/j.bmc.2024.117795_b0100","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data","volume":"9","author":"Roe","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"10.1016\/j.bmc.2024.117795_b0105","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA.py: An Efficient Program for End-State Free Energy Calculations","volume":"8","author":"Miller","year":"2012","journal-title":"J Chem Theory Comput"},{"key":"10.1016\/j.bmc.2024.117795_b0110","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A","article-title":"Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)","volume":"20","author":"Weiser","year":"1999","journal-title":"J Computat Chem."},{"key":"10.1016\/j.bmc.2024.117795_b0115","series-title":"The PyMOL Molecular Graphics System","author":"DeLano","year":"2008"},{"key":"10.1016\/j.bmc.2024.117795_b0120","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/978-1-4939-9752-7_2","article-title":"Integrating Molecular Docking and Molecular Dynamics Simulations","volume":"2053","author":"Santos","year":"2019","journal-title":"Methods Mol Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0125","doi-asserted-by":"crossref","unstructured":"Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamics simulations in drug design. Med Res Rev. 2996;26(5):531-568. 10.1002\/med.20067.","DOI":"10.1002\/med.20067"},{"key":"10.1016\/j.bmc.2024.117795_b0130","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.molcel.2018.04.006","article-title":"C-Terminal End-Directed Protein Elimination by CRL2 Ubiquitin Ligases","volume":"70","author":"Lin","year":"2018","journal-title":"Mol Cell"},{"key":"10.1016\/j.bmc.2024.117795_b0135","doi-asserted-by":"crossref","unstructured":"Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol. Published online April 29, 2024. 10.1038\/s41580-024-00729-9.","DOI":"10.1038\/s41580-024-00729-9"},{"key":"10.1016\/j.bmc.2024.117795_b0140","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2024.129864","article-title":"PROTAC-biomacromolecule conjugates for precise protein degradation in cancer therapy: A review","volume":"261","author":"Wang","year":"2024","journal-title":"Int J Biol Macromol"},{"key":"10.1016\/j.bmc.2024.117795_b0145","article-title":"N\/C-degron pathways and inhibitor development for PROTAC applications","volume":"1867","author":"Wu","year":"2024","journal-title":"Biochim Biophys Acta"},{"key":"10.1016\/j.bmc.2024.117795_b0150","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.cbpa.2017.05.016","article-title":"Targeted protein knockdown using small molecule degraders","volume":"39","author":"Raina","year":"2017","journal-title":"Curr Opin Chem Biol"},{"key":"10.1016\/j.bmc.2024.117795_b0155","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev-biochem-060815-014922","article-title":"Ubiquitin Ligases: Structure, Function, and Regulation","volume":"86","author":"Zheng","year":"2017","journal-title":"Annu Rev Biochem"},{"key":"10.1016\/j.bmc.2024.117795_b0160","doi-asserted-by":"crossref","unstructured":"Zhang P, Gao K, Zhang L, et al. CRL2-KLHDC3 E3 ubiquitin ligase complex suppresses ferroptosis through promoting p14ARF degradation. Cell Death Differ. 2022;29(4):758-771. 10.1038\/s41418-021-00890-0.","DOI":"10.1038\/s41418-021-00890-0"},{"key":"10.1016\/j.bmc.2024.117795_b0165","doi-asserted-by":"crossref","first-page":"7731","DOI":"10.1039\/c3cp00116d","article-title":"Comparison of MM\/GBSA calculations based on explicit and implicit solvent simulations","volume":"15","author":"Godschalk","year":"2013","journal-title":"PCCP"},{"key":"10.1016\/j.bmc.2024.117795_b0170","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1146\/annurev-biophys-052118-115325","article-title":"Generalized Born Implicit Solvent Models for Biomolecules","volume":"48","author":"Onufriev","year":"2019","journal-title":"Annu Rev Biophys"},{"key":"10.1016\/j.bmc.2024.117795_b0175","doi-asserted-by":"crossref","first-page":"4702","DOI":"10.1021\/ja8085643","article-title":"Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations","volume":"131","author":"Amaro","year":"2009","journal-title":"J Am Chem Soc"}],"container-title":["Bioorganic &amp; Medicinal Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0968089624002098?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0968089624002098?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T16:46:51Z","timestamp":1719420411000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0968089624002098"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7]]},"references-count":35,"alternative-id":["S0968089624002098"],"URL":"https:\/\/doi.org\/10.1016\/j.bmc.2024.117795","relation":{},"ISSN":["0968-0896"],"issn-type":[{"value":"0968-0896","type":"print"}],"subject":[],"published":{"date-parts":[[2024,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"How kelch domain-containing protein 3 distinguishes between the C-end degron of herpesviral protein UL49.5 and its mutants \u2013 Insights from molecular dynamics","name":"articletitle","label":"Article Title"},{"value":"Bioorganic & Medicinal Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.bmc.2024.117795","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"117795"}}