Integrative residue-intuitive machine learning and MD Approach to Unveil Allosteric Site and Mechanism for β2AR
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-024-52399-y
Download full text from publisher
References listed on IDEAS
- Yuanyuan Jiang & Zongwei Yang & Jiali Guo & Hongzhen Li & Yijing Liu & Yanzhi Guo & Menglong Li & Xuemei Pu, 2021. "Coupling complementary strategy to flexible graph neural network for quick discovery of coformer in diverse co-crystal materials," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- Jingxuan Zhu & Juexin Wang & Weiwei Han & Dong Xu, 2022. "Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Jie Zhao & Hong Fu & Jingjing Yu & Weiqi Hong & Xiaowen Tian & Jieyu Qi & Suyue Sun & Chang Zhao & Chao Wu & Zheng Xu & Lin Cheng & Renjie Chai & Wei Yan & Xiawei Wei & Zhenhua Shao, 2023. "Prospect of acromegaly therapy: molecular mechanism of clinical drugs octreotide and paltusotine," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Lei Huang & Tingyang Xu & Yang Yu & Peilin Zhao & Xingjian Chen & Jing Han & Zhi Xie & Hailong Li & Wenge Zhong & Ka-Chun Wong & Hengtong Zhang, 2024. "A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Christine Oswald & Mathieu Rappas & James Kean & Andrew S. Doré & James C. Errey & Kirstie Bennett & Francesca Deflorian & John A. Christopher & Ali Jazayeri & Jonathan S. Mason & Miles Congreve & Rob, 2016. "Intracellular allosteric antagonism of the CCR9 receptor," Nature, Nature, vol. 540(7633), pages 462-465, December.
- Anastasiia V. Sadybekov & Vsevolod Katritch, 2023. "Computational approaches streamlining drug discovery," Nature, Nature, vol. 616(7958), pages 673-685, April.
- Aaron M. Ring & Aashish Manglik & Andrew C. Kruse & Michael D. Enos & William I. Weis & K. Christopher Garcia & Brian K. Kobilka, 2013. "Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody," Nature, Nature, vol. 502(7472), pages 575-579, October.
- Ankita Srivastava & Jason Yano & Yoshihiko Hirozane & Georgia Kefala & Franz Gruswitz & Gyorgy Snell & Weston Lane & Anthony Ivetac & Kathleen Aertgeerts & Jasmine Nguyen & Andy Jennings & Kengo Okada, 2014. "High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875," Nature, Nature, vol. 513(7516), pages 124-127, September.
- Xiangyu Liu & Seungkirl Ahn & Alem W. Kahsai & Kai-Cheng Meng & Naomi R. Latorraca & Biswaranjan Pani & A. J. Venkatakrishnan & Ali Masoudi & William I. Weis & Ron O. Dror & Xin Chen & Robert J. Lefko, 2017. "Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure," Nature, Nature, vol. 548(7668), pages 480-484, August.
- Scott A. Hollingsworth & Brendan Kelly & Celine Valant & Jordan Arthur Michaelis & Olivia Mastromihalis & Geoff Thompson & A. J. Venkatakrishnan & Samuel Hertig & Peter J. Scammells & Patrick M. Sexto, 2019. "Cryptic pocket formation underlies allosteric modulator selectivity at muscarinic GPCRs," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Jie Heng & Yunfei Hu & Guillermo Pérez-Hernández & Asuka Inoue & Jiawei Zhao & Xiuyan Ma & Xiaoou Sun & Kouki Kawakami & Tatsuya Ikuta & Jienv Ding & Yujie Yang & Lujia Zhang & Sijia Peng & Xiaogang N, 2023. "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Janik B. Hedderich & Margherita Persechino & Katharina Becker & Franziska M. Heydenreich & Torben Gutermuth & Michel Bouvier & Moritz Bünemann & Peter Kolb, 2022. "The pocketome of G-protein-coupled receptors reveals previously untargeted allosteric sites," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Joshua A. Lees & João M. Dias & Francis Rajamohan & Jean-Philippe Fortin & Rebecca O’Connor & Jimmy X. Kong & Emily A. G. Hughes & Ethan L. Fisher & Jamison B. Tuttle & Gabrielle Lovett & Bethany L. K, 2023. "An inverse agonist of orphan receptor GPR61 acts by a G protein-competitive allosteric mechanism," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Artur Meller & Michael Ward & Jonathan Borowsky & Meghana Kshirsagar & Jeffrey M. Lotthammer & Felipe Oviedo & Juan Lavista Ferres & Gregory R. Bowman, 2023. "Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Alessio Fallani & Leonardo Medrano Sandonas & Alexandre Tkatchenko, 2024. "Inverse mapping of quantum properties to structures for chemical space of small organic molecules," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Arnau Comajuncosa-Creus & Guillem Jorba & Xavier Barril & Patrick Aloy, 2024. "Comprehensive detection and characterization of human druggable pockets through binding site descriptors," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
- Patrick Bryant & Atharva Kelkar & Andrea Guljas & Cecilia Clementi & Frank Noé, 2024. "Structure prediction of protein-ligand complexes from sequence information with Umol," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
- Minfei Su & Jinan Wang & Guoqing Xiang & Hung Nguyen Do & Joshua Levitz & Yinglong Miao & Xin-Yun Huang, 2023. "Structural basis of agonist specificity of α1A-adrenergic receptor," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Yosuke Toyoda & Angqi Zhu & Fang Kong & Sisi Shan & Jiawei Zhao & Nan Wang & Xiaoou Sun & Linqi Zhang & Chuangye Yan & Brian K. Kobilka & Xiangyu Liu, 2023. "Structural basis of α1A-adrenergic receptor activation and recognition by an extracellular nanobody," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Dawei Sun & Yonglian Sun & Eric Janezic & Tricia Zhou & Matthew Johnson & Caleigh Azumaya & Sigrid Noreng & Cecilia Chiu & Akiko Seki & Teresita L. Arenzana & John M. Nicoludis & Yongchang Shi & Baome, 2023. "Structural basis of antibody inhibition and chemokine activation of the human CC chemokine receptor 8," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Aslihan Shenol & Ricardo Tenente & Michael Lückmann & Thomas M. Frimurer & Thue W. Schwartz, 2024. "Multiple recent HCAR2 structures demonstrate a highly dynamic ligand binding and G protein activation mode," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
- Xinyu Xu & Jeremy Shonberg & Jonas Kaindl & Mary J. Clark & Anne Stößel & Luis Maul & Daniel Mayer & Harald Hübner & Kunio Hirata & A. J. Venkatakrishnan & Ron O. Dror & Brian K. Kobilka & Roger K. Su, 2023. "Constrained catecholamines gain β2AR selectivity through allosteric effects on pocket dynamics," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Zhenkai Guo & Dianlong Hou & Qiang He, 2024. "Hybrid Genetic Algorithm and CMA-ES Optimization for RNN-Based Chemical Compound Classification," Mathematics, MDPI, vol. 12(11), pages 1-18, May.
- David Jonathan Wasilko & Brian S. Gerstenberger & Kathleen A. Farley & Wei Li & Jennifer Alley & Mark E. Schnute & Ray J. Unwalla & Jorge Victorino & Kimberly K. Crouse & Ru Ding & Parag V. Sahasrabud, 2024. "Structural basis for CCR6 modulation by allosteric antagonists," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52399-y. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.