Article
Multidisciplinary Sciences
Kouki Kawakami, Masataka Yanagawa, Suzune Hiratsuka, Misaki Yoshida, Yuki Ono, Michio Hiroshima, Masahiro Ueda, Junken Aoki, Yasushi Sako, Asuka Inoue
Summary: This study uncovers the role of Gq heterotrimer in determining GRK subtype selectivity, which in turn regulates the conformation and functionality of β-arrestin. By investigating the angiotensin II type-1 receptor, the authors find that both GRK2/3 and GRK5/6 are recruited by Ang II, while only GRK5/6 is recruited by the β-arrestin-biased ligand TRV027. Additionally, inhibition of Gq shifts the GRK subtype selectivity and β-arrestin functionality to that of TRV027.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sigrun K. Maurer, Matthias P. Mayer, Stephanie J. Ward, Sana Boudjema, Mohamed Halawa, Jiatong Zhang, Simon G. Caulton, Jonas Emsley, Ingrid Dreveny
Summary: This study developed a fusion tag method to trap USP11 and determined its structure, revealing key interactions with a substrate and identifying the molecular basis for its high selectivity. The results have important implications for understanding the differences in selectivity between USP11 and USP15 as well as for targeted inhibitor development.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Sara Garcia-Alonso, Pablo Mesa, Laura de la Puente Ovejero, Gonzalo Aizpurua, Carmen G. Lechuga, Eduardo Zarzuela, Clara M. Santiveri, Manuel Sanclemente, Javier Munoz, Monica Musteanu, Ramon Campos-Olivas, Jorge Martinez-Torrecuadrada, Mariano Barbacid, Guillermo Montoya
Summary: This study describes the structure of the RAF1 protein in complex with HSP90 and CDC37. The research reveals that CDC37 can differentiate between different members of the RAF family. Additionally, the study shows that folded RAF1 assembles with 14-3-3 dimers, and disrupting the interaction between CDC37 and RAF1 may have potential therapeutic implications.
Article
Multidisciplinary Sciences
Maximilian Ruettermann, Michelle Koci, Pascal Lill, Ermis Dionysios Geladas, Farnusch Kaschani, Bjoern Udo Klink, Ralf Erdmann, Christos Gatsogiannis
Summary: This study provides cryo-EM structures of Pex1/Pex6 and reveals their mechanism of protein substrate translocation. Pex1/Pex6 generates mechanical forces through ATP hydrolysis to drive substrate transport across the peroxisomal membrane.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Volkan Yazar, Ismail Cem Yilmaz, Artun Bulbul, Dennis M. Klinman, Ihsan Gursel
Summary: This study investigated the immune suppression by A151 synthetic oligodeoxynucleotides (ODNs) in mouse splenocytes, revealing that A151 inhibits the immune response by interfering with immune cell adhesion through components of integrin complexes Itgam and Itga6.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Multidisciplinary Sciences
Russell A. Judge, Janani Sridar, Kathryn Tunyasunvunakool, Rinku Jain, John C. K. Wang, Christna Ouch, Jun Xu, Amirhossein Mafi, Aaron H. Nile, Clint Remarcik, Corey L. Smith, Crystal Ghosh, Chen Xu, Vincent Stoll, John Jumper, Amoolya H. Singh, Dan Eaton, Qi Hao
Summary: The study reveals the mechanism of PAPP-A substrate binding and selectivity, which underlies the tight regulation of IGF signaling.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Argha Mitra, Arijit Sarkar, Attila Borics
Summary: Research has revealed both structural similarities and receptor-specific differences between G protein-coupled receptors, which could be associated with different signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Bieke Decaesteker, Amber Louwagie, Siebe Loontiens, Fanny De Vloed, Sarah-Lee Bekaert, Juliette Roels, Suzanne Vanhauwaert, Sara De Brouwer, Ellen Sanders, Alla Berezovskaya, Geertrui Denecker, Eva D'haene, Stephane Van Haver, Wouter Van Loocke, Jo Van Dorpe, David Creytens, Nadine Van Roy, Tim Pieters, Christophe Van Neste, Matthias Fischer, Pieter Van Vlierberghe, Stephen S. Roberts, Johannes Schulte, Sara Ek, Rogier Versteeg, Jan Koster, Johan van Nes, Mark Zimmerman, Katleen De Preter, Frank Speleman
Summary: SOX11 is identified as a potential epigenetic master regulator upstream of the core regulatory circuitry in adrenergic high-risk neuroblastoma.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jana Skerlova, Jens Berndtsson, Hendrik Nolte, Martin Ott, Pal Stenmark
Summary: The pyruvate dehydrogenase complex (PDHc) is a multienzyme complex that converts pyruvate into acetyl-coenzyme A, linking glycolysis to the citric acid cycle. The core of PDHc is formed by dihydrolipoyl transacetylase, which provides binding sites for other enzymes and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The cryo-EM structure of the E. coli dihydrolipoyl transacetylase core in a resting state reveals molecular details of the assembly and interactions at the active site.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Marzieh Dehghan Shasaltaneh, Elmira Naghdi, Zahra Moosavi-Nejad
Summary: This study investigates the interactions between RNase A and cCMP through molecular docking and molecular dynamics simulation. The results indicate that cCMP-RNase A complexes are stabilized through hydrophobic interaction, hydrogen bonding, and π-π stacking interaction. The enzyme-ligand docking study shows three phases of binding modes, and experimental methods confirm the activation and inhibition of substrate at different concentrations of cCMP.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Medicine, Research & Experimental
Tingyuan Yang, Xiayu Shi, Shiliang Li, Zhenjiang Zhao, Junyi Wang, Panpan Yu, Honglin Li, Rui Wang, Zhuo Chen
Summary: In this study, researchers discovered that inhibition of dihydroorotate dehydrogenase (DHODH) overcame resistance to all-trans retinoic acid (ATRA) in high-risk acute promyelocytic leukemia (APL) patients. A potent DHODH inhibitor, 416, was found to effectively inhibit APL in cells and model mice. Additionally, 416 overcame ATRA resistance by inducing apoptosis and differentiation, and maintained its down-regulation effect on Bcl-2 and c-Myc in APL cells.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Medicine, Research & Experimental
Guang Xu, Shubin Fu, Xiaoyan Zhan, Zhilei Wang, Ping Zhang, Wei Shi, Nan Qin, Yuanyuan Chen, Chunyu Wang, Ming Niu, Yuming Guo, Jiabo Wang, Zhaofang Bai, Xiaohe Xiao
Summary: This study identified echinatin, a component of traditional herbal medicine licorice, as a potentially novel inhibitor of NLRP3 inflammasome activation in both in vitro and in vivo models. Echinatin was shown to exert inhibitory effects through its interaction with heat-shock protein 90 (HSP90), disrupting the formation of the HSP90-NLRP3 complex. The administration of echinatin demonstrated significant suppression of NLRP3 inflammasome activation and amelioration of inflammatory conditions in mouse models, suggesting its potential as a therapeutic approach for NLRP3-driven diseases.
Article
Pharmacology & Pharmacy
Senfeng Xiang, Xiaoxian Shi, Pengfei Chen, Yifan Chen, Shaowei Bing, Xizhi Jin, Ji Cao, Jinhu Wang, Bo Yang, Xuejing Shao, Qiaojun He, Meidan Ying
Summary: The research focuses on the substrate adaptors of CRL3, specifically the Kelch-like (KLHL) family proteins. The study identified 24 KLHL proteins with tumor promotion function and 13 KLHL proteins with high clinical significance in cancer therapy. Additionally, the novel biological function of KLHL13 as a vital factor contributing to malignant progression in lung cancer was clarified.
PHARMACOLOGICAL RESEARCH
(2021)
Article
Pharmacology & Pharmacy
Qianqian Wang, Xiaomin Shao, Elaine Lai Han Leung, Yingqing Chen, Xiaojun Yao
Summary: Research has shown that although bromodomain-containing proteins exhibit high structural similarity, individual bromodomains have distinct functions and can lead to different cellular phenotypes after pharmacological inhibition. Significant progress has been made in developing bromodomain-selective inhibitors targeting BET and non-BET proteins, enriching the knowledge base for bromodomain-selective drug discovery.
PHARMACOLOGICAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Laura C. Watkins, William F. DeGrado, Gregory A. Voth
Summary: The D44N mutation in the influenza A M2 channel opens the channel gate and increases proton conduction, leading to a loss of asymmetric conduction. This mutation lowers the energy barrier for His37 deprotonation in the activated state and facilitates proton flux through the Va127 tetrad. Increased hydration around the His37 tetrad enhances proton transport efficiency.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Medicinal
Brendan Kelly, Scott A. Hollingsworth, David C. Blakemore, Robert M. Owen, R. Ian Storer, Nigel A. Swain, Deniz Aydin, Rubben Torella, Joseph S. Warmus, Ron O. Dror
Summary: Biased agonists selectively stimulate certain signaling pathways controlled by GPCRs to maximize efficacy and minimize side effects. Designing biased agonists for the mu OR remains challenging due to unclear ligand-mediated interactions and differences in interaction with the binding pocket may lead to distinct bias profiles.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Koichiro E. Kishi, Yoon Seok Kim, Masahiro Fukuda, Masatoshi Inoue, Tsukasa Kusakizako, Peter Y. Wang, Charu Ramakrishnan, Eamon F. X. Byrne, Elina Thadhani, Joseph M. Paggi, Toshiki E. Matsui, Keitaro Yamashita, Takashi Nagata, Masae Konno, Sean Quirin, Maisie Lo, Tyler Benster, Tomoko Uemura, Kehong Liu, Mikihiro Shibata, Norimichi Nomura, So Iwata, Osamu Nureki, Ron O. Dror, Keiichi Inoue, Karl Deisseroth, Hideaki E. Kato
Summary: ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, has opened new possibilities in optogenetics with its unique properties. The cryo-EM structure of ChRmine, revealed at 2.0A resolution, uncovers architectural features distinct from other channelrhodopsins and lays the foundation for the creation of new channelrhodopsins for various biological applications.
Article
Multidisciplinary Sciences
Lei Han, Qianhui Qu, Deniz Aydin, Ouliana Panova, Michael J. Robertson, Yan Xu, Ron O. Dror, Georgios Skiniotis, Liang Feng
Summary: SGLTs are essential transporters responsible for glucose absorption in the intestine and kidney, targeted by multiple drugs for diabetes treatment. Besides glucose, some members within the SGLT family also transport other key metabolites.
Article
Biochemistry & Molecular Biology
Julian A. Harris, Bryan Faust, Arisbel B. Gondin, Marc Andre Damgen, Carl-Mikael Suomivuori, Nicholas A. Veldhuis, Yifan Cheng, Ron O. Dror, David M. Thal, Aashish Manglik
Summary: The neuropeptide substance P activates the neurokinin-1 receptor through interactions deep within the receptor, while interactions between the neuropeptide and the receptor extracellular loops regulate G protein signaling selectivity. This study sheds light on how different stimuli can lead to distinct G protein signaling at the same receptor.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Kaiming Zhang, Naoki Horikoshi, Shanshan Li, Alexander S. Powers, Mikhail A. Hameedi, Grigore D. Pintilie, Hee-Don Chae, Yousuf A. Khan, Carl-Mikael Suomivuori, Ron O. Dror, Kathleen M. Sakamoto, Wah Chiu, Soichi Wakatsuki
Summary: In this study, a protein double shell was engineered to overcome the size limitation of determining structures of flexible proteins smaller than 30 kDa. This approach successfully determined the structure of the 11 kDa KIX domain of CBP, and molecular dynamics simulations were used to design peptides that block protein-protein interactions. The findings provide insights for the development of next-generation inhibitors.
ACS CENTRAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Naotaka Tsutsumi, Shoji Maeda, Qianhui Qu, Martin Vogele, Kevin M. Jude, Carl-Mikael Suomivuori, Ouliana Panova, Deepa Waghray, Hideaki E. Kato, Andrew Velasco, Ron O. Dror, Georgios Skiniotis, Brian K. Kobilka, K. Christopher Garcia
Summary: This study reports the cryo-electron microscopy structures of HCMV-encoded GPCRs US28 and US27 forming nonproductive and productive complexes with host G proteins, providing new insights into their functional mechanisms in viral pathogenesis.
Article
Multidisciplinary Sciences
Bryan Faust, Christian B. Billesbolle, Carl-Mikael Suomivuori, Isha Singh, Kaihua Zhang, Nicholas Hoppe, Antonio F. M. Pinto, Jolene K. Diedrich, Yagmur Muftuoglu, Mariusz W. Szkudlinski, Alan Saghatelian, Ron O. Dror, Yifan Cheng, Aashish Manglik
Summary: Thyroid hormones play a crucial role in metabolism, growth, and development. In patients with Graves' disease, autoantibodies can pathologically increase thyroid hormone activity, but how they mimic the function of thyroid-stimulating hormone remains unclear. This study used cryo-electron microscopy to determine the structures of active and inactive thyroid-stimulating hormone receptor (TSHR). The findings reveal that the extracellular domain of TSHR undergoes a conformational change upon activation induced by thyroid-stimulating hormone or activating autoantibodies, providing insights into the mechanism of receptor activation.
Article
Neurosciences
Can Cao, Ximena Barros-Alvarez, Shicheng Zhang, Kuglae Kim, Marc A. Damgen, Ouliana Panova, Carl-Mikael Suomivuori, Jonathan F. Fay, Xiaofang Zhong, Brian E. Krumm, Ryan H. Gumpper, Alpay B. Seven, Michael J. Robertson, Nevan J. Krogan, Ruth Huttenhain, David E. Nichols, Ron O. Dror, Georgios Skiniotis, Bryan L. Roth
Summary: This study determines the binding of LSD to HTR2B receptors in different states using cryo-EM structures, providing molecular insights into the mechanism of LSD's psychedelic effects and accelerating the discovery of novel psychedelic drugs.
Article
Biochemistry & Molecular Biology
Qianhui Qu, Weijiao Huang, Deniz Aydin, Joseph M. Paggi, Alpay B. Seven, Haoqing Wang, Soumen Chakraborty, Tao Che, Jeffrey F. DiBerto, Michael J. Robertson, Asuka Inoue, Carl-Mikael Suomivuori, Bryan L. Roth, Susruta Majumdar, Ron O. Dror, Brian K. Kobilka, Georgios Skiniotis
Summary: This study investigated the mechanistic basis of action of two mu-opioid receptor (mu OR) agonists, LFT and MP, with different safety profiles, and found that they exhibited markedly different efficacy profiles for G protein subtype activation and beta-arrestin recruitment.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alexander S. Powers, Vi Pham, Wessel A. C. Burger, Geoff Thompson, Yianni Laloudakis, Patrick M. Sexton, Steven M. Paul, Arthur Christopoulos, David M. Thal, Christian C. Felder, Celine Valant, Ron O. Dror
Summary: The selectivity of a drug for target receptors is crucial but challenging when the receptors are similar. Serendipitous discovery of ligands that stimulate target receptors more strongly than closely related receptors provides a solution. This study reveals the structural basis for the efficacy-driven selectivity of xanomeline, a clinical drug candidate, between closely related muscarinic acetylcholine receptors (mAChRs), using atomic-level simulations. The results suggest strategies for rational design of ligands achieving efficacy-driven selectivity for G-protein-coupled receptors.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Stephan Eismann, Patricia Suriana, Bowen Jing, Raphael J. L. Townshend, Ron O. Dror
Summary: Machine learning research on protein structure has gained popularity, showing promising advances in basic science and drug discovery. Researchers have explored various numerical representations for macromolecular structure in a machine learning context, such as graphs, discretized 3D grids, and distance maps. In a blind experiment as part of CASP14, a new and conceptually simple representation of atoms as points in 3D was explored, and its features were updated using neural network layers with rotation-equivariant convolutions. This approach yielded competitive results in protein model quality assessment, despite its simplicity, minimal prior information, and training on relatively little data, showcasing its performance and generality in the era of complex machine learning methods like AlphaFold 2 dominating protein structure prediction.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Xinyu Xu, Jeremy Shonberg, Jonas Kaindl, Mary J. J. Clark, Anne Stoessel, Luis Maul, Daniel Mayer, Harald Huebner, Kunio Hirata, A. J. Venkatakrishnan, Ron O. O. Dror, Brian K. K. Kobilka, Roger K. K. Sunahara, Xiangyu Liu, Peter Gmeiner
Summary: Constrained catecholamines exhibit high selectivity for the beta(2)AR due to reduced ligand flexibility and a less stable binding pocket in the beta(1)AR. Surrounding residues in the extracellular loops (ECLs) of the receptors allosterically modify the binding pocket, resulting in different affinity and selectivity for the beta(2)AR. Exploiting these allosteric influences may lead to the development of more subtype-selective GPCR ligands.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Kaavya Krishna Kumar, Michael J. Robertson, Elina Thadhani, Haoqing Wang, Carl-Mikael Suomivuori, Alexander S. Powers, Lipin Ji, Spyros P. Nikas, Ron O. Dror, Asuka Inoue, Alexandros Makriyannis, Georgios Skiniotis, Brian Kobilka
Summary: Understanding the structure and function of the interaction between endocannabinoids (eCBs) and cannabinoid receptor 1 (CB1) is important for developing effective drugs targeting this receptor. In this study, the structure of the AMG315-bound CB1 signaling complex was determined, revealing differences in the ligand binding pocket compared to previous structures. The functional consequences of ligand interactions with specific residues were investigated, and it was found that intracellular rearrangements in the TM2 region are unique to CB1 and play a role in G protein activation. Additionally, a CB1-specific allosteric modulator exploits this activation mechanism.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Amal El Daibani, Joseph M. M. Paggi, Kuglae Kim, Yianni D. D. Laloudakis, Petr D. Popov, Sarah M. M. Bernhard, Brian E. E. Krumm, Reid H. J. Olsen, Jeffrey Diberto, F. Ivy Carroll, Vsevolod Katritch, Bernhard Wuensch, Ron O. O. Dror, Tao Che
Summary: Using structural determination, molecular dynamics simulations, and functional assays, the researchers identified molecular determinants of KOR signaling bias. They determined the crystal structure of KOR bound to the G protein-biased agonist nalfurafine and identified an arrestin-biased KOR agonist, WMS-X600. Through simulations and mutagenesis validation, they explained how agonists achieve biased signaling at KOR.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
S. Wenceslao Evans, Dong-Qing Shi, Mariya Chavarha, Mark H. Plitt, Jiannis Taxidis, Blake Madruga, Jiang Lan Fan, Fuu-Jiun Hwang, Siri C. van Keulen, Carl-Mikael Suomivuori, Michelle M. Pang, Sharon Su, Sungmoo Lee, Yukun A. Hao, Guofeng Zhang, Dongyun Jiang, Lagnajeet Pradhan, Richard H. Roth, Yu Liu, Conor C. Dorian, Austin L. Reese, Adrian Negrean, Attila Losonczy, Christopher D. Makinson, Sui Wang, Thomas R. Clandinin, Ron O. Dror, Jun B. Ding, Na Ji, Peyman Golshani, Lisa M. Giocomo, Guo-Qiang Bi, Michael Z. Lin
Summary: By inverting the fluorescence-voltage relationship, the photostability of ASAP family genetically encoded voltage indicators (GEVIs) has been enhanced. Two improved GEVIs, ASAP4b and ASAP4e, enable single-trial detection and recording in standard one- and two-photon microscopes with better temporal resolution. They can simultaneously detect voltage and calcium signals and extend the duration of voltage recordings.