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Heterogeneous sampled subgraph neural networks with knowledge distillation to enhance double-blind compound-protein interaction prediction Structure (IF 5.7) Pub Date : 2024-03-05 Ying Xia, Xiaoyong Pan, Hong-Bin Shen
Identifying binding compounds against a target protein is crucial for large-scale virtual screening in drug development. Recently, network-based methods have been developed for compound-protein interaction (CPI) prediction. However, they are difficult to be applied to unseen (i.e., never-seen-before) proteins and compounds. In this study, we propose SgCPI to incorporate local known interacting networks
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Insertases scramble lipids: Molecular simulations of MTCH2 Structure (IF 5.7) Pub Date : 2024-02-19 Ladislav Bartoš, Anant K. Menon, Robert Vácha
Scramblases play a pivotal role in facilitating bidirectional lipid transport across cell membranes, thereby influencing lipid metabolism, membrane homeostasis, and cellular signaling. MTCH2, a mitochondrial outer membrane protein insertase, has a membrane-spanning hydrophilic groove resembling those that form the lipid transit pathway in known scramblases. Employing both coarse-grained and atomistic
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EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry Structure (IF 5.7) Pub Date : 2024-02-16 Antoniya A. Aleksandrova, Edoardo Sarti, Lucy R. Forrest
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Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains Structure (IF 5.7) Pub Date : 2024-02-09 Ye-Jun Peng, Yuxing Chen, Cong-Zhao Zhou, Wei Miao, Yong-Liang Jiang, Xiaoli Zeng, Cheng-Cai Zhang
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Fluorinated cGAMP analogs, which act as STING agonists and are not cleavable by poxins: Structural basis of their function Structure (IF 5.7) Pub Date : 2024-02-06 Martin Klima, Milan Dejmek, Vojtech Duchoslav, Andrea Eisenreichova, Michal Sala, Karel Chalupsky, Dominika Chalupska, Barbora Novotná, Gabriel Birkuš, Radim Nencka, Evzen Boura
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Chaperone-assisted cryo-EM structure of P. aeruginosa PhuR reveals molecular basis for heme binding Structure (IF 5.7) Pub Date : 2024-02-06 Paweł P. Knejski, Satchal K. Erramilli, Anthony A. Kossiakoff
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De novo design of cavity-containing proteins with a backbone-centered neural network energy function Structure (IF 5.7) Pub Date : 2024-02-06 Yang Xu, Xiuhong Hu, Chenchen Wang, Yongrui Liu, Quan Chen, Haiyan Liu
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Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma Structure (IF 5.7) Pub Date : 2024-02-02 Longying Jiang, Xueke Liu, Xujun Liang, Shuyan Dai, Hudie Wei, Ming Guo, Zhuchu Chen, Desheng Xiao, Yongheng Chen
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Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2 Structure (IF 5.7) Pub Date : 2024-02-02 William J. Bradshaw, Emma C. Kennedy, Tiago Moreira, Luke A. Smith, Rod Chalk, Vittorio L. Katis, Justin L.P. Benesch, Paul E. Brennan, Emma J. Murphy, Opher Gileadi
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Understanding cytokinesis interaction by interaction Structure (IF 5.7) Pub Date : 2024-02-01 Andreas Haahr Larsen
In this issue of Structure, Hall et al.1 investigate the binding modes of anillin-like Mid1. During cytokinesis, Mid1 connects the contractile ring to the plasma membrane. Using computer simulations, the authors demonstrated how this connection is established via the L3 loop of the C2 domain.
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CELSR1, a core planar cell polarity protein, features a weakly adhesive and flexible cadherin ectodomain Structure (IF 5.7) Pub Date : 2024-02-01 Elakkiya Tamilselvan, Marcos Sotomayor
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Cryo-EM research in India Structure (IF 5.7) Pub Date : 2024-02-01 Arun K. Shukla, Manidipa Banerjee, Appu K. Singh, Aravind Penmatsa, Somnath Dutta, Ruchi Anand, Minhajuddin Sirajuddin, Shanti Swaroop Srivastava
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The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function Structure (IF 5.7) Pub Date : 2024-01-18 Daniel R. Eiler, Brian T. Wimberly, Danielle Y. Bilodeau, J. Matthew Taliaferro, Philip Reigan, Olivia S. Rissland, Jeffrey S. Kieft
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The series of conformational states adopted by rotorless F1-ATPase during its hydrolysis cycle Structure (IF 5.7) Pub Date : 2024-01-17 Meghna Sobti, Hiroshi Ueno, Simon H.J. Brown, Hiroyuki Noji, Alastair G. Stewart
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Structural determinants for tRNA selective cleavage by RNase 2/EDN Structure (IF 5.7) Pub Date : 2024-01-15 Jiarui Li, Xincheng Kang, Irene Guidi, Lu Lu, Pablo Fernández-Millán, Guillem Prats-Ejarque, Ester Boix
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Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1 Structure (IF 5.7) Pub Date : 2024-01-15 Tatsuhiko Ozawa, Yoshiki Ikeda, Liuan Chen, Rigel Suzuki, Atsushi Hoshino, Akira Noguchi, Shunsuke Kita, Yuki Anraku, Emiko Igarashi, Yumiko Saga, Noriko Inasaki, Shunta Taminishi, Jiei Sasaki, Yuhei Kirita, Hideo Fukuhara, Katsumi Maenaka, Takao Hashiguchi, Takasuke Fukuhara, Kenichi Hirabayashi, Hideki Tani, Hiroyuki Kishi, Hideki Niimi
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Structural insight into CD93 recognition by IGFBP7 Structure (IF 5.7) Pub Date : 2024-01-12 Yueming Xu, Yi Sun, Yuwen Zhu, Gaojie Song
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Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders Structure (IF 5.7) Pub Date : 2024-01-09 Dora Buzas, Huan Sun, Christine Toelzer, Sathish K.N. Yadav, Ufuk Borucu, Gunjan Gautam, Kapil Gupta, Joshua C. Bufton, Julien Capin, Richard B. Sessions, Frederic Garzoni, Imre Berger, Christiane Schaffitzel
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CRD: A de novo design algorithm for the prediction of cognate protein receptors for small molecule ligands Structure (IF 5.7) Pub Date : 2024-01-08 Santhosh Sankar, Sneha Vasudevan, Nagasuma Chandra
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Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy Structure (IF 5.7) Pub Date : 2024-01-08 Kayo Imamura, Ken-Ichi Akagi, Yohei Miyanoiri, Hirokazu Tsujimoto, Takatsugu Hirokawa, Hideo Ashida, Kaori Murakami, Asuka Inoue, Ryoji Suno, Takahisa Ikegami, Naotaka Sekiyama, So Iwata, Takuya Kobayashi, Hidehito Tochio
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Multiple masks of a Shigella podophage Structure (IF 5.7) Pub Date : 2024-01-04 Yong-Liang Jiang, Cong-Zhao Zhou
In this issue of Structure, Subramanian et al. present the cryo-EM structure of Shigella podophage HRP29, which possesses a T7-like tail complex surrounded by six P22/Sf6-like tailspikes and two unique decoration proteins. These colorful masks of HRP29 record the frequent events of horizontal gene transfer during evolution.
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Interplay between intrinsic flexibility and sugar coating in Contactin-2 homodimerization Structure (IF 5.7) Pub Date : 2024-01-04 Mehmet Sen
In this issue of Structure, Chataigner et al. reveal that Contactin-2’s homotypic interaction, a glycosylation-dependent process, generates a broad conformational landscape. This structural plasticity, driven by conformational equilibria and sugar coating, facilitates adaptation to diverse ligands and environmental conditions, highlighting its dynamic role in neuronal function.
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From simple to complex: Reconstructing all-atom structures from coarse-grained models using cg2all Structure (IF 5.7) Pub Date : 2024-01-04 Yui Tik Pang, Lixinhao Yang, James C. Gumbart
In this issue of Structure, Heo and Feig present cg2all, a novel deep-learning model capable of efficiently predicting all-atom protein structures from coarse-grained (CG) representations. The model maintains high accuracy, even when the CG model is simplified to a single bead per residue, and has a number of promising applications.
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3D animation as a tool for integrative modeling of dynamic molecular mechanisms Structure (IF 5.7) Pub Date : 2024-01-05 Margot Riggi, Rachel M. Torrez, Janet H. Iwasa
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Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase Structure (IF 5.7) Pub Date : 2024-01-04 Katharina Sievers, Piotr Neumann, Lukas Sušac, Stefano Da Vela, Melissa Graewert, Simon Trowitzsch, Dmitri Svergun, Robert Tampé, Ralf Ficner
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Structural comparison of typical and atypical E2 pestivirus glycoproteins Structure (IF 5.7) Pub Date : 2024-01-03 Hazel Aitkenhead, Christiane Riedel, Nathan Cowieson, Hans Tillmann Rümenapf, David I. Stuart, Kamel El Omari
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Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46 Structure (IF 5.7) Pub Date : 2023-12-29 Yutaka Mahana, Mariko Ariyoshi, Ryu-Suke Nozawa, Sachiko Shibata, Koji Nagao, Chikashi Obuse, Masahiro Shirakawa
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PAS domain of flagellar histidine kinase FlrB has a unique architecture and binds heme as a sensory ligand in an unconventional fashion Structure (IF 5.7) Pub Date : 2023-12-28 Peeali Mukherjee, Shubhangi Agarwal, Sritapa Basu Mallick, Jhimli Dasgupta
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Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain Structure (IF 5.7) Pub Date : 2023-12-28 Rajeshwer S. Sankhala, Vincent Dussupt, Wei-Hung Chen, Hongjun Bai, Elizabeth J. Martinez, Jaime L. Jensen, Phyllis A. Rees, Agnes Hajduczki, William C. Chang, Misook Choe, Lianying Yan, Spencer L. Sterling, Isabella Swafford, Caitlin Kuklis, Sandrine Soman, Jocelyn King, Courtney Corbitt, Michelle Zemil, Caroline E. Peterson, Letzibeth Mendez-Rivera, M. Gordon Joyce
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A combined biochemical and cellular approach reveals Zn2+-dependent hetero- and homodimeric CD4 and Lck assemblies in T cells Structure (IF 5.7) Pub Date : 2023-12-28 Anna M. Kocyła, Aleksander Czogalla, Inga Wessels, Lothar Rink, Artur Krężel
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Structural mechanism of TRPV5 inhibition by econazole Structure (IF 5.7) Pub Date : 2023-12-22 José J. De Jesús-Pérez, Matthew Gabrielle, Sumiyya Raheem, Edwin C. Fluck, Tibor Rohacs, Vera Y. Moiseenkova-Bell
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Accurate modeling of peptide-MHC structures with AlphaFold Structure (IF 5.7) Pub Date : 2023-12-18 Victor Mikhaylov, Chad A. Brambley, Grant L.J. Keller, Alyssa G. Arbuiso, Laura I. Weiss, Brian M. Baker, Arnold J. Levine
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Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain Structure (IF 5.7) Pub Date : 2023-12-15 Sebastian Jojoa-Cruz, Batuujin Burendei, Wen-Hsin Lee, Andrew B. Ward
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Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study Structure (IF 5.7) Pub Date : 2023-12-15 Aaron R. Hall, Yeol Kyo Choi, Wonpil Im, Dimitrios Vavylonis
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Functional dissection of KATP channel structures reveals the importance of a conserved interface Structure (IF 5.7) Pub Date : 2023-12-14 Yaxiong Yang, Lei Chen
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Unveiling the intriguing role of FAP20 in tubulin recruitment at the doublet microtubule inner junctions Structure (IF 5.7) Pub Date : 2023-12-07 Corbin S. Black, Khanh Huy Bui
In this issue of Structure, Bangera et al. investigate the role of the inner junction protein FAP20 in doublet microtubule assembly. Using cryo-EM and microtubule dynamic assays, they demonstrate that FAP20 recruits free tubulins to existing microtubule lattices, shedding light on B-tubule closure during doublet microtubule formation.
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Go big and go home: A bulky extension makes promiscuous ligands settle down Structure (IF 5.7) Pub Date : 2023-12-07 Xiaoyu Yu, Douglas J. Kojetin
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Treatment of noise caused by radiation damage during cryo-EM data collection Structure (IF 5.7) Pub Date : 2023-12-07 Rick Huang, Dan Shi
Here, we discuss how noise that is caused by radiation damage during cryo-EM data collections accumulates during single-particle analysis (SPA), MicroED, and cryo-ET. For MicroED and SPA, bad data can be identified and excluded during data collection and processing, whereas cryo-ET will require systematic radiation damage assessments that can be derived from SPA.
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The roles of FUS-RNA binding domain and low complexity domain in RNA-dependent phase separation Structure (IF 5.7) Pub Date : 2023-12-08 Laura R. Ganser, Amirhossein Ghanbari Niaki, Xincheng Yuan, Ethan Huang, Dahlia Deng, Nathalie A. Djaja, Yingda Ge, Alanna Craig, Olivia Langlois, Sua Myong
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Structural insights into the FtsEX-EnvC complex regulation on septal peptidoglycan hydrolysis in Vibrio cholerae Structure (IF 5.7) Pub Date : 2023-12-08 Aili Hao, Yang Suo, Seok-Yong Lee
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Strengthening E-cadherin adhesion via antibody-mediated binding stabilization Structure (IF 5.7) Pub Date : 2023-12-04 Bin Xie, Shipeng Xu, Leslayann Schecterson, Barry M. Gumbiner, Sanjeevi Sivasankar
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Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors Structure (IF 5.7) Pub Date : 2023-12-01 Tyler N. Vernon, J. Ross Terrell, Amanda V. Albrecht, Markus W. Germann, W. David Wilson, Gregory M.K. Poon
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One bead per residue can describe all-atom protein structures Structure (IF 5.7) Pub Date : 2023-11-23 Lim Heo, Michael Feig
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Structural aspects of RimP binding on small ribosomal subunit from Staphylococcus aureus Structure (IF 5.7) Pub Date : 2023-11-23 Nataliia Garaeva, Bulat Fatkhullin, Fadis Murzakhanov, Marat Gafurov, Alexander Golubev, Aydar Bikmullin, Maxim Glazyrin, Bruno Kieffer, Lasse Jenner, Vladimir Klochkov, Albert Aganov, Andrey Rogachev, Oleksandr Ivankov, Shamil Validov, Marat Yusupov, Konstantin Usachev
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Electron counting with direct electron detectors in MicroED Structure (IF 5.7) Pub Date : 2023-11-21 Johan Hattne, Max T.B. Clabbers, Michael W. Martynowycz, Tamir Gonen
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Contactin 2 homophilic adhesion structure and conformational plasticity Structure (IF 5.7) Pub Date : 2023-11-21 Lucas M.P. Chataigner, Lena Thärichen, J. Wouter Beugelink, Joke C.M. Granneman, Nadia J. Mokiem, Joost Snijder, Friedrich Förster, Bert J.C. Janssen
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Dissecting the molecular basis for the modulation of neurotransmitter GPCR signaling by GINIP Structure (IF 5.7) Pub Date : 2023-11-20 Alex Luebbers, Alberto J. Gonzalez-Hernandez, Myles Zhou, Stephen J. Eyles, Joshua Levitz, Mikel Garcia-Marcos
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The next decade in structural biology Structure (IF 5.7) Pub Date : 2023-11-02 Martin A. Walsh, Brent L. Nannenga, Tamir Gonen, Patrick M. Sexton, Denise Wootten, Wah Chiu, Fei Sun, Bridget Carragher, Clinton S. Potter, David Agard, Stephen K. Burley
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Ready for the sheet: β-strand folding of phosphorylation clusters guides GPCR binding to arrestin Structure (IF 5.7) Pub Date : 2023-11-02 Irene Coin, Daniel Huster
The molecular dynamics of arrestin binding to G protein-coupled receptors (GPCRs) are still poorly understood. In this issue of Structure, Guillien et al. show that negative charges in GPCR key phosphorylation clusters induce the formation of a transient β-strand that participates in an intermolecular β-sheet in the associated complex.
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Celebrating 30 years of Structure Structure (IF 5.7) Pub Date : 2023-11-02 Karin Kühnel
Abstract not available
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Chaperoning the major facilitator superfamily at single-molecule level Structure (IF 5.7) Pub Date : 2023-11-02 Eojin Kim, Duyoung Min
In this issue of Structure, Blaimschein et al. elucidate the chaperoning function of the insertase YidC during the insertion and folding of the melibiose permease MelB. Their single-molecule forced unfolding approach reveals that YidC significantly reduces the misfolding and enhances the folding of helices near the interface of two folding cores.
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Cullin(g) glutamate dehydrogenase: Insights into multivalent CRL3KLHL22 substrate recognition Structure (IF 5.7) Pub Date : 2023-11-02 David Schwefel
Substrate specificity is central to the regulation of cellular ubiquitylation. In this issue of Structure, Teng et al. employ biochemistry and cryo-EM single-particle reconstruction to clarify the intricate interaction of the dimeric CRL3KLHL22 E3 ligase assembly with a hexameric substrate and its possible implications for metabolic adaptation and oncogenesis.
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The solution structure of human leptin reveals a conformational plasticity important for receptor recognition Structure (IF 5.7) Pub Date : 2023-11-03 Xiao Fan, Ruiqi Qin, Wensu Yuan, Jing-Song Fan, Weidong Huang, Zhi Lin
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Modus operandi: Chromatin recognition by α-helical histone readers Structure (IF 5.7) Pub Date : 2023-11-02 Hossein Davarinejad, Alexis Arvanitis-Vigneault, Dallas Nygard, Mathieu Lavallée-Adam, Jean-François Couture
Histone reader domains provide a mechanism for sensing states of coordinated nuclear processes marked by histone proteins' post-translational modifications (PTMs). Among a growing number of discovered histone readers, the 14-3-3s, ankyrin repeat domains (ARDs), tetratricopeptide repeats (TPRs), bromodomains (BRDs), and HEAT domains are a group of domains using various mechanisms to recognize unmodified
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Architecture of the bacteriophage lambda tail Structure (IF 5.7) Pub Date : 2023-11-01 Chang Wang, Jinsong Duan, Zhiwei Gu, Xiaofei Ge, Jianwei Zeng, Jiawei Wang
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Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins Structure (IF 5.7) Pub Date : 2023-10-30 Sundharraman Subramanian, Silje M. Bergland Drarvik, Kendal R. Tinney, Kristin N. Parent
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Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook Structure (IF 5.7) Pub Date : 2023-10-27 Sabine Botha, Petra Fromme
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the
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Computational microbiology of bacteria: Advancements in molecular dynamics simulations Structure (IF 5.7) Pub Date : 2023-10-23 Syma Khalid, Astrid F. Brandner, Nikolai Juraschko, Kahlan E. Newman, Conrado Pedebos, Dheeraj Prakaash, Iain P.S. Smith, Callum Waller, Dhanushka Weerakoon
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GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution Structure (IF 5.7) Pub Date : 2023-10-23 Alejandro Hernández-Gómez, Iker Irisarri, David Fernández-Justel, Rafael Peláez, Alberto Jiménez, José Luis Revuelta, Mónica Balsera, Rubén M. Buey
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Biomolecular NMR spectroscopy in the era of artificial intelligence Structure (IF 5.7) Pub Date : 2023-10-16 Vaibhav Kumar Shukla, Gabriella T. Heller, D. Flemming Hansen