Ecosyste.ms: Papers

10.1016/j.jbc.2021.100360

Cross-linking and modification of fibronectin by peroxynitrous acid: Mapping and quantification of damage provides a new model for domain interactions
Cited by: 11
Author(s): Michele Mariotti, Adelina Rogowska-Wrzesińska, Per Hägglund, Michael J. Davies
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100350

Binding of calcium and magnesium to human cardiac troponin C
Cited by: 12
Author(s): Kaveh Rayani, Justin T Seffernick, Alison Yueh Li, Jonathan P. Davis, Anne M. Spuches, Filip Van Petegem, R. John Solaro, Steffen Lindert, Glen F. Tibbits
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100427

DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized and mismatch nucleotide insertion products in base excision repair
Cited by: 10
Author(s): Pradnya Kamble, Kalen Hall, Mahesh Chandak, Qun Tang, Melike Çağlayan
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100472

An experimental strategy to probe Gq contribution to signal transduction in living cells
Cited by: 16
Author(s): Julian Patt, Judith Alenfelder, Eva Marie Pfeil, Jan H. Voß, Nicole Merten, Funda Eryilmaz, Nina Heycke, Uli Rick, Asuka Inoue, Stefan Kehraus, Xavier Deupí, Christa E. Müller, Gabriele M. König, Max Crüsemann, Evi Kostenis
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100463

Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar
Cited by: 6
Author(s): M.P. Linehan, James B. Thoden, Hazel M. Holden
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100492

Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center
Cited by: 10
Author(s): Nicholas J York, Molly M. Lockart, Sinjinee Sardar, Nimesh Khadka, Wuxian Shi, Ronald E. Stenkamp, Jianye Zhang, Philip D. Kiser, Brad S. Pierce
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100458

Ca2+-saturated calmodulin binds tightly to the N-terminal domain of A-type fibroblast growth factor homologous factors
Cited by: 9
Author(s): Ryan Mahling, Cade R. Rahlf, Samuel C. Hansen, Matthew R. Hayden, Madeline A. Shea
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100545

TGF-β-induced cell motility requires downregulation of ARHGAPs to sustain Rac1 activity
Cited by: 3
Author(s): Mitsuyoshi Motizuki, Daizo Koinuma, Takashi Yokoyama, Yoshio Itoh, Chiho Omata, Kohei Miyazono, Masao Saitoh, Keiji Miyazawa
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100612

Functional mechanisms of MYRF DNA-binding domain mutations implicated in birth defects
Cited by: 7
Author(s): Chuandong Fan, Hongjoo An, Mohamed Sharif, Dongkyeong Kim, Yungki Park
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100693

Intrinsically disordered substrates dictate SPOP subnuclear localization and ubiquitination activity
Cited by: 13
Author(s): Grace A. Usher, Nafiseh Sabri, Roman Rohac, Amie K. Boal, Tanja Mittag, Scott A. Showalter
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100749

Moving beyond static snapshots: Protein dynamics and the Protein Data Bank
Cited by: 28
Author(s): Mitchell D. Miller, G.N. Phillips
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100715

Regulation of tau internalization, degradation, and seeding by LRP1 reveals multiple pathways for tau catabolism
Cited by: 42
Author(s): Joanna M. Cooper, Aurélien Lathuilière, Mary Migliorini, Allison L. Arai, Mashhood Wani, Simon Dujardin, Selen C. Muratoglu, Bradley T. Hyman, Dudley K. Strickland
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100658

Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium
Cited by: 4
Author(s): Gustavo Fernando Mercaldi, Maxuel O. Andrade, Jackeline de Lima Zanella, Artur T. Cordeiro, Celso Eduardo Benedetti
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100758

Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6
Cited by: 7
Author(s): Eugene Kuatsjah, Anson Chan, Rui Katahira, Stefan J. Haugen, Gregg T. Beckham, M.E.P. Murphy, Lindsay D. Eltis
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100772

Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1
Cited by: 5
Author(s): Christian J. Muñoz Sosa, Federico M. Issoglio, M.E. Carrizo
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100798

Functional impact of intramolecular cleavage and dissociation of adhesion G protein–coupled receptor GPR133 (ADGRD1) on canonical signaling
Cited by: 19
Author(s): Joshua D. Frenster, Gabriele Stephan, Niklas Ravn-Boess, Devin Bready, Jordan Wilcox, Bjoern Kieslich, Caroline Wilde, Norbert Sträter, Giselle R. Wiggin, Ines Liebscher, Torsten Schöneberg, Dimitris G. Placantonakis
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jbc.2021.100829

Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2
Cited by: 2
Author(s): Eva Absmeier, Karen Vester, Tahereh Ghane, Dmitry Burakovskiy, Pohl Milón, Petra Imhof, Marina V. Rodnina, K.F. Santos, Markus C. Wahl
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.100842

Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors
Cited by: 4
Author(s): Ekaterina Marakasova, Philip Olivares, Elena Karnaukhova, Haarin Chun, Nancy Hernandez, James H Kurasawa, Gabriela U. Hassink, Svetlana A Shestopal, Dudley K. Strickland, Andrey G. Sarafanov
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.100899

Regulation of a pentameric ligand-gated ion channel by a semiconserved cationic lipid-binding site
Cited by: 11
Author(s): Akshay Sridhar, Sarah C. R. Lummis, Diletta Pasini, Aujan Mehregan, Marijke Brams, Kumiko Kambara, Daniel Bertrand, Erik Lindahl, Rebecca J. Howard, Chris Ulens
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.100928

GSK137, a potent small-molecule BCL6 inhibitor with in vivo activity, suppresses antibody responses in mice
Cited by: 9
Author(s): Andrew C. Pearce, Mark J. Bamford, Ruth Barber, Angela Bridges, M.A. Convery, Constantinos Demetriou, Siân Evans, Thomas Gobbetti, David Hirst, Duncan S. Holmes, Jonathan P. Hutchinson, Sandrine Jayne, Larissa Lezina, Michael T. McCabe, Cassie Messenger, J. Morley, Melissa C. Musso, Paul Scott‐Stevens, Ana Sousa Manso, J. A. Schofield, Tom Slocombe, Don O. Somers, Ann L. Walker, Anastasia Wyce, Xiping Zhang, Simon D. Wagner
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.100966

Structural details of monoclonal antibody m971 recognition of the membrane-proximal domain of CD22
Cited by: 7
Author(s): June Ereño‐Orbea, Xianglei Liu, Taylor Sicard, Iga Kucharska, Wei Li, Dorota Borovsky, Hong Cui, Feng Yang, Dimiter S. Dimitrov, Jean-Philippe Julien
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.100981

Sequence variation in the β7–β8 loop of bacterial class A sortase enzymes alters substrate selectivity
Cited by: 10
Author(s): Isabel M. Piper, Sarah A. Struyvenberg, Jordan D. Valgardson, D. Alex Johnson, Melody Gao, Kerrylyn Johnston, Justin E. Svendsen, Hanna M. Kodama, Kelli L. Hvorecny, John M. Antos, J.F. Amacher
Software Mentions: 1
Published: over 3 years ago

10.1016/j.jbc.2021.101028

Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis
Cited by: 8
Author(s): Takamasa Teramoto, Takeshi Koyasu, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, T. Numata, Toshiya Senda, Yoshimitsu Kakuta
Software Mentions: 1
Published: about 3 years ago

10.1016/j.jbc.2021.101039

Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation
Cited by: 7
Author(s): Sebastián Esperante, Nathalia Varejão, Francisca Pinheiro, Ricardo Sant’Anna, Juan Román Luque‐Ortega, Carlos Alfonso, Valentina Sora, Elena Papaleo, Germán Rivas, David Reverter, Salvador Ventura
Software Mentions: 1
Published: about 3 years ago

10.1016/j.jbc.2021.101069

A three-pocket model for substrate coordination and selectivity by the nucleotide sugar transporters SLC35A1 and SLC35A2
Cited by: 2
Author(s): Danyang Li, Somshuvra Mukhopadhyay
Software Mentions: 1
Published: about 3 years ago

10.1016/j.jbc.2021.101095

PROFICS: A bacterial selection system for directed evolution of proteases
Cited by: 2
Author(s): Christina Kröß, Petra Engele, Bernhard Sprenger, Andreas Fischer, Nico Lingg, Magdalena Baier, Christoph Öhlknecht, Bettina Lier, Chris Oostenbrink, Monika Cserjan‐Puschmann, Gerald Striedner, Alois Jungbauer, Rainer Schneider
Software Mentions: 1
Published: about 3 years ago

10.1016/j.jbc.2021.101084

Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus
Cited by: 11
Author(s): Eva Madland, Zarah Forsberg, Yong Wang, Kresten Lindorff‐Larsen, Axel Niebisch, Jan Modregger, Vincent G. H. Eijsink, Finn Lillelund Aachmann, Gastón Courtade
Software Mentions: 1
Published: about 3 years ago

10.1007/s00775-018-1575-3

On how the binding cavity of AsqJ dioxygenase controls the desaturation reaction regioselectivity: a QM/MM study
Cited by: 26
Author(s): Zuzanna Wojdyła, Tomasz Borowski
Software Mentions: 1
Published: over 6 years ago

10.1007/s00775-018-1586-0

Preparation and characterization of metal-substituted carotenoid cleavage oxygenases
Cited by: 10
Author(s): Xuewu Sui, Erik R. Farquhar, Hannah Hill, Johannes von Lintig, Wuxian Shi, Philip D. Kiser
Software Mentions: 1
Published: over 6 years ago

10.1007/s00775-018-1583-3

Ether cross-link formation in the R2-like ligand-binding oxidase
Cited by: 8
Author(s): Julia J. Griese, Rui M. Branca, Vivek Srinivas, Martin Högbom
Software Mentions: 1
Published: over 6 years ago

10.1007/s00775-019-01703-z

Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access
Cited by: 9
Author(s): K. Grave, Wietske Lambert, Gustav Berggren, Julia J. Griese, M.D. Bennett, D.T. Logan, Martin Högbom
Software Mentions: 1
Published: over 5 years ago

10.1007/s00775-020-01759-2

Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions
Cited by: 2
Author(s): Dennis Huwald, Sabrina Duda, Raphael Gasper, V. Oliéric, Eckhard Hofmann, Anja Hemschemeier
Software Mentions: 1
Published: almost 5 years ago

10.1007/s00775-020-01782-3

The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron
Cited by: 14
Author(s): K. Grave, Julia J. Griese, Gustav Berggren, M.D. Bennett, Martin Högbom
Software Mentions: 1
Published: over 4 years ago

10.1007/s00775-020-01790-3

Metalation: nature’s challenge in bioinorganic chemistry
Cited by: 12
Author(s): Nigel J. Robinson, Arthur Glasfeld
Software Mentions: 1
Published: over 4 years ago

10.1007/s00775-020-01784-1

A traffic light enzyme: acetate binding reversibly switches chlorite dismutase from a red- to a green-colored heme protein
Cited by: 2
Author(s): Durga Mahor, Julia Püschmann, Menno van den Haak, Pepijn J. Kooij, David L. J. van Den Ouden, Marc J. F. Strampraad, Bérnard Srour, Peter‐Leon Hagedoorn
Software Mentions: 1
Published: over 4 years ago

10.1016/j.redox.2021.101975

Glutaredoxin: Discovery, redox defense and much more
Cited by: 43
Author(s): Fernando T. Ogata, Vasco Branco, Filipa F. Vale, Lucia Coppo
Software Mentions: 1
Published: over 3 years ago

10.1186/1477-7827-9-16

Anti-HSP90 autoantibodies in sera of infertile women identify a dominant, conserved epitope EP6 (380-389) of HSP90 beta protein
Cited by: 15
Author(s): Eusebio S. Pires, Asmita Choudhury, Susan Idicula‐Thomas, Vrinda Khole
Software Mentions: 1
Published: almost 14 years ago

10.1186/1477-7827-11-25

Inhibition of ovine in vitro fertilization by anti-Prt antibody: hypothetical model for Prt/ZP interaction
Cited by: 11
Author(s): Jorge Pimenta, João Sardinha, C.C. Marques, Ana Domingos, M.C. Baptista, J.P. Barbas, Ivo C. Martins, Patrı́cia Mesquita, Pedro Pessa, Rui Soares, Aldino Viegas, Eurico J. Cabrita, E M António Horta, Carlos M. G. A. Fontes, A M José Prates, Manuel F. O. Seabra Pereira
Software Mentions: 1
Published: over 11 years ago

10.21203/rs.3.rs-30374/v1

An in-silico approach to develop of a multi-epitope vaccine candidate against SARS-CoV-2 envelope (E) protein
Cited by: 8
Author(s): Fatemeh Ghafouri, Reza Ahangari Cohan, Farshid Noorbakhsh, Hilda Samimi, Vahid Haghpanah
Software Mentions: 1
Published: over 4 years ago

10.21203/rs.3.rs-49671/v1

Characterizing SARS-CoV-2 mutations in the United States
Cited by: 27
Author(s): Rui Wang, Jiahui Chen, Kaifu Gao, Yuta Hozumi, Changchuan Yin, Guowei Wei
Software Mentions: 1
Published: over 4 years ago

10.34133/2020/1658678

Nonhuman Primate Model of Oculocutaneous Albinism with <i>TYR</i> and <i>OCA2</i> Mutations
Cited by: 8
Author(s): Kun Wu, Ji‐Neng Lv, Hui Yang, Fengmei Yang, Rui Lin, Qiang Lin, Ren‐Juan Shen, Junbin Wang, Wenhua Duan, Min Hu, Jun Zhang, Zhanlong He, Zi‐Bing Jin
Software Mentions: 1
Published: almost 5 years ago

10.1186/1742-4690-4-19

Mutation in the loop C-terminal to the cyclophilin A binding site of HIV-1 capsid protein disrupts proper virus assembly and infectivity
Cited by: 12
Author(s): Samir Abdurahman, Stefan Höglund, Anders Höglund, Anders Vahlne
Software Mentions: 1
Published: over 17 years ago

10.1186/1742-4690-4-69

Characterization of the invariable residue 51 mutations of human immunodeficiency virus type 1 capsid protein on in vitro CA assembly and infectivity
Cited by: 22
Author(s): Samir Abdurahman, Masoud Youssefi, Stefan Höglund, Anders Vahlne
Software Mentions: 1
Published: about 17 years ago

10.1186/1742-4690-7-58

A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5α
Cited by: 25
Author(s): Ayumu Kuroishi, Katarzyna Bożek, Tatsuo Shioda, Emi E. Nakayama
Software Mentions: 1
Published: over 14 years ago

10.1186/1742-4690-8-78

Lack of adaptation to human tetherin in HIV-1 Group O and P
Cited by: 48
Author(s): Su Jung Yang, Lisa A. Lopez, Colin M. Exline, Kevin G. Haworth, Paula M. Cannon
Software Mentions: 1
Published: about 13 years ago

10.1186/1742-4690-8-101

The prototype HIV-1 maturation inhibitor, bevirimat, binds to the CA-SP1 cleavage site in immature Gag particles
Cited by: 62
Author(s): Angeline Nguyen, Christa L. Feasley, Ken W. Jackson, Theodore J. Nitz, Karl Salzwedel, Gillian M. Air, Michael Sakalian
Software Mentions: 1
Published: almost 13 years ago

10.1186/1742-4690-9-36

MiniCD4 protein resistance mutations affect binding to the HIV-1 gp120 CD4 binding site and decrease entry efficiency
Cited by: 18
Author(s): Katrijn Grupping, Philippe Selhorst, Johan Míchiels, Katleen Vereecken, Leo Heyndríckx, Pascal Kessler, Guido Vanham, Loı̈c Martin, Kevin K. Ariën
Software Mentions: 1
Published: over 12 years ago

10.1186/1742-4690-10-14

A systematic study of the N-glycosylation sites of HIV-1 envelope protein on infectivity and antibody-mediated neutralization
Cited by: 100
Author(s): Wenbo Wang, Jianhui Nie, Courtney Prochnow, Carolyn Truong, Jiajun Zheng, Suting Wang, Xiaojiang S. Chen, Youchun Wang
Software Mentions: 1
Published: almost 12 years ago

10.1186/1742-4690-10-65

Hypersusceptibility mechanism of Tenofovir-resistant HIV to EFdA
Cited by: 34
Author(s): Eleftherios Michailidis, Emily M. Ryan, Atsuko Hachiya, Karen A. Kirby, Bruno Marchand, Maxwell D. Leslie, Andrew D. Huber, Yee Tsuey Ong, Jacob C. Jackson, Kamalendra Singh, Eiichi Kodama, Hiroaki Mitsuya, Michael A. Parniak, Stefan G. Sarafianos
Software Mentions: 1
Published: over 11 years ago

10.1186/1742-4690-10-77

Heterogeneous susceptibility of circulating SIV isolate capsids to HIV-interacting factors
Cited by: 26
Author(s): João I. Mamede, Marc Sitbon, Jean-Luc Battini, Valérie Courgnaud
Software Mentions: 1
Published: over 11 years ago

10.1186/1742-4690-11-24

Structural basis for the inhibition of HIV-1 Nef by a high-affinity binding single-domain antibody
Cited by: 18
Author(s): Sebastian Lülf, Julie Matz, Marie‐Christine Rouyez, Annika Järviluoma, Kalle Saksela, Serge Bénichou, Matthias Geyer
Software Mentions: 1
Published: over 10 years ago

10.1186/1742-4690-11-38

Switching and emergence of CTL epitopes in HIV-1 infection
Cited by: 13
Author(s): Chungyong Han, Ai Kawana-Tachikawa, Akihisa Shimizu, Dayong Zhu, Hitomi Nakamura, Eisuke Adachi, Tadashi Kimura, Michiko Koga, Tomohiko Koibuchi, George F. Gao, Yusuke Sato, Atsushi Yamagata, Eric S. Martin, Shuya Fukai, Zabrina L. Brumme, Aikichi Iwamoto
Software Mentions: 1
Published: over 10 years ago

10.1186/s12977-014-0079-7

HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes
Cited by: 12
Author(s): Guangdi Li, Jens Verheyen, Kristof Theys, Supinya Piampongsant, Kristel Van Laethem, Anne‐Mieke Vandamme
Software Mentions: 1
Published: about 10 years ago

10.1186/1742-4690-10-144

Dual inhibition of HIV-1 replication by integrase-LEDGF allosteric inhibitors is predominant at the post-integration stage
Cited by: 106
Author(s): Erwann Le Rouzic, Damien Bonnard, Sophie Chasset, Jean-Michel Bruneau, Francis Chevreuil, Frédéric Le Strat, Juliette Nguyen, Roxane Beauvoir, Céline Amadori, Julie Brias, Sophie Vomscheid, Sylvia Eiler, Nicolas Lévy, Olivier Delelis, Eric Deprez, Ali Saı̈b, Alessia Zamborlini, Stéphane Emiliani, Marc Ruff, Benoît Ledoussal, F. Moreau, Richard Bénarous
Software Mentions: 1
Published: about 11 years ago

10.1186/s12977-015-0194-0

Determinants in HIV-2 Env and tetherin required for functional interaction
Cited by: 6
Author(s): Colin M. Exline, Su Jung Yang, Kevin G. Haworth, Srinivas Rengarajan, Lisa A. Lopez, Magali E. Droniou, Eduardo Seclén, Paula M. Cannon
Software Mentions: 1
Published: over 9 years ago

10.1186/s12977-016-0291-8

Mutagenesis of N-terminal residues of feline foamy virus Gag reveals entirely distinct functions during capsid formation, particle assembly, Gag processing and budding
Cited by: 5
Author(s): Yang Liu, Matthew J. Betts, Janet Lei-Rossmann, Guochao Wei, Qiuying Bao, Timo Kehl, Robert B. Russell, Martin Löchelt
Software Mentions: 1
Published: over 8 years ago

10.1186/s12977-018-0414-5

New World feline APOBEC3 potently controls inter-genus lentiviral transmission
Cited by: 7
Author(s): Yoriyuki Konno, Sumiharu Nagaoka, Izumi Kimura, Keisuke Yamamoto, Yumiko Kagawa, Ryuichi Kumata, Hirofumi Aso, Mahoko Takahashi Ueda, So Nakagawa, Tomoko Kobayashi, Yoshio Koyanagi, Kei Sato
Software Mentions: 1
Published: over 6 years ago

10.1186/s12977-018-0432-3

Myricetin antagonizes semen-derived enhancer of viral infection (SEVI) formation and influences its infection-enhancing activity
Cited by: 14
Author(s): Ruxia Ren, Sha Yin, B. Lai, Lingzhen Ma, Jiayong Wen, Xuanxuan Zhang, Fangyuan Lai, Shuwen Liu, Lin Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12284-020-00448-7

Exploring Natural Allelic Variations of the β-Triketone Herbicide Resistance Gene HIS1 for Application in indica Rice and Particularly in Two-Line Hybrid Rice
Cited by: 2
Author(s): Qiming Lv, Xiuli Zhang, Dingyang Yuan, Zhiyuan Huang, Rui Peng, Jiming Peng, Zuren Li, Li Tang, Ducai Liu, Xiaomao Zhou, Lifeng Wang, Lang Pan, Ye Shao, Bigang Mao, Yeyun Xin, Lihuang Zhu, Baisuo Zhao, Lianyang Bai
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12284-021-00499-4

Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability
Cited by: 4
Author(s): Kun‐Ting Hsieh, Yi-Ting Chen, Ting-Jen Hu, Shu‐Yuan Lin, Cheng-Yu Hsieh, Su-Hui Liu, Shiau-Yu Shiue, Shuen‐Fang Lo, I-Wen Wang, Chiu‐yu Tseng, Liang-Jwu Chen
Software Mentions: 1
Published: over 3 years ago

10.1126/sciadv.aat7052

Crystal structure of rhodopsin in complex with a mini-G _o sheds light on the principles of G protein selectivity
Cited by: 61
Author(s): Ching‐Ju Tsai, Filip Pamula, Rony Nehmé, Jonas Mühle, T. Weinert, Tilman Flock, Przemyslaw Nogly, Patricia C. Edwards, Byron Carpenter, Thomas Gruhl, Pikyee Ma, Xavier Deupí, Jörg Standfuss, Christopher G. Tate, Gebhard F. X. Schertler
Software Mentions: 1
Published: about 6 years ago

10.1126/sciadv.aau1199

The IgM pentamer is an asymmetric pentagon with an open groove that binds the AIM protein
Cited by: 74
Author(s): Emiri Hiramoto, Akihisa Tsutsumi, Risa Suzuki, Shigeru Matsuoka, Satoko Arai, Masahide Kikkawa, Toru Miyazaki
Software Mentions: 1
Published: about 6 years ago

10.1126/sciadv.aau6769

HIV-1 vaccine design through minimizing envelope metastability
Cited by: 65
Author(s): Linling He, Sonu Kumar, Joel D. Allen, Deli Huang, Xue Lin, Colin Mann, Karen L. Saye-Francisco, Jeffrey Copps, Achyut Sarkar, Gabrielle S Blizard, Gabriel Ozorowski, Devin Sok, Max Crispin, Andrew B. Ward, David Nemazee, Dennis R. Burton, Ian A. Wilson, Jiang Zhu
Software Mentions: 1
Published: about 6 years ago

10.1126/sciadv.aaw1567

Olanzapine: A potent agonist at the hM4D(Gi) DREADD amenable to clinical translation of chemogenetics
Cited by: 42
Author(s): Mikail Weston, Teresa Kaserer, Angela Wu, Alexandre Mouravlev, Jenna C. Carpenter, Albert Snowball, Samuel Knauß, Melanie von Schimmelmann, Matthew J. During, Gabriele Lignani, Stephanie Schorge, Deborah Young, Dimitri M. Kullmann, Andreas Lieb
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.aav7574

Asymmetry in catalysis by <i>Thermotoga maritima</i> membrane-bound pyrophosphatase demonstrated by a nonphosphorus allosteric inhibitor
Cited by: 13
Author(s): Keni Vidilaseris, Alexandros Kiriazis, Ainoleena Turku, Ayman Khattab, Niklas G. Johansson, Teppo O. Leino, Paula Kiuru, Gustav Boije af Gennäs, Seppo Meri, Jari Yli‐Kauhaluoma, Henri Xhaard, Adrian Goldman
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.aax1803

Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo–electron microscopy
Cited by: 14
Author(s): Chai Gopalasingam, Rachel M. Johnson, George N. Chiduza, Takehiko Tosha, Masaki Yamamoto, Yoshitsugu Shiro, S.V. Antonyuk, Stephen P. Muench, S.S. Hasnain
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.aax3567

Human adenovirus type 26 uses sialic acid–bearing glycans as a primary cell entry receptor
Cited by: 62
Author(s): Alex Baker, R.M. Mundy, James A. Davies, P.J. Rizkallah, Alan L. Parker
Software Mentions: 1
Published: about 5 years ago

10.1126/sciadv.aax3641

RNA binding activates RIG-I by releasing an autorepressed signaling domain
Cited by: 13
Author(s): Thayne H. Dickey, Brian Song, Anna Marie Pyle
Software Mentions: 1
Published: about 5 years ago

10.1126/sciadv.aay6415

The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis
Cited by: 43
Author(s): Christopher J. Gisriel, Gaozhong Shen, Vasily Kurashov, Ming Yang Ho, Shangji Zhang, Dewight Williams, John H. Golbeck, Petra Fromme, Donald A. Bryant
Software Mentions: 1
Published: almost 5 years ago

10.1126/sciadv.aax5783

Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions
Cited by: 71
Author(s): Miguel A. Gonzalez‐Lozano, Frank Koopmans, Patrick F. Sullivan, Jonas Protze, Gerd Krause, Matthijs Verhage, K. W. Li, Fan Liu, August B. Smit
Software Mentions: 1
Published: almost 5 years ago

10.1126/sciadv.abb5924

Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease
Cited by: 81
Author(s): Gabriella T. Heller, Francesco A. Aprile, Thomas C. T. Michaels, Ryan Limbocker, Michele Perni, Francesco Simone Ruggeri, Benedetta Mannini, Thomas Löhr, Massimiliano Bonomi, Carlo Camilloni, Alfonso De Simone, Isabella C. Felli, Roberta Pierattelli, Tuomas P. J. Knowles, Christopher M. Dobson
Software Mentions: 1
Published: about 4 years ago

10.1126/sciadv.abg4403

Crystal structure of ADAMTS13 CUB domains reveals their role in global latency
Cited by: 20
Author(s): H. J. Kim, Yingqi Xu, Anastasis Petri, Karen Vanhoorelbeke, James T. B. Crawley, Jonas Emsley
Software Mentions: 1
Published: over 3 years ago

10.1126/sciadv.abf6744

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping
Cited by: 9
Author(s): M.A. Marquez-Monino, Raquel Ortega-García, Megan L. Shipton, Elsa Franco-Echevarría, Andrew M. Riley, J. Sanz‐Aparicio, Barry V. L. Potter, Beatriz González
Software Mentions: 1
Published: over 3 years ago

10.1126/sciadv.abg4000

Cork-in-bottle mechanism of inhibitor binding to mammalian complex I
Cited by: 31
Author(s): Injae Chung, Riccardo Serreli, Jason B. Cross, Maria Emilia Di Francesco, Joseph R. Marszalek, Judy Hirst
Software Mentions: 1
Published: over 3 years ago

10.1126/sciadv.abf8864

Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-Å resolution
Cited by: 27
Author(s): Laura Bracun, Atsushi Yamagata, Bern M. Christianson, Tohru Terada, Daniel P. Canniffe, Mikako Shirouzu, Luning Liu
Software Mentions: 1
Published: over 3 years ago

10.1126/sciadv.abi6856

Rare genetic variability in human drug target genes modulates drug response and can guide precision medicine
Cited by: 14
Author(s): Yitian Zhou, Gabriel Herras Arribas, Ainoleena Turku, Tuuli Jürgenson, Souren Mkrtchian, Kristi Krebs, Yì Wáng, Barbora Svobodová, Lili Milani, Gunnar Schulte, Jan Korábečný, Stefano Gastaldello, Volker M. Lauschke
Software Mentions: 1
Published: about 3 years ago

10.1038/s41597-020-00652-6

Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design
Cited by: 23
Author(s): Marija Sorokina, João M.C. Teixeira, Susana Barrera-Vilarmau, Ralf Paschke, Ioannis Papasotiriou, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis
Software Mentions: 1
Published: about 4 years ago

10.1126/sciimmunol.aao1384

A molecular basis of human T cell receptor autoreactivity toward self-phospholipids
Cited by: 36
Author(s): Adam Shahine, Ildiko Van Rhijn, Tan-Yun Cheng, Sarah K. Iwany, Stéphanie Gras, D. Branch Moody, Jamie Rossjohn
Software Mentions: 1
Published: about 7 years ago

10.1038/srep02318

Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China
Cited by: 18
Author(s): Yongbo Wang, Zhangyan Dai, Han Cheng, Zexian Liu, Zhicheng Pan, Wankun Deng, Tianshun Gao, Xiaotong Li, Yuangen Yao, Jian Ren, Yu Xue
Software Mentions: 1
Published: over 11 years ago

10.1038/srep04942

High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
Cited by: 135
Author(s): Nicholas C. Wu, Arthur P. Young, Laith Q. Al‐Mawsawi, C. Anders Olson, Jun Feng, Hangfei Qi, Shu Hwa Chen, I-Hsuan Lu, Chung Yen Lin, Robert Chin, Harding H. Luan, Nguyen Nguyen, Stanley F. Nelson, Xinmin Li, Ting Wu, Ren Sun
Software Mentions: 1
Published: over 10 years ago

10.1038/srep04965

Selective Small Molecule Compounds Increase BMP-2 Responsiveness by Inhibiting Smurf1-mediated Smad1/5 Degradation
Cited by: 58
Author(s): Ya Cao, Cheng Wang, Xueli Zhang, Guichun Xing, Kefeng Lu, Yongqing Gu, Fuchu He, Lingqiang Zhang
Software Mentions: 1
Published: over 10 years ago

10.1038/srep07322

Structural insight into substrate recognition by the endoplasmic reticulum folding-sensor enzyme: crystal structure of third thioredoxin-like domain of UDP-glucose:glycoprotein glucosyltransferase
Cited by: 34
Author(s): Tong Zhu, Tadashi Satoh, Koichi Kato
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep08026

Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway
Cited by: 561
Author(s): Joana S. Fraga, Ana Maranha, V. Mendes, Pedro José Barbosa Pereira, Nuno Empadinhas, Sandra Macedo-Ribeiro
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep08361

A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline
Cited by: 28
Author(s): Xin Chen, Shanshan Qin, Shuai Chen, Jinxin Li, Lixin Li, Zhongling Wang, Quan Wang, Jianping Lin, Cheng Yang, Shui Wang
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep08769

Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels
Cited by: 24
Author(s): G.A. Bezerra, E. Dobrovetsky, A. Seitova, Sofiya Fedosyuk, Sirano Dhe‐Paganon, Karl Gruber
Software Mentions: 1
Published: over 9 years ago

10.1038/srep09375

Enhanced photocurrent production by bio-dyes of photosynthetic macromolecules on designed TiO2 film
Cited by: 54
Author(s): Daoyong Yu, Mengfei Wang, Guangpu Zhu, Baosheng Ge, Shuang Liu, Fang Huang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep09449

Structure and function of a Clostridium difficile sortase enzyme
Cited by: 22
Author(s): Christopher J. Chambers, April K. Roberts, Clifford C. Shone, K. Ravi Acharya
Software Mentions: 1
Published: over 9 years ago

10.1038/srep09641

Ryanodine receptors are targeted by anti-apoptotic Bcl-XL involving its BH4 domain and Lys87 from its BH3 domain
Cited by: 30
Author(s): Tim Vervliet, Irma Lemmens, Elien Vandermarliere, Elke Decrock, Hristina Ivanova, Giovanni Monaco, Vincenzo Sorrentino, Nael Nadif Kasri, Ludwig Missiaen, Lennart Martens, Humbert De Smedt, Luc Leybaert, Jan B. Parys, Jan Tavernier, Geert Bultynck
Software Mentions: 1
Published: over 9 years ago

10.1038/srep10447

Structural and functional characterization of a novel scFv anti-HSP60 of Strongyloides sp.
Cited by: 16
Author(s): Marcelo Arantes Levenhagen, Francisco Abad Santos, Patrícia Tiemi Fujimura, Ana Paula Caneiro, Julia Maria Costa‐Cruz, Luiz Ricardo Goulart
Software Mentions: 1
Published: over 9 years ago

10.1038/srep11581

Structural and Physical Basis for Anti-IgE Therapy
Cited by: 40
Author(s): Jon D. Wright, Hsing-Mao Chu, Chun‐Hsiang Huang, Che Ma, Tse Wen Chang, Carmay Lim
Software Mentions: 1
Published: over 9 years ago

10.1038/srep11629

Highly homologous proteins exert opposite biological activities by using different interaction interfaces
Cited by: 10
Author(s): Anat Amir, Martijn van Rosmalen, Guy Mayer, Mario Lebendiker, Tsafi Danieli, Assaf Friedler
Software Mentions: 1
Published: over 9 years ago

10.1038/srep11648

Molecular evolution of haemagglutinin (H) gene in measles virus
Cited by: 32
Author(s): Hirokazu Kimura, Masaaki Saitoh, Miho Kobayashi, Haruyuki Ishii, Takeshi Saraya, Daisuke Kurai, Hiroyuki Tsukagoshi, Komei Shirabe, Atsuyoshi Nishina, Kunihisa Kozawa, Makoto Kuroda, Fumihiko Takeuchi, Tsuyoshi Sekizuka, Hisanori Minakami, Akihide Ryo, Makoto Takeda
Software Mentions: 1
Published: over 9 years ago

10.1038/srep10270

Optimizing fluorescent protein trios for 3-Way FRET imaging of protein interactions in living cells
Cited by: 21
Author(s): Brandon L. Scott, Adam D. Hoppe
Software Mentions: 1
Published: over 9 years ago

10.1038/srep11674

Crystal Structures of a Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest a Novel Cofactor Binding Mode for Oxidoreductases
Cited by: 14
Author(s): Junji Hayashi, Shota Inoue, Kwang Jin Kim, Kazunari Yoneda, Yutaka Kawarabayasi, Toshihisa Ohshima, Haruhiko Sakuraba
Software Mentions: 1
Published: over 9 years ago

10.1038/srep12052

Ortho-methylated 3-hydroxypyridines hinder hen egg-white lysozyme fibrillogenesis
Cited by: 16
Author(s): Luca Marino, Kris Pauwels, Rodrigo Casasnovas, Pilar Sanchís, Bartolomé Vilanova, Francisco Muñoz, Josefa Donoso, Miquel Adrover
Software Mentions: 1
Published: over 9 years ago

10.1038/srep12583

Molecular mechanisms of the non-coenzyme action of thiamin in brain: biochemical, structural and pathway analysis
Cited by: 90
Author(s): Garik Mkrtchyan, Vasily A. Aleshin, Yu. M. Parkhomenko, Thilo Kaehne, Martino L. di Salvo, Alessia Parroni, Roberto Contestabile, А. I. Vovk, Lucien Bettendorff, Victoria I. Bunik
Software Mentions: 1
Published: over 9 years ago

10.1038/srep12905

Conserved features in TamA enable interaction with TamB to drive the activity of the translocation and assembly module
Cited by: 31
Author(s): Joel Selkrig, Matthew J. Belousoff, Stephen J. Headey, Eva Heinz, Takuya Shiota, Hsin‐Hui Shen, Simone A. Beckham, Rebecca S. Bamert, Minh-Duy Phan, Mark A. Schembri, Matthew C. J. Wilce, M.J. Scanlon, Richard A. Strugnell, Trevor Lithgow
Software Mentions: 1
Published: over 9 years ago

10.1038/srep13038

Two single amino acid substitutions in the intervening region of Newcastle disease virus HN protein attenuate viral replication and pathogenicity
Cited by: 12
Author(s): Bin Liu, Yanhong Ji, Lin Zheng, Yue Fu, Rihab Muhammad Dafallah, Qing Zhu
Software Mentions: 1
Published: over 9 years ago

10.1038/srep12828

Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus
Cited by: 9
Author(s): Sun‐Woo Yoon, Noam Chen, Mariette Ducatez, Ryan McBride, Subrata Barman, Thomas Fabrizio, Robert G. Webster, Türkan Haliloğlu, James C. Paulson, Charles J. Russell, Tomer Hertz, Nir Ben‐Tal, Richard J. Webby
Software Mentions: 1
Published: over 9 years ago

10.1038/srep13180

Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations
Cited by: 40
Author(s): Ramin Ekhteiari Salmas, Mine Yurtsever, Serdar Durdağı
Software Mentions: 1
Published: over 9 years ago