Article
Biochemistry & Molecular Biology
Lev Khmelnitsky, Ayala Milo, Orly Dym, Deborah Fass
Summary: CysD domains are important for intermolecular adhesion in the formation and secretion of mucin polymers. The crystal structure of the seventh CysD domain from MUC5AC provided experimental data on a representative CysD in a larger branch of the fold family. The structure revealed differences in calcium-binding sites and an additional α-helix with potential functional implications.
Article
Materials Science, Multidisciplinary
Nanna Zhou Hagstrom, Rahul Jangid, Meera Madhavi, Diego Turenne, Jeffrey A. Brock, Erik S. Lamb, Boyan Stoychev, Justine Schlappa, Natalia Gerasimova, Benjamin Van Kuiken, Rafael Gort, Laurent Mercadier, Loic Le Guyader, Andrey Samartsev, Andreas Scherz, Giuseppe Mercurio, Hermann A. Durr, Alexander H. Reid, Monika Arora, Hans T. Nembach, Justin M. Shaw, Emmanuelle Jal, Eric E. Fullerton, Mark W. Keller, Roopali Kukreja, Stefano Bonetti, Thomas J. Silva, Ezio Iacocca
Summary: The study reveals that the ultrafast response of magnetic domain patterns is related to spatial features, and far-from-equilibrium magnetization dynamics offer alternative pathways for spatiotemporal manipulation of magnetism.
Article
Materials Science, Multidisciplinary
Dmitriy Zusin, Ezio Iacocca, Loic Le Guyader, Alexander H. Reid, William F. Schlotter, Tian-Min Liu, Daniel J. Higley, Giacomo Coslovich, Scott F. Wandel, Phoebe M. Tengdin, Sheena K. K. Patel, Anatoly Shabalin, Nelson Hua, Stjepan B. Hrkac, Hans T. Nembach, Justin M. Shaw, Sergio A. Montoya, Adam Blonsky, Christian Gentry, Mark A. Hoefer, Margaret M. Murnane, Henry C. Kapteyn, Eric E. Fullerton, Oleg Shpyrko, Hermann A. Durr, T. J. Silva
Summary: In this study, the laser-induced dynamics of labyrinth domain networks in ferromagnetic CoFe/Ni multilayers were investigated using ultrafast x-ray diffraction. It was observed that the amplitudes of the magnetic diffraction rings decreased to different degrees within a short period of time and the rings also broadened and contracted radially. By analyzing the diffraction rings using Fourier analysis, the broadening of the domain walls was quantitatively determined. These findings provide important evidence for understanding the dynamics of labyrinth domain structures under far-from-equilibrium conditions.
Article
Crystallography
Woong Choi, Jonghyeon Son, Aekyung Park, Hongshi Jin, Seung Chul Shin, Jun Hyuck Lee, T. Doohun Kim, Han-Woo Kim
Summary: Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA metabolism and have potential applications in molecular biology and analytical methods. This study purified, characterized, and analyzed a psychrophilic SSB (LjSSB) isolated from Lacinutrix jangbogonensis PAMC 27137 in the Antarctic region. The crystal structure of LjSSB was obtained, and its complete structural information will provide novel strategies for protein engineering and molecular biological techniques.
Article
Chemistry, Multidisciplinary
Abigail R. Orun, Ethan T. Shields, Sara Dmytriw, Ananya Vajapayajula, Caroline K. Slaughter, Christopher D. Snow
Summary: Researchers have designed isoreticular cocrystals as scaffolds for DNA-binding molecules. These cocrystals have tunable DNA-DNA junctions and can accommodate different guest molecules during crystallization. The design principles can be applied to existing cocrystals to develop programmable scaffolds for DNA-binding molecules.
Article
Multidisciplinary Sciences
Ea Kristine Clarisse Tulin, Chiaki Nakazawa, Tomomi Nakamura, Shion Saito, Naoki Ohzono, Keiko Hiemori, Shin-ichi Nakakita, Hiroaki Tateno, Takashi Tonozuka, Atsushi Nishikawa
Summary: The study utilized HA1 mutants in complex with HA2 WT and HA3 WT to produce glycan detecting tools with high binding affinity, specifically targeting Gal, GalNAc, and Neu5Ac terminal epitopes on the cell surface. The specificities of these lectins were identified using glycan microarray and competitive sugar inhibition experiments on cells, showing clear differences in staining patterns depending on cell type. This provides new promising tools for understanding the functional role of glycans in physiological and pathological events.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Dmitry Makarov, Anastasia Kharlamova
Summary: This study develops a theory of X-ray ultrashort pulse scattering that takes into account the interaction between ultrashort pulses and complex polyatomic structures. The obtained expressions have a simple analytical form that can be used in diffraction analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Michelangelo Marasco, John Kirkpatrick, Teresa Carlomagno, Jochen S. Hub, Massimiliano Anselmi
Summary: SHP2 is a critical protein involved in regulating cellular processes, and its mutations can lead to developmental disorders and cancer. The protein consists of multiple domains, including two SH2 domains and a catalytic PTP domain. The relative orientation and spacing between the SH2 domains play a crucial role in enzymatic activation. Previous studies have not provided a clear picture of the SH2 domain structure, but experiment-guided molecular simulations have revealed the structural flexibility of the tandem SH2 in solution, suggesting its importance in SHP2's functional activity.
Article
Genetics & Heredity
Line J. Manceau, Julien E. Richard Albert, Pier-Luigi J. Lollini, Maxim V. C. E. Greenberg, Pascale J. Gilardi-Hebenstreit, Vanessa E. Ribes
Summary: The chimeric proteins PAX3-FOXO1 and PAX7-FOXO1, derived from chromosomal translocations, exhibit distinct genomic occupancy and transcriptional activity, leading to different pathological manifestations in alveolar rhabdomyosarcoma.
Article
Multidisciplinary Sciences
Akinobu Niozu, Yoshiaki Kumagai, Toshiyuki Nishiyama Hiraki, Hironobu Fukuzawa, Koji Motomura, Maximilian Bucher, Kazuki Asa, Yuhiro Sato, Yuta Ito, Daehyun You, Taishi Ono, Yiwen Li, Edwin Kukk, Catalin Miron, Liviu Neagu, Carlo Callegari, Michele Di Fraia, Giorgio Rossi, Davide Emilio Galli, Tommaso Pincelli, Alessandro Colombo, Shigeki Owada, Kensuke Tono, Takashi Kameshima, Yasumasa Joti, Tetsuo Katayama, Tadashi Togashi, Makina Yabashi, Kazuhiro Matsuda, Christoph Bostedt, Kiyoshi Ueda, Kiyonobu Nagaya
Summary: This study explores the formation process of solid Xe nanoparticles in an expanding supercooled Xe jet under vacuum conditions using X-ray diffraction experiments. It is found that the structure of Xe nanoparticles is a mixture of face-centered cubic and randomly stacked hexagonal close-packed structures, rather than pure face-centered cubic. Instantaneous coexistence of comparably sized face-centered cubic and hexagonal close-packed domains in single Xe nanoparticles is observed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Marie S. Prevost, Nathalie Barilone, Gabrielle Dejean de la Batie, Steprimephanie Pons, Gabriel Ayme, Patrick England, Marc Gielen, Francois Bontems, Gerard Pehau-Arnaudet, Uwe Maskos, Pierre Lafaye, Pierre-Jean Corringer
Summary: The study presents the cryo-EM structures of alpha 7 in complex with single-chain antibodies, revealing an original mechanism of potentiation that is significant for the design of pro-cognitive drugs.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Longlong Wu, Pavol Juhas, Shinjae Yoo, Ian Robinson
Summary: This study presents a method to estimate the complex single-particle image quickly and accurately using a deep neural network model, and further enhance the accuracy of the reconstructed results by combining it with traditional iterative methods. Improved convergence is demonstrated with experimental BCDI data.
Article
Chemistry, Multidisciplinary
Katarzyna Kluska, Giulia Veronesi, Aurelien Deniaud, Balint Hajdu, Bela Gyurcsik, Wojciech Bal, Artur Krezel
Summary: It has been demonstrated that Ag-I can replace Zn-II in zinc fingers, leading to the loss of biological function. X-ray absorption spectroscopy (XAS) study reveals the structural features of AgnSn clusters formed in zinc fingers. The study shows that Ag-I predominantly coordinates with two sulfur donors with an average Ag-S distance of 2.41 angstrom. A mixed AgS2/AgS3 geometry is found in CCCH Ag-I-ZF. Furthermore, cooperative replacement of Zn-II ions with Ag2S2 clusters is observed in a three-zinc finger transcription factor protein 1MEY#, causing dissociation from its cognate DNA complex.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Nina Schmolka, Ino D. D. Karemaker, Richard Cardoso da Silva, Davide C. C. Recchia, Vincent Spegg, Jahnavi Bhaskaran, Michael Teske, Nathalie P. P. de Wagenaar, Matthias Altmeyer, Tuncay Baubec
Summary: The Nucleosome Remodeling and Deacetylation (NuRD) complex, consisting of MBD2 and MBD3 subunits, is crucial for cellular differentiation. In this study, the authors investigated the role of different MBD2 and MBD3 isoforms in rescuing the differentiation block observed in Mbd3 knockout mouse embryonic stem cells. They found that MBD3 is essential for neuronal differentiation, but its MBD domain is not required. Additionally, they identified that MBD2 isoforms can replace MBD3 during lineage commitment, with MBD2b fully rescuing the phenotype.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Mustafa Bal, Aysegul Kose, Seyit Ali Gungor
Summary: This study synthesized benzimidazole compounds containing benzophenone group according to the literature and investigated their DNA binding properties using UV-vis and photoluminescence spectroscopy. The structures of the compounds were determined using methods such as FT-IR, H-1, C-13 NMR, UV-vis, photoluminescence spectroscopy, and X-ray crystallography. Information about the binding types, binding mode, and binding energies of the compounds with DNA were collected using UV-vis, photoluminescence spectroscopy, and viscosity tests. Binding interactions were also investigated using molecular docking. The calculated binding constants (Kb) for substances A, B, and C were found to be 3.0 x 10(4), 7.0 x 10(4), and 3.0 x 10(4) M-1, respectively. Compound B showed the best DNA binding activity in in vitro studies. It is believed that these synthesized compounds may have potential in cancer drug research as DNA binding agents.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Alok K. Sharma, Gabriel Birrane, Clemens Anklin, Alan C. Rigby, Seth L. Alper
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Multidisciplinary Sciences
Thiago J. Borges, Naoka Murakami, Felipe D. Machado, Ayesha Murshid, Benjamin J. Lang, Rafael L. Lopes, Laura M. Bellan, Mayuko Uehara, Krist H. Antunes, Maria Jose Perez-Saez, Gabriel Birrane, Priscila Vianna, Joao Ismael B. Goncalves, Rafael F. Zanin, Jamil Azzi, Reza Abdi, Satoshi Ishido, Jeoung-Sook Shin, Ana Paula D. Souza, Stuart K. Calderwood, Leonardo V. Riella, Cristina Bonorino
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Gabriel Birrane, Anne P. Beigneux, Brian Dwyer, Bettina Strack-Logue, Kristian Kolby Kristensen, Omar L. Francone, Loren G. Fong, Haydyn D. T. Mertens, Clark Q. Pan, Michael Ploug, Stephen G. Young, Muthuraman Meiyappan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Gabriel Birrane, Anne-Laure Dassier, Alla Romashko, Dianna Lundberg, Kevin Holmes, Thomas Cottle, Angela W. Norton, Bohong Zhang, Michael F. Concino, Muthuraman Meiyappan
JOURNAL OF STRUCTURAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Anne P. Beigneux, Christopher M. Allan, Norma P. Sandoval, Geoffrey W. Cho, Patrick J. Heizer, Rachel S. Jung, Kimber L. Stanhope, Peter J. Havel, Gabriel Birrane, Muthuraman Meiyappan, John E. Gill, Masami Murakami, Kazuya Miyashita, Katsuyuki Nakajima, Michael Ploug, Loren G. Fong, Stephen G. Young
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Review
Cell Biology
Stephen G. Young, Loren G. Fong, Anne P. Beigneux, Christopher M. Allan, Cuiwen He, Haibo Jiang, Katsuyuki Nakajima, Muthuraman Meiyappan, Gabriel Birrane, Michael Ploug
Article
Biology
Tobias W. Giessen, Benjamin J. Orlando, Andrew A. Verdegaal, Melissa G. Chambers, Jules Gardener, David C. Bell, Gabriel Birrane, Maofu Liao, Pamela A. Silver
Article
Multidisciplinary Sciences
Kristian K. Kristensen, Katrine Zinck Leth-Espensen, Haydyn D. T. Mertens, Gabriel Birrane, Muthuraman Meiyappan, Gunilla Olivecrona, Thomas J. D. Jorgensen, Stephen G. Young, Michael Ploug
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Rutuja Kulkarni, Shuxian Jiang, Gabriel Birrane, Anil Prasad
Article
Biochemistry & Molecular Biology
John G. Luz, Anne P. Beigneux, DeeAnn K. Asamoto, Cuiwen He, Wenxin Song, Christopher M. Allan, Jazmin Morales, Yiping Tu, Adam Kwok, Thomas Cottle, Muthuraman Meiyappan, Loren G. Fong, Judy E. Kim, Michael Ploug, Stephen G. Young, Gabriel Birrane
JOURNAL OF LIPID RESEARCH
(2020)
Article
Urology & Nephrology
Di Feng, Mukesh Kumar, Jan Muntel, Susan B. Gurley, Gabriel Birrane, Isaac E. Stillman, Lai Ding, Minxian Wang, Saima Ahmed, Johannes Schlondorff, Seth L. Alper, Tom Ferrante, Susan L. Marquez, Carlos F. Ng, Richard Novak, Donald E. Ingber, Hanno Steen, Martin R. Pollak
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2020)
Article
Biochemistry & Molecular Biology
Adele Gabba, Agnieszka Bogucka, John G. Luz, Ana Diniz, Helena Coelho, Francisco Corzana, Francisco Javier Canada, Filipa Marcelo, Paul Murphy, Gabriel Birrane
Summary: The MGL protein is an important immunoregulatory receptor that can bind a variety of glycans, with a preference for the glycan GalNAc. New structural studies provide insights into substrate recognition by MGL.
Article
Multidisciplinary Sciences
Stephen G. Young, Wenxin Song, Ye Yang, Gabriel Birrane, Haibo Jiang, Anne P. Beigneux, Michael Ploug, Loren G. Fong
Summary: GPIHBP1 is a crucial partner for LPL in lipolytic processing of lipoproteins, stabilizing LPL structure and preserving activity. It captures LPL and shuttles it to the capillary lumen. The AD of GPIHBP1 accelerates LPL binding, preserves LPL activity, and allows LPL to move across ECs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Adele Gabba, Riem Attariya, Sandra Behren, Christian Pett, Joost C. van der Horst, Hajime Yurugi, Jin Yu, Moritz Urschbach, Juan Sabin, Gabriel Birrane, Edgar Schmitt, Sandra J. van Vliet, Pol Besenius, Ulrika Westerlind, Paul V. Murphy
Summary: The expression and glycosylation patterns of mucin on cancer cells differ from healthy cells, making them attractive targets for immunotherapy. In this study, a modular tripartite vaccine targeting macrophage galactose-type lectin (MGL) on antigen presenting cells was prepared using solid phase peptide synthesis. The vaccine induced a higher antibody response against tumor-associated carbohydrate antigens (TACAs) compared to TACAs alone, highlighting its potential as an anticancer vaccine.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Hematology
Shannon Elf, Nouran S. Abdelfattah, April J. Baral, Danielle Beeson, Jeanne F. Rivera, Amy Ko, Natalie Florescu, Gabriel Birrane, Edwin Chen, Ann Mullally