PeSTo: parameter-free geometric deep learning for accurate prediction of protein binding interfaces

Autor: Lucien F. Krapp, Luciano A. Abriata, Fabio Cortés Rodriguez, Matteo Dal Peraro

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-11 (2023)

Abstract Proteins are essential molecular building blocks of life, responsible for most biological functions as a result of their specific molecular interactions. However, predicting their binding interfaces remains a challenge. In this study, we pre

Externí odkaz: https://doaj.org/article/082cd95ef19544f996bec815b6afa158

CERT1 mutations perturb human development by disrupting sphingolipid homeostasis

Autor: Charlotte Gehin, Museer A. Lone, Winston Lee, Laura Capolupo, Sylvia Ho, Adekemi M. Adeyemi, Erica H. Gerkes, Alexander P.A. Stegmann, Estrella López-Martín, Eva Bermejo-Sánchez, Beatriz Martínez-Delgado, Christiane Zweier, Cornelia Kraus, Bernt Popp, Vincent Strehlow, Daniel Gräfe, Ina Knerr, Eppie R. Jones, Stefano Zamuner, Luciano A. Abriata, Vidya Kunnathully, Brandon E. Moeller, Anthony Vocat, Samuel Rommelaere, Jean-Philippe Bocquete, Evelyne Ruchti, Greta Limoni, Marine Van Campenhoudt, Samuel Bourgeat, Petra Henklein, Christian Gilissen, Bregje W. van Bon, Rolph Pfundt, Marjolein H. Willemsen, Jolanda H. Schieving, Emanuela Leonardi, Fiorenza Soli, Alessandra Murgia, Hui Guo, Qiumeng Zhang, Kun Xia, Christina R. Fagerberg, Christoph P. Beier, Martin J. Larsen, Irene Valenzuela, Paula Fernández-Álvarez, Shiyi Xiong, Robert Śmigiel, Vanesa López-González, Lluís Armengol, Manuela Morleo, Angelo Selicorni, Annalaura Torella, Moira Blyth, Nicola S. Cooper, Valerie Wilson, Renske Oegema, Yvan Herenger, Aurore Garde, Ange-Line Bruel, Frederic Tran Mau-Them, Alexis B.R. Maddocks, Jennifer M. Bain, Musadiq A. Bhat, Gregory Costain, Peter Kannu, Ashish Marwaha, Neena L. Champaigne, Michael J. Friez, Ellen B. Richardson, Vykuntaraju K. Gowda, Varunvenkat M. Srinivasan, Yask Gupta, Tze Y. Lim, Simone Sanna-Cherchi, Bruno Lemaitre, Toshiyuki Yamaji, Kentaro Hanada, John E. Burke, Ana Marjia Jakšić, Brian D. McCabe, Paolo De Los Rios, Thorsten Hornemann, Giovanni D’Angelo, Vincenzo A. Gennarino

Publikováno v: The Journal of Clinical Investigation, Vol 133, Iss 10 (2023)

Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesi

Externí odkaz: https://doaj.org/article/47a113198d5649e88315ddec99f2067f

3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme

Autor: Melisa Lázaro, Roberto Melero, Charlotte Huet, Jorge P. López-Alonso, Sandra Delgado, Alexandra Dodu, Eduardo M. Bruch, Luciano A. Abriata, Pedro M. Alzari, Mikel Valle, María-Natalia Lisa

Publikováno v: Communications Biology, Vol 4, Iss 1, Pp 1-8 (2021)

Lázaro et. al. report the first 3D structure of a large glutamate dehydrogenase (L-GDH), the one corresponding to the Mycobacterium smegmatis enzyme composed of 180 kDa subunits (mL-GDH180), obtained by X-ray crystallography and cryo-electron micros

Externí odkaz: https://doaj.org/article/ee3d06ba507e400089d1f6209e598b96

Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis

Autor: Martina K. Ried, Rebekka Wild, Jinsheng Zhu, Joka Pipercevic, Kristina Sturm, Larissa Broger, Robert K. Harmel, Luciano A. Abriata, Ludwig A. Hothorn, Dorothea Fiedler, Sebastian Hiller, Michael Hothorn

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021)

Plants regulate phosphate homeostasis via the interaction of PHR transcription factors with SPX receptors bound to inositol pyrophosphate signaling molecules. Here the authors show that inositol pyrophosphate-bound SPX interacts with the coiled-coil

Externí odkaz: https://doaj.org/article/00e29285b86d4975ada814bc3bd2fb9d

Investigating Crosstalk Among PTMs Provides Novel Insight Into the Structural Basis Underlying the Differential Effects of Nt17 PTMs on Mutant Httex1 Aggregation

Autor: Anass Chiki, Zhidian Zhang, Kolla Rajasekhar, Luciano A. Abriata, Iman Rostami, Lucien F. Krapp, Driss Boudeffa, Matteo Dal Peraro, Hilal A. Lashuel

Publikováno v: Frontiers in Molecular Biosciences, Vol 8 (2021)

Post-translational modifications (PTMs) within the first 17 amino acids (Nt17) of the Huntingtin protein (Htt) have been shown to inhibit the aggregation and attenuate the toxicity of mutant Htt proteins in vitro and in various models of Huntington�

Externí odkaz: https://doaj.org/article/045b674b456b4b079baf7f9bee17020f