The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin and related phage defence systems

Autor: Karin Ernits, Chayan Kumar Saha, Tetiana Brodiazhenko, Bhanu Chouhan, Aditi Shenoy, Julian J Duque-Pedraza, Veda Bojar, Jose A Nakamoto, Tatsuaki Kurata, Artyom Egorov, Lena Shyrokova, Marcus J. O. Johansson, Toomas Mets, Aytan Rustamova, Jelisaveta Dzigurski, Tanel Tenson, Abel Garcia-Pino, Arne Elofsson, Vasili Hauryliuk, Gemma Catherine Atkinson

Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode two proteins: a toxin and neutralising antitoxin. Us

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::19bb730b2ee9c3d9501b3ecede3018f2
https://doi.org/10.1101/2023.03.22.533649

Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

Autor: Arne Elofsson, Patrick Bryant, Gabriele Pozzati, Wensi Zhu, Aditi Shenoy, Petras Kundrotas

Publikováno v: Nature Communications. 13

AlphaFold can predict the structure of single- and multiple-chain proteins with very high accuracy. However, the accuracy decreases with the number of chains, and the available GPU memory limits the size of protein complexes which can be predicted. H

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https://doi.org/10.1038/s41467-022-33729-4

Effects of fire severity on plant nutrient uptake reinforce alternate pathways of succession in boreal forests

Autor: Knut Kielland, Aditi Shenoy, Jill F. Johnstone

Publikováno v: Plant Ecology. 214:587-596

Fire activity in the North American boreal region is projected to increase under a warming climate and trigger changes in vegetation composition. In black spruce forests of interior Alaska, fire severity impacts residual organic layer depth which is

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https://doi.org/10.1007/s11258-013-0191-0

Streamline based design guideline for deterministic microfluidic hydrodynamic single cell traps

Autor: Aditi Shenoy, Richard Smith, Allan Guan, Zhenyu Li

Publikováno v: Biomicrofluidics. 9:024103

A prerequisite for single cell study is the capture and isolation of individual cells. In microfluidic devices, cell capture is often achieved by means of trapping. While many microfluidic trapping techniques exist, hydrodynamic methods are particula

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https://doi.org/10.1063/1.4914469

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

Autor: Valentin Iglesias, Vasilis J. Promponas, Alexander Miguel Monzon, Konstantinos D. Tsirigos, Juliet F Nilsson, Attila Mészáros, Samuel Peña-Díaz, Edoardo Salladini, Silvio C. E. Tosatto, Peter Tompa, Zsuzsanna Dosztányi, Zsofia E. Kalman, Norman E. Davey, Christos A. Ouzounis, Nazanin Farahi, Giovanni Minervini, Martín N. Salas, Arne Elofsson, Mátyás Pajkos, Julia Marchetti, Maria Cristina Aspromonte, Elena Papaleo, Sonia Longhi, Juliana Glavina, Anastasia Chasapi, Federica Quaglia, Gabriele Pozzati, Tamás Szaniszló, Rita Pancsa, Damiano Piovesan, András Hatos, Aditi Shenoy, Bálint Mészáros, Suvarna Nadendla, Javier Iserte, Pascale Gaudet, Lucía B. Chemes, Emanuela Leonardi, Jaime Santos, Radoslav Davidovic, Michelle G. Giglio, Gábor Erdős, Eva Schad, Emiliano Maiani, Salvador Ventura, Pedro Pereira, László Dobson, Nevena Veljkovic, Jordi Pujols, Claudio Bassot, Alma Carolina Sanchez Rocha, Veronika Ács, Cristina Marino-Buslje, Erzsébet Fichó, Gustavo Parisi, Sandra Macedo-Ribeiro, Nicolas Palopoli, Luciana Rodriguez Sawicki, Marian Novotný, Tamas Lazar, Matteo Lambrughi

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2021, ⟨10.1093/nar/gkab1082⟩
Nucleic Acids Research, 2022, 50 (D1), pp.D480-D487. ⟨10.1093/nar/gkab1082⟩
Nucleic acids research
Nuclei Acids Research
Quaglia, F, Mészáros, B, Salladini, E, Hatos, A, Pancsa, R, Chemes, L B, Pajkos, M, Lazar, T, Peña-Díaz, S, Santos, J, Ács, V, Farahi, N, Fichó, E, Aspromonte, M C, Bassot, C, Chasapi, A, Davey, N E, Davidović, R, Dobson, L, Elofsson, A, Erdős, G, Gaudet, P, Giglio, M, Glavina, J, Iserte, J, Iglesias, V, Kálmán, Z, Lambrughi, M, Leonardi, E, Longhi, S, Macedo-Ribeiro, S, Maiani, E, Marchetti, J, Marino-Buslje, C, Mészáros, A, Monzon, A M, Minervini, G, Nadendla, S, Nilsson, J F, Novotný, M, Ouzounis, C A, Palopoli, N, Papaleo, E, Pereira, P J B, Pozzati, G, Promponas, V J, Pujols, J, Rocha, A C S, Salas, M, Sawicki, L R, Schad, E, Shenoy, A, Szaniszló, T, Tsirigos, K D, Veljkovic, N, Parisi, G, Ventura, S, Dosztányi, Z, Tompa, P, Tosatto, S C E & Piovesan, D 2022, ' DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation ', Nucleic Acids Research, vol. 50, no. D1, pp. D480–D487 . https://doi.org/10.1093/nar/gkab1082

The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisPr

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