Athi N. Naganathan on Muck Rack

Athi N. Naganathan

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Articles

Diverse conformational ensembles define the shared folding-allosteric landscapes of protein kinases

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By Dhruv Kumar Chaurasiya, Athi N. Naganathan
| buff.ly
Get full text access Log in, subscribe or purchase for full access. References 1. Colicelli, J. ABL Tyrosine Kinases: Evolution of Function, Regulation, and Specificity Sci. Sig. 2010; 3:re6 2. Kazanietz, M.G. ∙ Cooke, M. Protein kinase C signaling “in” and “to” the nucleus: Master kinases in transcriptional regulation J. Biol. Chem. 2024; 300, 105692 3. Akabane, S. ∙ Oka, T. Insights into the regulation of mitochondrial functions by protein kinase A-mediated phosphorylation J. Biochem. 2023; 175:1-7 4.
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Polyphosphate discriminates protein conformational ensembles more efficiently than DNA promoting diverse assembly and maturation behaviors

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By Saloni Goyal, Divya Rajendran, Anup Kumar Mani, Athi N. Naganathan
| eLife
eLife Assessment This manuscript offers important insights into how polyphosphate (polyP) influences protein phase separation differently from DNA. The authors present compelling evidence that polyP distinguishes among protein conformational ensembles, leading to divergent condensate maturation behaviors that include unfolding and polyproline II formation.
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The need to implement FAIR principles in biomolecular simulations - Nature Methods

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By Rommie Amaro, Ivet Bahar, Massimiliano Bonomi, Gregory Bowman, Giovanni Bussi, Christophe Chipot, G. Andrés Cisneros, Peter Coveney, Roberto Covino, Matteo Dal Peraro, Lucie Delemotte, Jonathan W. Essex, Franca Fraternali, Francesco L. Gervasio, Fernando González-Nilo, Helmut Grubmüller, Marina G. Guenza, Horacio V. Guzman, Teresa Head-Gordon, Niu Huang, Xuhui Huang, Gerhard Hummer, Wanting Jiao, Syma Khalid, Charles A. Laughton, Kresten Lindorff-Larsen, Sharon M. Loverde, Magnus Lundborg, Yun Luo, F. Javier Luque, Charlotte Lynch, Siewert J. Marrink, J. Andrew McCammon, Kenneth M. Merz, Adrian J. Mulholland, Athi N. Naganathan, Frank Noe, Agnes Noy, Megan L. O’Mara, Mary Jo Ondrechen, José N. Onuchic, Alberto Perez, Alberto Pérez, Juan Perilla, Jean-Philip Piquemal, Adolfo B. Poma, Matej Praprotnik, Nathalie Reuter, Carme Rovira, Benoît Roux, Ursula Rothlisberger, Karissa Y. Sanbonmatsu, Carlos Simmerling, Jeremy Smith, Yuji Sugita, Katarzyna Świderek, Peng Tao, D. Peter Tieleman, Irina G. Tikhonova, Julian Tirado-Rives, Sameer Velankar, Stacey D. Wetmore, Lee-Wei Yang, Martin Zacharias, Josep Ll. Gelpí, Ariel Warshel
| Nature Verified
In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.
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