Transcriptome and Redox Proteome Reveal Temporal Scales of Carbon Metabolism Regulation in Model Cyanobacteria Under Light Disturbance

Autor: Johnson, Connah G. M., Johnson, Zachary, Mackey, Liam S., Li, Xiaolu, Sadler, Natalie C., Zhang, Tong, Qian, Wei-Jun, Bohutskyi, Pavlo, Feng, Song, Cheung, Margaret S.

We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins and nucleic acids interactions in multi-layered protein-DNA regulatory networks under l

Externí odkaz: http://arxiv.org/abs/2410.09346

The need to implement FAIR principles in biomolecular simulations

Autor: Amaro, Rommie, Åqvist, Johan, Bahar, Ivet, Battistini, Federica, Bellaiche, Adam, Beltran, Daniel, Biggin, Philip C., Bonomi, Massimiliano, Bowman, Gregory R., Bryce, Richard, Bussi, Giovanni, Carloni, Paolo, Case, David, Cavalli, Andrea, Chang, Chie-En A., Cheatham III, Thomas E., Cheung, Margaret S., Chipot, Cris, Chong, Lillian T., Choudhary, Preeti, Cisneros, Gerardo Andres, Clementi, Cecilia, Collepardo-Guevara, Rosana, Coveney, Peter, Covino, Roberto, Crawford, T. Daniel, Peraro, Matteo Dal, de Groot, Bert, Delemotte, Lucie, De Vivo, Marco, Essex, Jonathan, Fraternali, Franca, Gao, Jiali, Gelpí, Josep Lluís, Gervasio, Francesco Luigi, Gonzalez-Nilo, Fernando Danilo, Grubmüller, Helmut, Guenza, Marina, Guzman, Horacio V., Harris, Sarah, Head-Gordon, Teresa, Hernandez, Rigoberto, Hospital, Adam, Huang, Niu, Huang, Xuhui, Hummer, Gerhard, Iglesias-Fernández, Javier, Jensen, Jan H., Jha, Shantenu, Jiao, Wanting, Jorgensen, William L., Kamerlin, Shina Caroline Lynn, Khalid, Syma, Laughton, Charles, Levitt, Michael, Limongelli, Vittorio, Lindahl, Erik, Lindorff-Larsen, Kresten, Loverde, Sharon, Lundborg, Magnus, Luo, Yun Lyna, Luque, Francisco Javier, Lynch, Charlotte I., MacKerell, Alexander, Magistrato, Alessandra, Marrink, Siewert J., Martin, Hugh, McCammon, J. Andrew, Merz, Kenneth, Moliner, Vicent, Mulholland, Adrian, Murad, Sohail, Naganathan, Athi N., Nangia, Shikha, Noe, Frank, Noy, Agnes, Oláh, Julianna, O'Mara, Megan, Ondrechen, Mary Jo, Onuchic, José N., Onufriev, Alexey, Osuna, Silvia, Panchenko, Anna R., Pantano, Sergio, Parish, Carol, Parrinello, Michele, Perez, Alberto, Perez-Acle, Tomas, Perilla, Juan R., Pettitt, B. Montgomery, Pietropalo, Adriana, Piquemal, Jean-Philip, Poma, Adolfo, Praprotnik, Matej, Ramos, Maria J., Ren, Pengyu, Reuter, Nathalie, Roitberg, Adrian, Rosta, Edina, Rovira, Carme, Roux, Benoit, Röthlisberger, Ursula, Sanbonmatsu, Karissa Y., Schlick, Tamar, Shaytan, Alexey K., Simmerling, Carlos, Smith, Jeremy C., Sugita, Yuji, Świderek, Katarzyna, Taiji, Makoto, Tao, Peng, Tikhonova, Irina G., Tirado-Rives, Julian, Tunón, Inaki, Van Der Kamp, Marc W., Van der Spoel, David, Velankar, Sameer, Voth, Gregory A., Wade, Rebecca, Warshel, Ariel, Welborn, Valerie Vaissier, Wetmore, Stacey, Wong, Chung F., Yang, Lee-Wei, Zacharias, Martin, Orozco, Modesto

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a data

Externí odkaz: http://arxiv.org/abs/2407.16584

Graph identification of proteins in tomograms (GRIP-Tomo)

Autor: George, August, Kim, Doo Nam, Moser, Trevor, Gildea, Ian T., Evans, James E., Cheung, Margaret S.

In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinem

Externí odkaz: http://arxiv.org/abs/2210.08194

CTRAMER: An open source software package for correlating interfacial charge transfer rate constants with donor acceptor geometries in organic photovoltaic materials

Autor: Tinnin, Jacob, Aksu, Huseyin, Tong, Zhengqing, Zhang, Pengzhi, Geva, Eitan, Dunietz, Barry D., Sun, Xiang, Cheung, Margaret S.

Publikováno v: J. Chem. Phys. 154, 214108 (2021)

In this paper we present CTRAMER (Charge Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory), an open source software package for calculating interfacial charge transfer (CT) rate constants in organic photovoltaic (OPV) mat

Externí odkaz: http://arxiv.org/abs/2105.05936

Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif

Autor: Zhang, Pengzhi, Han, Jaebeom, Cieplak, Piotr, Cheung, Margaret. S.

Publikováno v: J. Chem. Phys. 154, 124104 (2021)

It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed wide variation

Externí odkaz: http://arxiv.org/abs/2011.07639