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1. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

Author

Bottaro, Sandro, Bussi, Giovanni, Lindorff-Larsen, Kresten, Bottaro, Sandro, Bussi, Giovanni, and Lindorff-Larsen, Kresten

Abstract

The 5′ untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5′-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.

Published
2021

2. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

Author

Bottaro, Sandro, Bussi, Giovanni, Lindorff-Larsen, Kresten, Bottaro, Sandro, Bussi, Giovanni, and Lindorff-Larsen, Kresten

Abstract

The 5′ untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5′-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.

Published
2021

4. Promoting transparency and reproducibility in enhanced molecular simulations

Author

Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Tribello, Gareth A., Banas, Pavel, Barducci, Alessandro, Bernetti, Mattia, Bolhuis, Peter G., Bottaro, Sandro, Branduardi, Davide, Capelli, Riccardo, Carloni, Paolo, Ceriotti, Michele, Cesari, Andrea, Chen, Haochuan, Chen, Wei, Colizzi, Francesco, De, Sandip, De La Pierre, Marco, Donadio, Davide, Drobot, Viktor, Ensing, Bernd, Ferguson, Andrew L., Filizola, Marta, Fraser, James S., Fu, Haohao, Gasparotto, Piero, Gervasio, Francesco Luigi, Giberti, Federico, Gil-Ley, Alejandro, Giorgino, Toni, Heller, Gabriella T., Hocky, Glen M., Iannuzzi, Marcella, Invernizzi, Michele, Jelfs, Kim E., Jussupow, Alexander, Kirilin, Evgeny, Laio, Alessandro, Limongelli, Vittorio, Lindorff-Larsen, Kresten, Lohr, Thomas, Marinelli, Fabrizio, Martin-Samos, Layla, Masetti, Matteo, Meyer, Ralf, Michaelides, Angelos, Molteni, Carla, Morishita, Tetsuya, Nava, Marco, Paissoni, Cristina, Papaleo, Elena, Parrinello, Michele, Pfaendtner, Jim, Piaggi, Pablo, Piccini, GiovanniMaria, Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Provasi, Davide, Quigley, David, Raiteri, Paolo, Raniolo, Stefano, Rydzewski, Jakub, Salvalaglio, Matteo, Sosso, Gabriele Cesare, Spiwok, Vojtech, Sponer, Jiri, Swenson, David W. H., Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A., White, Andrew, Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Tribello, Gareth A., Banas, Pavel, Barducci, Alessandro, Bernetti, Mattia, Bolhuis, Peter G., Bottaro, Sandro, Branduardi, Davide, Capelli, Riccardo, Carloni, Paolo, Ceriotti, Michele, Cesari, Andrea, Chen, Haochuan, Chen, Wei, Colizzi, Francesco, De, Sandip, De La Pierre, Marco, Donadio, Davide, Drobot, Viktor, Ensing, Bernd, Ferguson, Andrew L., Filizola, Marta, Fraser, James S., Fu, Haohao, Gasparotto, Piero, Gervasio, Francesco Luigi, Giberti, Federico, Gil-Ley, Alejandro, Giorgino, Toni, Heller, Gabriella T., Hocky, Glen M., Iannuzzi, Marcella, Invernizzi, Michele, Jelfs, Kim E., Jussupow, Alexander, Kirilin, Evgeny, Laio, Alessandro, Limongelli, Vittorio, Lindorff-Larsen, Kresten, Lohr, Thomas, Marinelli, Fabrizio, Martin-Samos, Layla, Masetti, Matteo, Meyer, Ralf, Michaelides, Angelos, Molteni, Carla, Morishita, Tetsuya, Nava, Marco, Paissoni, Cristina, Papaleo, Elena, Parrinello, Michele, Pfaendtner, Jim, Piaggi, Pablo, Piccini, GiovanniMaria, Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Provasi, Davide, Quigley, David, Raiteri, Paolo, Raniolo, Stefano, Rydzewski, Jakub, Salvalaglio, Matteo, Sosso, Gabriele Cesare, Spiwok, Vojtech, Sponer, Jiri, Swenson, David W. H., Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A., and White, Andrew

Published
2019

6. Promoting transparency and reproducibility in enhanced molecular simulations

Author

Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Tribello, Gareth A., Banas, Pavel, Barducci, Alessandro, Bernetti, Mattia, Bolhuis, Peter G., Bottaro, Sandro, Branduardi, Davide, Capelli, Riccardo, Carloni, Paolo, Ceriotti, Michele, Cesari, Andrea, Chen, Haochuan, Chen, Wei, Colizzi, Francesco, De, Sandip, De La Pierre, Marco, Donadio, Davide, Drobot, Viktor, Ensing, Bernd, Ferguson, Andrew L., Filizola, Marta, Fraser, James S., Fu, Haohao, Gasparotto, Piero, Gervasio, Francesco Luigi, Giberti, Federico, Gil-Ley, Alejandro, Giorgino, Toni, Heller, Gabriella T., Hocky, Glen M., Iannuzzi, Marcella, Invernizzi, Michele, Jelfs, Kim E., Jussupow, Alexander, Kirilin, Evgeny, Laio, Alessandro, Limongelli, Vittorio, Lindorff-Larsen, Kresten, Lohr, Thomas, Marinelli, Fabrizio, Martin-Samos, Layla, Masetti, Matteo, Meyer, Ralf, Michaelides, Angelos, Molteni, Carla, Morishita, Tetsuya, Nava, Marco, Paissoni, Cristina, Papaleo, Elena, Parrinello, Michele, Pfaendtner, Jim, Piaggi, Pablo, Piccini, GiovanniMaria, Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Provasi, Davide, Quigley, David, Raiteri, Paolo, Raniolo, Stefano, Rydzewski, Jakub, Salvalaglio, Matteo, Sosso, Gabriele Cesare, Spiwok, Vojtech, Sponer, Jiri, Swenson, David W. H., Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A., White, Andrew, Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Tribello, Gareth A., Banas, Pavel, Barducci, Alessandro, Bernetti, Mattia, Bolhuis, Peter G., Bottaro, Sandro, Branduardi, Davide, Capelli, Riccardo, Carloni, Paolo, Ceriotti, Michele, Cesari, Andrea, Chen, Haochuan, Chen, Wei, Colizzi, Francesco, De, Sandip, De La Pierre, Marco, Donadio, Davide, Drobot, Viktor, Ensing, Bernd, Ferguson, Andrew L., Filizola, Marta, Fraser, James S., Fu, Haohao, Gasparotto, Piero, Gervasio, Francesco Luigi, Giberti, Federico, Gil-Ley, Alejandro, Giorgino, Toni, Heller, Gabriella T., Hocky, Glen M., Iannuzzi, Marcella, Invernizzi, Michele, Jelfs, Kim E., Jussupow, Alexander, Kirilin, Evgeny, Laio, Alessandro, Limongelli, Vittorio, Lindorff-Larsen, Kresten, Lohr, Thomas, Marinelli, Fabrizio, Martin-Samos, Layla, Masetti, Matteo, Meyer, Ralf, Michaelides, Angelos, Molteni, Carla, Morishita, Tetsuya, Nava, Marco, Paissoni, Cristina, Papaleo, Elena, Parrinello, Michele, Pfaendtner, Jim, Piaggi, Pablo, Piccini, GiovanniMaria, Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Provasi, Davide, Quigley, David, Raiteri, Paolo, Raniolo, Stefano, Rydzewski, Jakub, Salvalaglio, Matteo, Sosso, Gabriele Cesare, Spiwok, Vojtech, Sponer, Jiri, Swenson, David W. H., Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A., and White, Andrew

Published
2019

8. Asymmetric base-pair opening drives helicase unwinding dynamics

Author

European Commission, Colizzi, Francesco, Pérez-González, Cibran, Fritzen, Remi, Levy, Yaakov, White, Malcolm F., Penedo, J. Carlos, Bussi, Giovanni, European Commission, Colizzi, Francesco, Pérez-González, Cibran, Fritzen, Remi, Levy, Yaakov, White, Malcolm F., Penedo, J. Carlos, and Bussi, Giovanni

Abstract

The opening of a Watson–Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix

Published
2019

10. RNA Structural Dynamics As Captured by Molecular Simulations:A Comprehensive Overview

Author

Sponer, Jiri, Bussi, Giovanni, Krepl, Miroslav, Banás, Pavel, Bottaro, Sandro, Cunha, Richard A., Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simon, Jureacka, Petr, Walter, Nils G., Otyepka, Michal, Sponer, Jiri, Bussi, Giovanni, Krepl, Miroslav, Banás, Pavel, Bottaro, Sandro, Cunha, Richard A., Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simon, Jureacka, Petr, Walter, Nils G., and Otyepka, Michal

Published
2018

13. RNA Unwinding from Reweighted Pulling Simulations

Author

Colizzi, Francesco, Bussi, Giovanni, Colizzi, Francesco, and Bussi, Giovanni

Abstract

The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively characterized at the molecular level. In this work, the base opening process was first enforced by atomistic pulling simulations and then analyzed with a novel reweighting scheme, which allowed the free-energy profile along any suitable reaction coordinate, for example, solvation, to be reconstructed. The systematic application of such approach to different base-pair combinations provides a molecular motion picture of helix opening, which is validated by comparison with an extensive set of experimental observations and links them to the enzyme-dependent unwinding mechanism. The RNA intrinsic dynamics disclosed in this work could rationalize the directionality observed in RNA-processing molecular machineries

Published
2012

14. [Historiae romanae decades]

Author

Livio, Tito, Floro, Lucio Anneo Epitome rerum Romanarum, Bussi, Giovanni Andrea 1417-1475 autor, Cornarius, Benedictus destinatario, Sabellico, Marco Antonio Cocio 1436-1506 editor, Rosso, Giovanni fl. 1480-1519 impresor, Iglesia Católica Papa (1464-1471 Pablo II) destinatario, Livio, Tito, Floro, Lucio Anneo Epitome rerum Romanarum, Bussi, Giovanni Andrea 1417-1475 autor, Cornarius, Benedictus destinatario, Sabellico, Marco Antonio Cocio 1436-1506 editor, Rosso, Giovanni fl. 1480-1519 impresor, and Iglesia Católica Papa (1464-1471 Pablo II) destinatario

Abstract

[Carta a Benedictus Cornarius] (h. *2v); In Livium annotationes / Marcus Antonius Sabellicus (h. *3r-*5v). [Carta a Pablo II] / Johannes Andreas de Bussis (h. a2r-a3r). [Periochae] / Florus (h. a3r-c1r). Capita operum (h. c1r-c1v), H, IBP, Goff, BSB-Ink, IGI, IBE, Bod-inc, GW, ISTC, El pie de imprenta consta en colofón, con la fecha: M.cccclxxxxi.die.v.nouembris, Sign.: [ ]6, a10, b6, c10, d–n8 aa–ii8, kk-ll6, A–G8, H10, Letra redonda, Títulos marginales, Huecos para iniciales

15. [Opera]

Author

Lactancio, Lucio Celio Firmiano, Bussi, Giovanni Andrea 1417-1475 editor literario, Sweynheim, Konrad impresor, Pannartz, Arnold impresor, Pseudo-Lactancio De Phoenice carmen, Fortunato, Venancio Honorio Clemenciano De Pascha, Lactancio, Lucio Celio Firmiano, Bussi, Giovanni Andrea 1417-1475 editor literario, Sweynheim, Konrad impresor, Pannartz, Arnold impresor, Pseudo-Lactancio De Phoenice carmen, and Fortunato, Venancio Honorio Clemenciano De Pascha

Abstract

[De divinis institutionibus adversus gentes ; De ira Dei ; De opificio Dei seu De formatione hominis / Lactancio. De Phoenice carmen / Seudo-Lactancio. De Pascha vel de resurrectione Christi carmen / Fortunato], HCR, BMC, IGI, Goff, IDL, IBE, ISTC, Martín Abad, Editado por Giovanni Andrea Bussi (h. a2), Datos de impresión tomados del colofón, Sign.: [a¹² b–x¹⁰ y¹²], Texto a línea tirada (38 líneas), Huecos para inicial, En blanco h. b1v y h. y11v

16. Caii Plynii Secundi naturalis historiae libri

Author

Plinio Segundo, Cayo, Bussi, Giovanni Andrea 1417-1475 editor, Jenson, Nicolas impresor, Plinio Segundo, Cayo, Bussi, Giovanni Andrea 1417-1475 editor, and Jenson, Nicolas impresor

Abstract

HC, Pol, BMC, IGI, Goff, IBP, CIH, IDL, IJL, IBE, ISTC, Martín Abad, Título tomado del colofón, Datos de impresión tomados del colofón, Sign.: [a¹² b⁸ c–h¹⁰ i¹² k–p¹⁰ q⁸ r–z¹⁰ A–D¹⁰ E⁶ F–G¹⁰ H–M⁸ N¹⁰ O¹²], Letra romana: 115R, Texto a línea tirada (50 líneas), Huecos para iniciales, letras de aviso

17. M. Tul. Ciceronis ad M. Brutum et ceteros epistole

Author

Cicerón, Marco Tulio, Sweynheym, Konrad impresor, Pannartz, Arnold impresor, Bussi, Giovanni Andrea 1417-1475 editor, Cicerón, Marco Tulio, Sweynheym, Konrad impresor, Pannartz, Arnold impresor, and Bussi, Giovanni Andrea 1417-1475 editor

Abstract

[Epistola ad] Paulum II, Pont. Max. / [Johannes Andreas de Bussis] (h. a1v). Epistolae ad Marcum Brutum (h. a2r-b2r); Epistolae ad Quintum fratrem (h. b2r-d6r) / Marcus Tullius Cicero. Epistola ad Octavianum / [Pseudo- Cicero] (h. d6r-d7v). Epistolae ad Atticum / Marcus Tullius Cicero (h. d7v-v10v), HC, Pell, GW, BMC, IGI, Goff, IBE, ISTC, Bod-Inc, Martín Abad, Título tomado de h. a2r, Pie de imprenta tomado del colofón (h. v10v), en el que consta la fecha: Anno dominici natalis M.cccc.lxx., Sign.: [a–e¹⁰ f¹² g–k¹⁰ l⁸ m–v¹⁰], Letra romana (2:115R), Texto a línea tirada (38 líneas), Huecos para iniciales

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