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  1. No Access

    Article

    DNA cleavage by endonuclease I-DmoI: a QM/MM study and comparison with experimental data provide indications on the environmental effects

    Here, we present the theoretical–computational modelling of the free energy barrier of the phosphodiester bond cleavage as occurring in the mesophilic variant of endonuclease I-DmoI bound to DNA. Our data, obt...

    Giuseppe E. Segreto, Josephine Alba, Riccardo Salvio… in Theoretical Chemistry Accounts (2020)

  2. No Access

    Article

    Evolutionary Modes in Protein Observable Space: The Case of Thioredoxins

    In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from...

    Sara Del Galdo, Josephine Alba, Andrea Amadei… in Journal of Molecular Evolution (2019)

  3. No Access

    Article

    On the activation and deactivation pathways of the Lck kinase domain: a computational study

    Here we report the description of the conformational pathways connecting the Lck active and inactive states by means of all-atoms molecular dynamics simulations coupled to an enhancing sampling methodology. By...

    Josephine Alba, Edoardo Milanetti… in Journal of Computer-Aided Molecular Design (2019)

  4. Article

    Open Access

    Understanding the indirect DNA read-out specificity of I-CreI Meganuclease

    The high DNA specificity of homing endonucleases makes them a powerful protein scaffold to engineer enzymes for genome manipulation. Understanding their molecular recognition of DNA is an important prerequisit...

    Jesús Prieto, Pilar Redondo, Blanca López-Méndez, Marco D’Abramo… in Scientific Reports (2018)

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  5. No Access

    Article

    Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

    I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target seq...

    Josephine Alba, Maria Jose Marcaida… in Journal of Computer-Aided Molecular Design (2017)

  6. No Access

    Article

    Photoinduced electron transfer in a dichromophoric peptide: a numerical experiment

    In this study, we have applied a theoretical–computational methodology, developed in our laboratory and based on molecular dynamics simulations and quantum-chemical calculations, for modelling the kinetics of ...

    Massimiliano Aschi, Marco D’Abramo, Andrea Amadei in Theoretical Chemistry Accounts (2016)

  7. No Access

    Article

    Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state

    Intramolecular charge transfer (ICT) of gaseous π-conjugated oligo-phenyleneethynylenes (OPE) induced by a homogeneous applied electric field has been theoretically investigated using a combined approach integrat...

    Massimiliano Aschi, Maira D’Alessandro, Monica Pellegrino… in Theoretical Chemistry Accounts (2008)

  8. No Access

    Article

    Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin

    The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase may be well modelled theoretically by means of molecular dynamics simulations, the perturbed matrix method (...

    Andrea Amadei, Marco D’Abramo, Isabella Daidone… in Theoretical Chemistry Accounts (2007)