title: Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni(2.).
abstract: An integrated approach, combining atomistic molecular dynamics simulations, coarse-grained models, and solution NMR, was used to characterize the internal dynamics of HpNikR, a Ni-dependent transcription factor. Specifically, these methods were used to ascertain how the presence of bound Ni(2+) ions affects the stability of the known open, cis, and trans forms observed in the crystal structures of this protein as well as their interconversion capability. The consensus picture emerging from all the collected data hints at the interconversion of NikR among the three types of conformations, regardless of the content of bound Ni(2+). On the basis of atomistic and coarse-grained simulations, we deduce that the interconversion capability is particularly effective between the cis and the open forms and appreciably less so between the trans conformer and the other two forms. The presence of the bound Ni(2+) ions does, however, affect significantly the degree of the correlations on the two DNA-binding domains of NikR, which is significantly suppressed as compared to the apo form. Overall, the findings suggest that the binding of HpNikR to DNA occurs through a sophisticated multistep process involving both a conformational selection and an induced fit.
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Musiani
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Branimir
authors.initials: B
authors.lastname: Bertoša
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Magistrato
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Barbara
authors.initials: B
authors.lastname: Zambelli
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Paola
authors.initials: P
authors.lastname: Turano
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Valeria
authors.initials: V
authors.lastname: Losasso
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Cristian
authors.initials: C
authors.lastname: Micheletti
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Ciurli
authors.affiliation: Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni