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Pregled bibliografske jedinice broj: 511970

Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+


Musiani, Francesco; Bertoša, Branimir; Magistrato, Alessandra; Zambelli, Barbara; Turano, Paola; Losasso, Valeria; Micheletti, Cristian; Ciurli, Stefano; Carloni, Paolo
Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+ // Journal of chemical theory and computation, 6 (2010), 11; 3503-3515 doi:10.1021/ct900635z (međunarodna recenzija, članak, znanstveni)


Naslov
Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+

Autori
Musiani, Francesco ; Bertoša, Branimir ; Magistrato, Alessandra ; Zambelli, Barbara ; Turano, Paola ; Losasso, Valeria ; Micheletti, Cristian ; Ciurli, Stefano ; Carloni, Paolo

Izvornik
Journal of chemical theory and computation (1549-9618) 6 (2010), 11; 3503-3515

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Molecular-dynamics simulations; decomposing proteins; receptor; system

Sažetak
An integrated approach, combining atomistic molecular dynamics simulations, coarsegrained 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 Ni2+ 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 Ni2+. 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 Ni2+ 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.

Izvorni jezik
Engleski

Znanstvena područja
Fizika, Kemija, Biologija



POVEZANOST RADA


Projekt / tema
098-1191344-2860 - Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (Sanja Tomić, )

Ustanove
Institut "Ruđer Bošković", Zagreb

Autor s matičnim brojem:
Branimir Bertoša, (243230)

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus


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