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Nuclear receptor-DNA binding specificity : a combine and Free-Wilson QSAR ananlysis


Tomić, Sanja; Nillson, Lennart; Wade, Rebecca
Nuclear receptor-DNA binding specificity : a combine and Free-Wilson QSAR ananlysis // Journal of medicinal chemistry, 43 (2000), 9; 1780-1792 (međunarodna recenzija, članak, znanstveni)


Naslov
Nuclear receptor-DNA binding specificity : a combine and Free-Wilson QSAR ananlysis

Autori
Tomić, Sanja ; Nillson, Lennart ; Wade, Rebecca

Izvornik
Journal of medicinal chemistry (0022-2623) 43 (2000), 9; 1780-1792

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

Ključne riječi
Quantitative Structure-Activity Relationship (QSAR); COMBINE analysis; molecular modeling; transcription factor; DNA binding; glucocorticoid receptor

Sažetak
Specific binding of transcription factors to DNA is crucial for gene regulation. We derived models for the binding specificity of transcription factors of the nuclear receptor family to DNA using two QSAR methods: a Free-Wilson-like method and Comparative Binding Energy (COMBINE) analysis. The analysis is based on experimental data for the interaction of 20 mutant glucocorticoid receptor DNA-binding domains with 16 different response elements in a total of 320 complexes (Zilliacus, J.; Wright, A.P.; Carlstedt-Duke, J.; Nilsson, L.; Gustafsson, J.A. Proteins 1995 21, 57-67). The predictive abilities of the models obtained by the two methods are similar. The COMBINE analysis indicates that the most important properties for determining binding specificity for this dataset are the changes upon binding of the solvation free energies of the bases that are mutated in the dataset and the electrostatic interactions of the mutated nucleotides with certain charged amino acids. Further important descriptors are the changes of solvation free energy and surface area of the side chain of the mutated residue. It is clear, however, that there are additional features important for the specificity of binding that are not included in the models, such as differences in interfacial hydration of the complexes.

Izvorni jezik
Engleski

Znanstvena područja
Kemija



POVEZANOST RADA


Projekt / tema
00980608

Ustanove
Institut "Ruđer Bošković", Zagreb

Autor s matičnim brojem:
Sanja Tomić, (113604)

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
  • MEDLINE