Modeling the zing finger protein SmZF1 from Schistosoma mansoni: Insights into DNA binding and gene regulation

Mainá Bitar, Marcela Gonçalves Drummond, Mauricio Garcia Souza Costa, Francisco Pereira Lobo, Carlos Eduardo Calzavara-Silva, Paulo Mascarello Bisch, Carlos Renato MacHado, Andréa Mara MacEdo, Raymond J. Pierce, Glória Regina Franco

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Zinc finger proteins are widely found in eukaryotes, representing an important class of DNA-binding proteins frequently involved in transcriptional regulation. Zinc finger motifs are composed by two antiparallel β-strands and one α-helix, stabilized by a zinc ion coordinated by conserved histidine and cysteine residues. In Schistosoma mansoni, these regulatory proteins are known to modulate morphological and physiological changes, having crucial roles in parasite development. A previously described C 2H2 zinc finger protein, SmZF1, was shown to be present in cell nuclei of different life stages of S. mansoni and to activate gene transcription in a heterologous system. A high-quality SmZF1 tridimensional structure was generated using comparative modeling. Molecular dynamics simulations of the obtained structure revealed stability of the zinc fingers motifs and high flexibility on the terminals, comparable to the profile observed on the template X-ray structure based on thermal b-factors. Based on the protein tridimensional features and amino acid composition, we were able to characterize four C2H2 zinc finger motifs, the first involved in protein-protein interactions while the three others involved in DNA binding. We defined a consensus DNA binding sequence using three distinct algorithms and further carried out docking calculations, which revealed the interaction of fingers 2-4 with the predicted DNA. A search for S. mansoni genes presenting putative SmZF1 binding sites revealed 415 genes hypothetically under SmZF1 control. Using an automatic annotation and GO assignment approach, we found that the majority of those genes code for proteins involved in developmental processes. Taken together, these results present a consistent base to the structural and functional characterization of SmZF1.

Original languageEnglish
Pages (from-to)29-38
Number of pages10
JournalJournal of Molecular Graphics and Modelling
Volume39
DOIs
StatePublished - Feb 2013
Externally publishedYes

Keywords

  • Comparative modeling
  • Molecular dynamics
  • Schistosoma mansoni
  • SmZF1
  • Transcriptional regulation
  • Zinc finger

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