title: Modeling the zing finger protein SmZF1 from Schistosoma mansoni: Insights into DNA binding and gene regulation.
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(2)H(2) 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 C(2)H(2) 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.
authors.affiliation: Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Mainá
authors.initials: M
authors.lastname: Bitar
authors.forename: Marcela Gonçalves
authors.initials: MG
authors.lastname: Drummond
authors.forename: Mauricio Garcia Souza
authors.initials: MG
authors.lastname: Costa
authors.forename: Francisco Pereira
authors.initials: FP
authors.lastname: Lobo
authors.forename: Carlos Eduardo
authors.initials: CE
authors.lastname: Calzavara-Silva
authors.forename: Paulo Mascarello
authors.initials: PM
authors.lastname: Bisch
authors.forename: Carlos Renato
authors.initials: CR
authors.lastname: Machado
authors.forename: Andréa Mara
authors.initials: AM
authors.lastname: Macedo
authors.forename: Raymond J
authors.initials: RJ
authors.lastname: Pierce
authors.forename: Glória Regina
authors.initials: GR
authors.lastname: Franco
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D015801:Helminth Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D055550:Protein Stability; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D015801:Helminth Proteins; C440069:SmZF1 protein, Schistosoma mansoni; D014157:Transcription Factors