title: Identifying key interactions stabilizing DOF zinc finger-DNA complexes using in silico approaches.
abstract: DOF (DNA-binding with one finger) proteins, a family of DNA-binding transcription factors, are members of zinc fingers unique to plants. They are associated with different plant specific phenomena including germination, dormancy, light and defense responses. Until now, there is no report of experimentally solved structure for DOF proteins, making empirical investigation of DOF-DNA interaction more challenging. It has been shown that comparative modeling can be used to reliably predict the three-dimensional (3D) model of structurally unknown proteins whenever a suitable template is available. Furthermore, current molecular mechanics force fields allow prediction of interaction energies for macromolecular complexes. Therefore, the approaches considered in this work were to model the 3D structures of DOF zinc fingers (ZFs) from Arabidopsis thaliana complexed with DNA molecule, to calculate their binding energies, to identify key interactions established between ZFs and DNA, and to determine the impact of the different interactions on the binding energies. The results were used to predict the binding affinities for the novel designed ZFs and may be used in engineering DNA binding proteins.
authors.affiliation: Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Hamzeh-Mivehroud
authors.affiliation: Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
authors.forename: Hakimeh
authors.initials: H
authors.lastname: Moghaddas-Sani
authors.affiliation: Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
authors.forename: Mahdieh
authors.initials: M
authors.lastname: Rahbar-Shahrouziasl
authors.affiliation: Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. Electronic address: dastmalchi.s@tbzmed.ac.ir.
authors.forename: Siavoush
authors.initials: S
authors.lastname: Dastmalchi
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013816:Thermodynamics; D016335:Zinc Fingers
chemical_list: D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D004247:DNA
keywords: Binding free energy calculation; DNA-binding proteins; DOF proteins; Homology modeling; Zinc fingers