title: Towards computational specificity screening of DNA-binding proteins.
abstract: DNA-binding proteins are key players in the regulation of gene expression and, hence, are essential for cell function. Chimeric proteins composed of DNA-binding domains and DNA modifying domains allow for precise genome manipulation. A key prerequisite is the specific recognition of a particular nucleotide sequence. Here, we quantitatively assess the binding affinity of DNA-binding proteins by molecular dynamics-based alchemical free energy simulations. A computational framework was developed to automatically set up in silico screening assays and estimate free energy differences using two independent procedures, based on equilibrium and non-equlibrium transformation pathways. The influence of simulation times on the accuracy of both procedures is presented. The binding specificity of a zinc-finger transcription factor to several sequences is calculated, and agreement with experimental data is shown. Finally we propose an in silico screening strategy aiming at the derivation of full specificity profiles for DNA-binding proteins.
authors: Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
authors: Daniel
authors: D
authors: Seeliger
authors: Floris P
authors: FP
authors: Buelens
authors: Maik
authors: M
authors: Goette
authors: Bert L
authors: BL
authors: de Groot
authors: Helmut
authors: H
authors: Grubmüller
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011485:Protein Binding; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry*; D016335:Zinc Fingers
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA