title: Structure-based DNA-binding prediction and design.
abstract: Structure-based DNA-binding prediction is a powerful tool to infer protein-binding sites and design new specificities. It can limit experiments in scope and help focus them toward candidates with higher chances of success. The zinc finger domain is an excellent scaffold for design due to its small and robust fold and relatively simple interaction pattern. It presents some degree of modularity, and modeling can be used to guide experiments and help increase zinc finger module libraries. In this chapter we present a fast and simple but still powerful method for predicting and designing DNA-binding specificities applied to C(2)H(2) zinc finger proteins, based on FoldX, a semiautomatic protein design tool. Given a template structure, this method generates candidate mutants for a given target DNA sequence selected by energetic criteria.
authors.affiliation: EMBL-CRG Systems Biology Unit, Centre de Regulació Genòmica, PRBB-UPF, Barcelona, Spain.
authors.forename: Andreu
authors.initials: A
authors.lastname: Alibés
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
authors.forename: Alejandro D
authors.initials: AD
authors.lastname: Nadra
mesh_terms: D000595:Amino Acid Sequence; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D030562:Databases, Protein; D008954:Models, Biological; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins