title: Conformational selection or induced fit for Brinker and DNA recognition.
abstract: Brinker is the key target protein of the Drosophila Decapentaplegic morphogen signalling pathway. Brinker is widely expressed and can bind with DNA. NMR spectra suggest that apo-Brinker is intrinsically unstructured and undergoes a folding transition upon DNA-binding. However, the coupled mechanism of binding and folding is poorly understood. Here, we performed molecular dynamics (MD) simulations for both bound and apo-Brinker to study the mechanism. Room-temperature MD simulations suggest that Brinker becomes more rigid and stable upon DNA-binding. Kinetic analysis of high-temperature MD simulations shows that both bound and apo-Brinker unfold via a two-state process. The time scale of tertiary unfolding is significantly different between bound and apo-Brinker. The predicted Φ-values suggest that there are more residues with native-like transition state ensembles (TSEs) for bound Brinker than for apo-Brinker. The average RMSD differences between bound and apo-Brinker and Kolmogorov-Smirnov (KS) test analysis illustrate that Brinker folding upon DNA-binding might obey induced-fit mechanism based on MD simulations. These methods can be used for the research of other biomolecular folding upon ligand-binding.
authors.affiliation: College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Qin
authors.forename: Yaobin
authors.initials: Y
authors.lastname: Jiang
authors.forename: Yue
authors.initials: Y
authors.lastname: Chen
authors.forename: Maoying
authors.initials: M
authors.lastname: Wu
authors.forename: Guanwen
authors.initials: G
authors.lastname: Yan
authors.forename: Wenjun
authors.initials: W
authors.lastname: Ye
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.forename: Hai-Feng
authors.initials: HF
authors.lastname: Chen
mesh_terms: D000818:Animals; D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D029721:Drosophila Proteins / Q000737:chemistry* / Q000378:metabolism*; D004331:Drosophila melanogaster; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D058767:Protein Unfolding; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry; D013379:Substrate Specificity
chemical_list: D001059:Apoproteins; D029721:Drosophila Proteins; D012097:Repressor Proteins; D012997:Solvents; C118082:brk protein, Drosophila; D004247:DNA