title: Structure/function of KRAB repression domains: structural properties of KRAB modules inferred from hydrodynamic, circular dichroism, and FTIR spectroscopic analyses.
abstract: The abundant zinc finger proteins (ZFPs) sharing the KRAB motif, a potent transcription repression domain, direct the assembly on templates of multiprotein repression complexes. A pivotal step in this pathway is the assembly of a KRAB domain-directed complex with a primary corepressor, KAP1/KRIP-1/TIF1beta. The structure/function dependence of KRAB/TIF1beta protein-protein interaction and properties of the complex, therefore, play pivotal roles in diverse cellular processes depending on KRAB-ZFPs regulation. KRAB domains are functionally bipartite. The 42 amino acid-long KRAB-A module, indeed, is necessary and sufficient for transcriptional repression and for the interaction with the tripartite RBCC region of TIF1beta, while the KRAB-B motif seems to potentiate the assembly of the complex. The structural properties of KRAB-A and KRAB-AB domains from the human ZNF2 protein have been investigated by characterizing highly purified lone (A) and composite (AB) modules. Hydrodynamic and spectroscopic features, investigated by means of gel filtration, circular dichroism, and infrared spectroscopy, provide evidence that both KRAB-A and KRAB-AB domains present low compactness, structural disorder, residual secondary structure content, flexibility, and tendency to molecular aggregation. Comparative analysis among KRAB-A and KRAB-AB modules suggests that the presence of the -B module may influence the properties of lone KRAB-A by affecting the structural flexibility and stability of the conformers. The combined experimental data and the intrinsic features of KRAB-A and KRAB-AB primary structures indicate a potential role of specific subregions within the modules in driving structural flexibility, which is proposed to be of importance for their function.
authors.affiliation: Istituto di Genetica e Biofisica Adriano Buzzati-Traverso, CNR, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Mannini
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Rivieccio
authors.forename: Sabato
authors.initials: S
authors.lastname: D'Auria
authors.forename: Fabio
authors.initials: F
authors.lastname: Tanfani
authors.forename: Alessio
authors.initials: A
authors.lastname: Ausili
authors.forename: Angelo
authors.initials: A
authors.lastname: Facchiano
authors.forename: Aangelo
authors.initials: A
authors.lastname: Facchiano
authors.forename: Carlo
authors.initials: C
authors.lastname: Pedone
authors.forename: Giovanna
authors.initials: G
authors.lastname: Grimaldi
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D005822:Genetic Vectors; D006801:Humans; D007700:Kinetics; D008239:Lysine; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D011994:Recombinant Proteins / Q000737:chemistry; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012995:Solubility; D017550:Spectroscopy, Fourier Transform Infrared; D014466:Ultraviolet Rays; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; D011994:Recombinant Proteins; D012097:Repressor Proteins; C422407:ZNF350 protein, human; D008239:Lysine