Selected article for: "SUD core and zone interference"
Author: Tan, Jinzhi; Vonrhein, Clemens; Smart, Oliver S.; Bricogne, Gerard; Bollati, Michela; Kusov, Yuri; Hansen, Guido; Mesters, Jeroen R.; Schmidt, Christian L.; Hilgenfeld, Rolf
Title: The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes
  • Document date: 2009_5_15
    • ID: 1aqt65cc_21
    Snippet: Inspection of the structure of the SUD dimer reveals a central narrow cleft running across the dimer surface, but distinct from the monomer-monomer interface ( Figure 3C ), which could be a binding site for another protein. In addition, there are several positively charged patches in the center of the dimer ( Figure 3B ), and on its backside ( Figure 3C ), which could be involved in binding to G-quadruplexes. We have prepared four sets of mutatio.....
    Document: Inspection of the structure of the SUD dimer reveals a central narrow cleft running across the dimer surface, but distinct from the monomer-monomer interface ( Figure 3C ), which could be a binding site for another protein. In addition, there are several positively charged patches in the center of the dimer ( Figure 3B ), and on its backside ( Figure 3C ), which could be involved in binding to G-quadruplexes. We have prepared four sets of mutations by replacing lysine residues (and one glutamate) in these patches by alanines. The first two pairs of mutations, K505A+K506A (M1, at the end of helix aN4) and K476A+K477A (M2, in the loop between aN3 and bN5), are located on the surface of the SUD-N subdomain and lead to reduced shifts with G-quadruplexes in the zone-interference gel electrophoresis experiment, both with the G-quadruplex from the The narrow cleft running across the dimer surface (with a ,45u orientation relative to the monomer-monomer interface, which runs horizontal in this illustration) could be a potential protein-binding site. The monomer-monomer interface is largely hydrophilic and buries ,1130 Ã… 2 of exposed surface per monomer. doi:10.1371/journal.ppat.1000428.g003 10 , or (dT) 10 shows that the binding is specific for (dG) 10 . ''H'' stands for A, C, or T. (B) Binding of increasing concentrations (indicated above the lanes) of the quadruplex-forming oligodeoxynucleotide 59-GGGCGCGGGAG-GAATTGGGCGGG-39 (labeled ''Bcl-2'') as occurring within the bcl-2 promoter region, in the presence and absence of 100 mM KCl, which is known to promote quadruplex formation. Left panel, full-length SUD; right panel, SUD core . The reverse-complementary oligodeoxynucleotide (labeled ''rc''), which fails to form a quadruplex but exceeds the minimum length of ,15 nucleotides for non-quadruplex interaction with SUD, is also bound, but with reduced affinity and independently of KCl. (dG) 10

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