Top2 localizes Ipl1 to mitotic inner centromeres independently of the SPR core

t. bend region. Here we constructed A where the residues from Asp-30-Gln-34 have been deleted and E where two extra alanines are now flanking 626 The ColEl Rop protein Fig. 7. Localization of active and inactive mutants of the Rop molecule. Three different views of the Rop dimer. The amino acid side chains that have been tested by site directed mutagenesis were identified by their van der Waal surfaces. Side chains whose alteration caused a non-functional protein have red PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19828691 surfaces while the side chains that have been mutated and have not been found to be important for function have blue surfaces. Relevant amino acids have been identified with numbers, indicating their position along the polypeptide chain, preceded either by an A or by a B to distinguish identical residues on the two monomers. The pictures were drawn using the Insight graphic program. 627 L.Castagnoli et al. are not important for function as assayed in our two in vivo tests and none of them prevents folding. We are forced to conclude that either our assays do not completely cover the function of Rop or that subtle quantitative changes that we cannot detect are, or have been, selectively not neutral in the natural evolutionary niche of these bacterial plasmids. The loop region To localize further the essential information that has been affected in the mutant A we have constructed mutants in which the solvent-exposed amino acids from Glu-24 to Asp-36 have been modified by site directed mutagenesis. The only solvent-exposed amino acid that has not been modified is Asp-30. That the role of this amino acid is not critical, however, has already been demonstrated by the construction of mutant E in which two alanines have been inserted on both sides of Asp-30. The mutants at position Asp-32 were obtained by random mutagenesis with an oligonucleotide carrying degenerate sequences in place of the Asp-32 coding triplet. As indicated in the by neutralizing the negative charge barrier thus favouring the approach of the protein to the nucleic acid. As shown by Bedouelle and Winter three clusters of Arg and Lys residues are involved in the interaction between the tyrosil tRNA synthetase from Bacillus stearothermophilus and tRNATYr. Rop is a rather acidic protein, having only seven positively charged amino acids compared with the 14 Asp or Glu residues. We have modified to Cys two of the three Lys and three of the four Arg residues and we have tested whether any of these changes affected the activity of the protein. The results shown in Other mutants on the 487-52-5 lateral surface of the Rop cylinder Most of the remaining mutants, constructed by altering the solvent exposed side chains in the lateral surface of the Rop cylinder, do not alter the function of the protein. The aromatic ring of Phe-14, however, is indicated by our experiments as playing an important role. Although it has been recently appreciated that aromatic rings can act as hydrogen bond acceptors, the side chain of Phe is rather hydrophobic and it is therefore unlikely to contribute to the RNA binding process by specifically recognizing a pattern of complementary hydrogen bond donors and acceptors on the bases. It is tempting to speculate that while side chains near the bend provide the pattern of hydrogen bonds that permits recognition, the aromatic ring of Phe-14 contributes to stabilize the Rop-RNAI-RNAII complex by stacking between two consecutive bases. In Positively charged side chains Proteins interacting with nucleic ac