A simple formula based on linear response theory is proposed to explain and predict the structural change of proteins upon ligand binding. By regarding ligand binding as an external perturbation, the structural change as a response is described by atomic fluctuations in the ligand-free form and the protein-ligand interactions. The results for three protein systems of various sizes are consistent with the observations in the crystal structures, confirming the validity of the linear relationship between the equilibrium fluctuations and the structural change upon ligand binding.

The proper location and timing of Dnmt1 activation are essential for DNA methylation maintenance. We demonstrate here that Dnmt1 utilizes two-mono-ubiquitylated histone H3 as a unique ubiquitin mark for its recruitment to and activation at DNA methylation sites. The crystal structure of the replication foci targeting sequence (RFTS) of Dnmt1 in complex with H3-K18Ub/23Ub reveals striking differences to the known ubiquitin-recognition structures. The two ubiquitins are simultaneously bound to the RFTS with a combination of canonical hydrophobic and atypical hydrophilic interactions. The C-lobe of RFTS, together with the K23Ub surface, also recognizes the N-terminal tail of H3. The binding of H3-K18Ub/23Ub results in spatial rearrangement of two lobes in the RFTS, suggesting the opening of its active site. Actually, incubation of Dnmt1 with H3-K18Ub/23Ub increases its catalytic activity in vitro. Our results therefore shed light on the essential role of a unique ubiquitin-binding module in DNA methylation maintenance.

Homologous recombination is an important biological process that occurs in all organisms and facilitates genome rearrangements and repair of DNA double-strand breaks. Eukaryotic Rad51 proteins (Rad51 sp or Rhp51 in fission yeast) are functional and structural homologs of bacterial RecA protein, an evolutionarily conserved protein that plays a key role in homologous pairing and strand exchange between homologous DNA molecules in vitro. Here we show that the fission yeast swi5 ؉ gene, which was originally identified as a gene required for normal mating-type switching, encodes a protein conserved among eukaryotes and is involved in a previously uncharacterized Rhp51 (Rad51 sp )-dependent recombination repair pathway that does not require the Rhp55͞57 (Rad55͞57 sp ) function. Protein interactions with both Swi5 and Rhp51 were found to be mediated by a domain common to Swi2 and Sfr1 (Swi five-dependent recombination repair protein 1, a previously uncharacterized protein with sequence similarity to the C-terminal part of Swi2). Genetic epistasis analyses suggest that the Swi5-Sfr1-Rhp51 interactions function specifically in DNA recombination repair, whereas the Swi5-Swi2-Rhp51 interactions may function, together with chromodomain protein Swi6 (HP1 homolog), in mating-type switching.D NA double-strand breaks (DSBs) are caused by DNAdamaging agents, such as ionizing irradiation, and also arise during normal DNA replication. These accidentally generated DSBs are critical genotoxic lesions in all organisms. However, the DSBs can be repaired efficiently by several cellular mechanisms that maintain genome stability. Homologous recombination is one of the most important pathways for DSB repair.Eukaryotic Rad51 protein is regarded as the structural and functional counterpart of the Escherichia coli RecA protein and plays a central role in homologous recombination in eukaryotic cells (1). Purified Rad51 forms nucleoprotein filaments, like RecA (2), and promotes homologous pairing and strand exchange between homologous DNA strands in vitro (3, 4). However, eukaryotes possess additional RecA-like proteins such as Rad55 sc ͞ Rhp55 (Rad55 sp ) and Rad57 sc ͞Rhp57 (Rad57 sp ) in Saccharomyces cerevisiae and Schizosaccharomyces pombe and Rad51B, Rad51C, Rad51D, Xrcc2, and Xrcc3 in vertebrates (1).Biochemical studies have demonstrated that these RecA paralogs stimulate Rad51-mediated strand exchange (1, 5, 6). Rad55 (Rhp55) and Rad57 (Rhp57) form heterodimers and bind to Rad51 (Rhp51) (7,8). Null mutants of the S. pombe rhp51 gene are hypersensitive to DNA-damaging agents, and rhp51 mutations are epistatic to rhp55 or rhp57 mutations. In addition, paralog mutants are cold-sensitive, and overexpression of Rad51 (Rhp51) partially suppresses their DNA repair defects (9-12). Furthermore, the formation of Rhp51 foci in irradiated S. pombe cells depends on the rhp55 function (13). The dependence of Rad51 foci on paralogs has also been demonstrated in S. cerevisiae (14) and in chicken DT40 cells (12,15). These observations are consistent wi...