"η6"-Type anion-π in biomolecular recognition.

Theoretical and compelling experimental evidence indicates that the interaction between an anion and an aromatic π system when the anion is directly above the ring face ("η(6)"-type anion-π), can be attractive. This may play an important role in the formation and recognition of biomolecular structures. We examined high-resolution structures of proteins and nucleic acids for the presence of "η(6)"-type anion-π. Though less frequent than its counterpart cation-π, "η(6)"-type anion-π is observed unambiguously, occurring in protein/nucleic acid loops and often involving conserved/coevolving sites in proteins, suggesting it plays an important role in macromolecular folding and function.

[Functional site prediction of BRCT domain containing phosphate binding pocket].

The BRCT domain (after the C-terminal domain of a breast cancer susceptibility protein) is an important signaling and protein targeting motif in the DNA damage response system. To clarify possible interaction mechanisms between the BRCT domain, which contains phosphate binding pocket and its phosphorylated ligand, we analyzed the structural conservation and electrostatic surface potentials of XRCC1 BRCT1, PTIP BRCT4, ECT2 BRCT1 and TopBP1 BRCT1. The results showed common structurally conserved and positively charged grooves located around the phosphate binding pockets of these domains. These grooves possibly act as functional sites in the four BRCT domains due to the extensive existence of similar grooves in the BRCT domains containing phosphate binding pocket. The two sides of the groove were composed of positively charged and hydrophilic residues and the bottom was composed of hydrophobic and hydrophilic residues, suggesting that the groove binds to BRCT domain ligand mainly through electrostatic and hydrophobic interactions. The groove was mainly located in individual BRCT domains and differences in shape and charge distribution among the four BRCT domain grooves were observed, indicating that ligand binding specificity was predominantly determined by individual BRCT domains. The groove was centered by the phosphate binding pocket, implying that the groove interacted with residues located at both the N-terminal and C-terminal sides of the phosphorylated residue.

Functional Evolution of BRCT Domains from Binding DNA to Protein.

The BRCT domain (BRCA1 C-terminal domain) is an important signaling and protein targeting motif in the DNA damage response system. The BRCT domain, which mainly occurs as a singleton (single BRCT) or tandem pair (double BRCT), contains a phosphate-binding pocket that can bind the phosphate from either the DNA end or a phosphopeptide. In this work, we performed a database search, phylogeny reconstruction, and phosphate-binding pocket comparison to analyze the functional evolution of the BRCT domain. We identified new BRCT-containing proteins in bacteria and eukaryotes, and found that the number of BRCT-containing proteins per genome is correlated with genome complexity. Phylogeny analyses revealed that there are two groups of single BRCT domains (sGroup I and sGroup II) and double BRCT domains (dGroup I and dGroup II). These four BRCT groups differ in their phosphate-binding pockets. In eukaryotes, the evolution of the BRCT domain can be divided into three phases. In the first phase, the sGroup I BRCT domain with the phosphate-binding pocket that can bind the phosphate of nicked DNA invaded eukaryotic genome. In the second phase, the phosphate-binding pocket changed from a DNA-binding type to a protein-binding type in sGroup II. The tandem duplication of sGroup II BRCT domain gave birth to double BRCT domain, from which two structurally and functionally distinct groups were evolved. The third phase is after the divergence between animals and plants. Both sGroup I and sGroup II BRCT domains originating in this phase lost the phosphate-binding pocket and many evolved protein-binding sites. Many dGroup I members were evolved in this stage but few dGroup II members were observed. The results further suggested that the BRCT domain expansion and functional change in eukaryote may be driven by the evolution of the DNA damage response system.