Toward understanding protein-DNA interactions
Knowledge of protein-DNA interactions has important implications in understandingbiological activities and developing therapeutic drugs. Two types of protein-DNAinteractions exist: (1) interactions between double-stranded DNA-binding proteins(DSBs) and double-stranded DNA (dsDNA), and (2) those between single-strandedDNA-binding proteins (SSBs) and single-stranded DNA (ssDNA). DSB-dsDNA interactionshave been extensively studied but are still not completely understood. Incontrast, less attention has been paid to SSB-ssDNA interactions. To expand ourknowledge of DSB-dsDNA interactions, we investigated the roles of individual DNAstrands and protein secondary structure types in specific DSB-dsDNA recognitionbased on side chain-base hydrogen bonds. By comparing the contribution of eachDNA strand to the overall binding specificity, we found that highly specific DSBsshow balanced hydrogen bonding with each of the two DNA strands, while multi-specificDSBs are generally biased towards one strand. In addition, amino acidsinvolved in side chain-base hydrogen bonds in these two groups of proteins favordifferent secondary structure types. To advance our understanding of SSB-ssDNAinteractions, we performed a comparative structural analysis on known SSB-ssDNAcomplex structures. Structural features such as DNA binding propensities and secondarystructure types of amino acids involved in SSB-ssDNA interactions, protein-DNA contact area, residue-base contacts, protein-ssDNA hydrogen bonding and π-πinteractions, were analyzed and compared between specific and non-specific ssDNA-bindingproteins. Our results suggest that side chain-base hydrogen bonds play majorroles in protein-ssDNA binding specificity, while protein-ssDNA π-π interactions maycontribute to binding affinity. In addition, bound and unbound conformations of the same ssDNA-binding domains were compared to investigate the conformationalchanges upon ssDNA binding, and the results indicate that conformational changesof ssDNA-binding proteins might not be a major contributor in conferring bindingspecificity. These studies provide new insights into the mechanisms of specific protein-DNA interactions and can help therapeutic drug design.