A comparative study of protein–ssDNA interactions

Abstract

Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein–ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB–ssDNA interactions, protein–ssDNA hydrogen bonding and π–π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein–ssDNA binding specificity, while π–π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein–double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.

Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches

“…Aliphatic amino acids alanine, isoleucine, leucine, and valine show low propensity in both binding specificity groups. Interestingly, the negatively charged aspartate is also enriched in the specific protein-ssDNA interactions as we demonstrated in specific protein-dsDNA interactions [ 23 , 27 ]. π–π interactions may primarily contribute to binding affinity as there are no apparent difference of π–π interactions between the two binding specificity groups.…”

“…Even though binding specificity is a relative term and is difficult to define with a hard cutoff, proteins can be grouped based on the differences of binding affinity among a large number of sequences [ 23 ]. In both protein-dsDNA interaction and protein-ssDNA interaction, hydrogen bonds (HBs) between DNA bases and protein sidechain atoms are considered the major contributor to binding specificity [ 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. Some OB fold proteins bind ssDNA with very high sequence specificity.…”

“…While there are quite a number of studies on structural features in protein-dsDNA binding specificity [ 23 , 24 , 26 , 40 , 41 , 42 , 43 , 44 ], the specificity investigation of protein-ssDNA interaction is underexplored due to the limited availability of protein-ssDNA complex structures. We recently performed a comparative study of protein–ssDNA interactions in terms of binding specificity [ 27 ]. A non-redundant dataset of SSB–ssDNA complexes with high structural quality was generated and classified into two groups: specific and non-specific, based on their binding specificity, which was manually annotated by searching the primary references of these SSB–ssDNA complexes and their homologs in Protein Data Bank (PDB) [ 45 , 46 ] as well as relevant information in UniProt [ 47 ].…”

“…A non-redundant dataset of SSB–ssDNA complexes with high structural quality was generated and classified into two groups: specific and non-specific, based on their binding specificity, which was manually annotated by searching the primary references of these SSB–ssDNA complexes and their homologs in Protein Data Bank (PDB) [ 45 , 46 ] as well as relevant information in UniProt [ 47 ]. We then compared the key structural features in protein-ssDNA interaction, including binding propensities and secondary structure types of ssDNA base-interacting residues, hydrogen bonds, π–π interactions between residue side chains and DNA bases, interaction interfaces, and protein conformational changes upon ssDNA binding [ 27 ].…”

“…Hydrogen bonds and amino acid binding propensities were found to be the key discriminating features between specific and non-specific ssDNA binding proteins [ 27 ] ( Figure 2 for comparison of sidechain-base hydrogen bonds). As for amino acid binding propensities, while aromatic and positively charged amino acids, phenylalanine, tryptophan, tyrosine, histidine, lysine, and arginine are enriched in both specific and non-specific protein-ssDNA complexes, three amino acids (histidine, tyrosine, and arginine) are more enriched in the specific group than those in the non-specific group.…”