Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins

Abstract

Recognition of single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) is important for many fundamental cellular functions. A variety of single-stranded DNA-binding proteins (ssDBPs) and single-stranded RNA-binding proteins (ssRBPs) have evolved that bind ssDNA and ssRNA, respectively, with varying degree of affinities and specificities to form complexes. Structural studies of these complexes provide key insights into their recognition mechanism. However, computational modeling of the specific recognition process and to predict the structure of the complex is challenging, primarily due to the heterogeneity of their binding energy landscape and the greater flexibility of ssDNA or ssRNA compared with double-stranded nucleic acids. Consequently, considerably fewer computational studies have explored interactions between proteins and single-stranded nucleic acids compared with protein interactions with double-stranded nucleic acids. Here, we report a newly developed energy-based coarse-grained model to predict the structure of ssDNA–ssDBP and ssRNA–ssRBP complexes and to assess their sequence-specific interactions and stabilities. We tuned two factors that can modulate specific recognition: base–aromatic stacking strength and the flexibility of the single-stranded nucleic acid. The model was successfully applied to predict the binding conformations of 12 distinct ssDBP and ssRBP structures with their cognate ssDNA and ssRNA partners having various sequences. Estimated binding energies agreed well with the corresponding experimental binding affinities. Bound conformations from the simulation showed a funnel-shaped binding energy distribution where the native-like conformations corresponded to the energy minima. The various ssDNA–protein and ssRNA–protein complexes differed in the balance of electrostatic and aromatic energies. The lower affinity of the ssRNA–ssRBP complexes compared with the ssDNA–ssDBP complexes stems from lower flexibility of ssRNA compared to ssDNA, which results in higher rate constants for the dissociation of the complex ( k off ) for complexes involving the former.

A comparative study of protein–ssDNA interactions

“…Our comparative analyses show that the SP group proteins form more contacts with DNA bases than those in the NS group (Figure 6 ), and the propensities of amino acids that involved in protein–ssDNA contacts show that both groups prefer aromatic residues and positively charged residues, but residues H, Y and R are more enriched in the SP group (Figure 2 ). These findings are consistent with previous studies ( 50 , 84 , 85 ). The enrichment of all aromatic residues can be attributed to the increased accessibility of ssDNA.…”

“…An analysis of crystal structures of 10 different non-cognate ssDNA ligands complexed with the Oxytricha nova telomere end-binding protein ( On TEBP) revealed that the overall protein conformation in all complexes remained nearly identical to that of the cognate complex, but the ssDNA exhibited subtle to dramatic conformational changes ( 49 ). Pal and Levy also found that the ssDNA molecules were more flexible than the proteins, but they suggested that the sequence specificity was mostly introduced by the stacking interactions between aromatic residues and DNA bases ( 50 ).…”

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

“…DNA is well known as the repository of genetic information shared by all forms of eukaryote life. Compare the fragility of single-stranded DNA (ssDNA) with the unparalleled stability of double-stranded DNA (dsDNA) 67 , 68 . The paired strands of dsDNA, bound together, are relatively resistant to random damage because each strand is in constant interaction with its sister strand; the two strands can be perceived to be in continuous cooperation; essentially all potentially reactive, non-covalent bonding energy is engaged in cooperative interactions between the strands.…”

Comprehensive Analysis of the Safety Profile of a Single-Stranded RNA Nano-Structure Adjuvant

“…Single-stranded RNA (ssRNA) is also known to serve as an agonist of TLR-7/8 and retinoic acid-inducible gene I (RIG-I), which can induce innate immune responses and increase immunogenicity [26,27]. Compared to dsRNA, ssRNA can induce appropriate immune responses and does not remain in the body for a long time [28,29], resulting in fewer intense adverse effects. Currently, ssRNA is being studied as an intrinsic adjuvant in tumor-vaccination studies [30,31,32].…”