Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides

pKa calculations based on the Poisson–Boltzmann equation have been widely used to study proteins and, more recently, DNA. However, much less attention has been paid to the calculation of pKa shifts in RNA. There is accumulating evidence that protonated nucleotides can stabilize RNA structure and participate in enzyme catalysis within ribozymes. Here, we calculate the pKa shifts of nucleotides in RNA structures using numerical solutions to the Poisson–Boltzmann equation. We find that significant shifts are predicted for several nucleotides in two catalytic RNAs, the hairpin ribozyme and the hepatitis delta virus ribozyme, and that the shifts are likely to be related to their functions. We explore how different structural environments shift the pKas of nucleotides from their solution values. RNA structures appear to use two basic strategies to shift pKas: (a) the formation of compact structural motifs with structurally-conserved, electrostatic interactions; and (b) the arrangement of the phosphodiester backbone to focus negative electrostatic potential in specific regions.