Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions

Abstract

Many nucleic acid-protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer-protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid-protein structures discriminated peculiarities of high-affinity nucleic acid-protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer-protein complexes. These results are of great importance for a design of efficient aptamers.

Keywords: affinity; aptamer; energy dissipation; protein; structure-activity relationship.

Figure 1

Aptamer–protein complexes. Dependencies of the mean length of the sidechain of amino acids within 4 Å proximity to polar contacts (A), number of polar contacts (B), mean number of carbon atoms in aromatic or aliphatic groups of the sidechain (C), and total number of atoms in amino acids within 4 Å proximity to polar contacts (D) versus change in Gibbs free energy during binding. The data are clustered—G-quadruplex aptamers with thrombin are colored in red, and all other aptamer complexes are colored in black.

Figure 2

Analysis of kinetic parameters of aptamer–protein complexes. (A) The dependencies of number of polar contacts (PC) from kinetic constants of association, k_on. (B) The mean length sidechain of amino-acid-formed PC from kinetic constant of dissociation, k_off. (C) The mean length sidechain of amino acids within 4 Å proximity to “hot spots” (HS) versus k_off. (D) Total number of atoms in amino acids within 4 Å proximity to HS versus, k_off (D). Logarithmic (y = a × ln(x) + b) approximations were used.

Figure 3

Selection of high-affinity complexes based on the parameters of the interface. Complexes with high values of the parameters of the number of polar contacts (PC), the mean length sidechain of amino-acid-formed PC and amino acids within 4 Å proximity to “hot spots” (HS), and the total number of atoms in amino acids within 4 Å proximity to HS (green dots) have the highest changes in Gibbs free energy during binding compared to other complexes (black dots).

Figure 4

Comparison of aptamer–protein and DNA helix–protein complexes plotted in the coordinates mean lengths of sidechain of amino acids within 4 Å vicinity of polar contacts versus changes in Gibbs free energy during binding. (A) HTH-type proteins from mesophiles with human-like conditions (blue dots), and other organisms (Bacillus and a thermophile = green dots) were plotted with aptamer–protein complexes (black dots). (B) Complexes of fis protein with optimal and non-optimal DNA helices (magenta dots) were plotted with aptamer–protein complexes (black dots).

Figure 5

Capacity of energy transfer (C_y′) plotted versus changes in Gibbs free energy. (A) Aptamer–protein complexes: G-quadruplex aptamers to thrombin are shown as red dots; all other aptamers are shown as black dots; and 7 dots chosen for linearization are shown with blue circles. The linear dependence is described with the equation y = 19.9x − 818 with R² = 0.97. Examples of improvement of aptamer affinity are shown with orange arrows that are drawn from non-optimal to optimal complexes. (B) DNA helix–protein complexes: HTH-type proteins are shown as red dots; complexes of fis protein with different DNA helices are shown as blue dots; and linearized efficient aptamer–protein complexes are shown in black dots.