Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations  Till Siebenmorgen, Martin Zacharias  Biophysical Journal  Volume 112, Issue 11, Pages 2280-2290 (June 2017) DOI: 10.1016/j.bpj.2017.04.036 Copyright © 2017 Biophysical Society Terms and Conditions

Figure 1 Structure and strand topology of the G-quadruplex PDB: 143D (A) and PDB: 2GKU (B), respectively. The quadruplex-forming G3 segments are shown in blue (first segment), red (second segment), yellow (third segment), and green (fourth segment) stick representation. The backbone of the connecting loop segments is shown as a more narrow pink-colored stick model. To further emphasize the different directions of the segments, the thymine nucleotides 3′ to the second segment (red) and 3′ to the third segment are also indicated as bold sticks. For clarity, the bound cations (in the central cavity) are not shown. To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 2 Calculated binding free energy difference ΔΔGbind (kcal·mol−1) for binding of different ions to the central pore of the G-quadruplex structures (PDB code indicated). The reference corresponds to bound K+ ions. The position of the ions (Li+→Cs+) on the x axis has been scaled according to the difference in aqueous ion solvation free energy. The dashed lines indicate calculated relative binding free energies for artificial ions with the same attractive LJ parameter as the K+ (marked by an asterisk in the legend). Relative binding free energy differences are given for two centrally bound ions. To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 3 Snapshots of conformations close to the average structure found during MD simulations with different centrally bound ions. The nucleobases are atom-color coded whereas the backbone color changes from blue to red along the 5′–3′ chain direction. The two centrally bound ions are shown as van der Waals spheres with increasing size from Li+ (left panel) to Cs+ (rightmost panel) indicating approximately the size of the ions. To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 4 Probability histograms of the sampled reciprocal distances between the bound ions and the coordinating O6 atoms of the G-quartet guanines during MD simulations. Note that the reciprocal distance is the relevant quantity for the strong Coulomb interaction between ion and central guanine tetrads. For clarity, the Li+ case is not shown because of a less localized distribution (see Table 3 for average distance and variance). To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 5 Transient ion binding sites were found for the 143D G-quartet structure (A, stick model with centrally bound ions indicated as gray van der Waals spheres) shown as orange spheres. The size of the spheres indicates approximately the occupancy during the simulations of 63% for the location of the largest sphere (interacting with nucleotides 10 and 11), 51% for the second largest sphere (interacting with nucleotides 15 and 20), and 8% occupancy for the smallest sphere. Occupancy is defined as simulation time with ions contacting the site versus total simulation time. An ion was considered as transiently bound to a nucleotide if the distance to the center of mass was <7 Å (see Materials and Methods). In the case of the PDB: 2GKU G-quartet (B), interaction sites near nucleotides 8 and 9 (largest orange sphere with 55% occupancy) and close to residues 15, 23, and 25 with an occupancy of 33% were identified. The ions at the surface pockets interacted mostly with nucleotide phosphate groups. To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 6 Mean calculated energy contributions to G-quadruplex ion binding. Different components are indicated. Ion-Q4 indicates the mean interaction between centrally bound ions and the complete quadruplex. Note that an offset has been subtracted for the Ion-Q4 interaction to adjust it to the range of interactions for the guanine ion interactions alone. GG, guanine-guanine interactions of the guanine tetrads; IG, ion-guanine interactions. To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 7 Mean calculated energy contributions to G-quadruplex ion binding for artificial ions with the same attractive LJ parameter (taken from the K+ ion). Different components are indicated. GG, guanine-guanine interactions of the guanine tetrads; IG, ion-guanine interactions. To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 8 Average calculated binding energy (ΔE′bind) versus quadruplex-bound cation type (see main text) for binding of artificial ions (same LJ attractive parameter, upper panel) and for binding of native ions (lower panel). Contributions are given for the two bound ions. Note that the binding energe (ΔE′bind) as defined in the main text also contains the difference in free energy of ion solvation (not only purely energetic interaction contributions). To see this figure in color, go online. Biophysical Journal 2017 112, 2280-2290DOI: (10.1016/j.bpj.2017.04.036) Copyright © 2017 Biophysical Society Terms and Conditions