Nucleotide conformations

Based on traditional definitions of nucleotide conformations, their symbolic characterization takes place on two levels. The first one is the position of the furanose ring atoms relative to the general plane of the ring, which determines the sugar puckering mode. The values of the pseudorotation phase angle for furanose rings described by Altona et al. [1] are divided into the ten classes shown in Table 3.2. The second is the orientation of the nitrogen base relative to the sugar, which can be determined by the angle around the glycosyl bond, $\chi$, defined by the atoms O4', C1', N9 and C4 for purines and the atoms O4', C1', N1 and C2 for pyrimidines. As accepted by the IUPAC-IUB commision [12], values of $\chi$ in the range $[-90^\circ,90^\circ[$ indicate a syn orientation whereas other values indicate a trans orientation. Since the other parts of a nucleotide are mostly rigid, the two above properties represent a fair qualitative description of nucleotide conformations. The class of a nucleotide conformation can thus be defined by its sugar puckering mode and nitrogen base orientation around the glycosyl bond. The corresponding symbols assigned by MC-Annotate are summerized in Table 3.2.

Figure: Symbols used in classification. Two symbols from the base type and interacting edges are used, one for each nucelotide involved in the base-pair as indicated by the exponent 2. The MC-Sym numbers for base-pairs of two or more H-bonds are in roman, whereas arabic numbers are used for one H-bond base-pairing patterns.

The distance, $d(\mathbf{b}_1,\mathbf{b}_2)$, between two nucleotide conformations, $\mathbf{b}_1$ and $\mathbf{b}_2$, can be defined by the root mean square deviation (RMSD) between the heavy atoms in the backbone of the two nucleotides, a posteriori of optimal superimposition of their local referentials in 3-D space [9]. Our metric is in good correlation with the more standard all-atom superposition and RMSD metric, $d_a(\mathbf{b}_1,\mathbf{b}_2)$, performed using the analytical method described by Kabsch [13,14] and places the emphasis on the backbone atom positions and orientation relative to the nitrogen base.