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Loop flexibility in human telomeric quadruplex small-molecule complexes.

Collie GW, Campbell NH, Neidle S - Nucleic Acids Res. (2015)

Bottom Line: Sugar conformation and backbone angles have also been examined and trends highlighted.One particular loop class has been found to be most prevalent.Implications for in particular, rational drug design, are discussed.

View Article: PubMed Central - PubMed

Affiliation: UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK.

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(A) Views of the various TTA loop types (coloured as in Figure 1), grouped into 12 distinct categories. (B) (i) The two sub-types of type-1 loops. Sub-type 1 (left) is from PDB structure 1KF1, sub-type 2 (right) is from PDB structure 3T5E. The structures shown here have been structurally aligned and are presented in the same orientation. (ii) An example of the structural diversity of non-type-1 loops: overlay of a type-4 loop (pink, from PDB structure 3CCO), a type-10 loop (green, from PDB structure 3SC8) and a type-1 loop (red, from PDB structure 1KF1). The non-type-1 loops are dramatically different to the ‘native’ type-1 TTA loop—as well as to one another. Note the retention of base-stacking interactions in the type-10 loop arrangement, which is a common feature of non-type-1 loops.
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Figure 2: (A) Views of the various TTA loop types (coloured as in Figure 1), grouped into 12 distinct categories. (B) (i) The two sub-types of type-1 loops. Sub-type 1 (left) is from PDB structure 1KF1, sub-type 2 (right) is from PDB structure 3T5E. The structures shown here have been structurally aligned and are presented in the same orientation. (ii) An example of the structural diversity of non-type-1 loops: overlay of a type-4 loop (pink, from PDB structure 3CCO), a type-10 loop (green, from PDB structure 3SC8) and a type-1 loop (red, from PDB structure 1KF1). The non-type-1 loops are dramatically different to the ‘native’ type-1 TTA loop—as well as to one another. Note the retention of base-stacking interactions in the type-10 loop arrangement, which is a common feature of non-type-1 loops.

Mentions: (A) View of the human telomeric quadruplex native and ligand complex crystal structures, with nucleic acids drawn in stick form and ligands in surface representation. Metal ions (potassiums) are shown as purple spheres. Individual loops are highlighted with sticks in single colours. The colour coding corresponds to the more detailed view of each loop type shown in Figure 2. (B) Structures of individual ligands, shown with the PDB IDs for the structures in which they occur.


Loop flexibility in human telomeric quadruplex small-molecule complexes.

Collie GW, Campbell NH, Neidle S - Nucleic Acids Res. (2015)

(A) Views of the various TTA loop types (coloured as in Figure 1), grouped into 12 distinct categories. (B) (i) The two sub-types of type-1 loops. Sub-type 1 (left) is from PDB structure 1KF1, sub-type 2 (right) is from PDB structure 3T5E. The structures shown here have been structurally aligned and are presented in the same orientation. (ii) An example of the structural diversity of non-type-1 loops: overlay of a type-4 loop (pink, from PDB structure 3CCO), a type-10 loop (green, from PDB structure 3SC8) and a type-1 loop (red, from PDB structure 1KF1). The non-type-1 loops are dramatically different to the ‘native’ type-1 TTA loop—as well as to one another. Note the retention of base-stacking interactions in the type-10 loop arrangement, which is a common feature of non-type-1 loops.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4446451&req=5

Figure 2: (A) Views of the various TTA loop types (coloured as in Figure 1), grouped into 12 distinct categories. (B) (i) The two sub-types of type-1 loops. Sub-type 1 (left) is from PDB structure 1KF1, sub-type 2 (right) is from PDB structure 3T5E. The structures shown here have been structurally aligned and are presented in the same orientation. (ii) An example of the structural diversity of non-type-1 loops: overlay of a type-4 loop (pink, from PDB structure 3CCO), a type-10 loop (green, from PDB structure 3SC8) and a type-1 loop (red, from PDB structure 1KF1). The non-type-1 loops are dramatically different to the ‘native’ type-1 TTA loop—as well as to one another. Note the retention of base-stacking interactions in the type-10 loop arrangement, which is a common feature of non-type-1 loops.
Mentions: (A) View of the human telomeric quadruplex native and ligand complex crystal structures, with nucleic acids drawn in stick form and ligands in surface representation. Metal ions (potassiums) are shown as purple spheres. Individual loops are highlighted with sticks in single colours. The colour coding corresponds to the more detailed view of each loop type shown in Figure 2. (B) Structures of individual ligands, shown with the PDB IDs for the structures in which they occur.

Bottom Line: Sugar conformation and backbone angles have also been examined and trends highlighted.One particular loop class has been found to be most prevalent.Implications for in particular, rational drug design, are discussed.

View Article: PubMed Central - PubMed

Affiliation: UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK.

Show MeSH
Related in: MedlinePlus