G4-quadruplex-binding proteins: review and insights into selectivity

Abstract

There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.

Keywords: DNA–protein interactions; G4-quadruplexes; Quadruplex-binding proteins; RNA–protein interactions.

Fig. 1

Schematic of G4-quadruplexes (G4Qs), showing the G-tetrad’s planar orientation (A), formed by Hoogsteen bonds and stabilized by a metal ion, typically potassium (K +), which can stack upon one another in various orientations (B). These structures interact with various cellular proteins, which may bind in a number of different manners (C), including top-stacking (i), groove-binding (ii), and loop-binding (iii)

Fig. 2

Example of groove-binding mode—telomeric end-binding protein of Oxytricha nova (OnTEBP), a protozoan analogue of human POT1 protein (PDB 1JB7) broad-view (A) and close-up (B), showing the Tyr142 in proximity to several of the G4Q guanosines and residues Lys105 and Asn139 nearer to the phosphate backbone facilitating H-bonding opportunities

Fig. 3

Example of top-stacking—DHX36 with c-MYC promoter region G4Q. A High-level orientation of the structural arrangement showing the DSM helix sitting atop the G4Q, the lateral OB domain loop contacting the G4Q from the side, while the G4Q is pulled through the RecA-like domains (see text; PDB 5VHE); B DSM helix showing the Tyr69 oriented parallel with an upper guanosine from the tetrad facilitating π-π stacking. Other hydrophobic residues make up the remainder of the downward facing helical residues (Ile65, Trp68, and Ala70); C OB domain showing the proximity for the extensive hydrogen-bonding network between the phosphate backbone of the G4Q and Lys860, Asn851, Gly853, and Lys 855. D Independent study of the DHX36 DSM domain with c-MYC showing similar top-stacking binding mode (PDB 6Q6R)

Fig. 4

FMRP’s 13-amino acid β turn folding into the groove at the junction of duplex and G4Q DNA (PDB 5DE5). The uppermost amino acid, Arg15, interacts with G7 and A17 nucleotides, which are not part of the G4Q structure. Binding is thought to promote stabilization of the G4Q (see text)

Fig. 5

Example of loop-binding mode—synthetic zinc finger, Gq1 targeting a telomeric G4Q. Computationally derived model (PDB from Ladame, et al. 2006), showing overall arrangement (center) and key residues from A the first “finger,” whereby His125, Arg124, and Arg127 interact with the two outward-directed T12 and A13 nucleotides; B the second “finger,” where His153 and Thr156 bind with phosphate backbone of G10, while Arg142 wraps under to bind the other protruding nucleotide, T11; and C the third “finger,” where the Ser175, Arg178, and Thr182 create extensive H-bonds with the phosphate backbone of the loop