Structure-based modeling of protein: DNA specificity

Abstract

Protein:DNA interactions are essential to a range of processes that maintain and express the information encoded in the genome. Structural modeling is an approach that aims to understand these interactions at the physicochemical level. It has been proposed that structural modeling can lead to deeper understanding of the mechanisms of protein:DNA interactions, and that progress in this field can not only help to rationalize the observed specificities of DNA-binding proteins but also to allow researchers to engineer novel DNA site specificities. In this review we discuss recent developments in the structural description of protein:DNA interactions and specificity, as well as the challenges facing the field in the future.

Keywords: Binding specificity; Molecular modeling; Protein:DNA interactions; Structural modeling; Structure prediction; Transcription factor binding sites.

Figure 1:

Atomically detailed structures of protein:DNA complexes illuminate the molecular mechanisms underlying sequence-specific binding: the overall structure (with protein shown in cartoon representation, the DNA in sticks, zinc ions as spheres and crystal waters as crosses) (A) and per-position specificity-determining interactions (B) seen in the high-resolution crystal structure of the C2H2 zinc finger Zif268 bound to a high-affinity target site (PDB ID 1aay [11]; PWM data downloaded from the Uniprobe database [12]; structure figures generated in PyMOL [13]). (A colour version of this figure is available online at: http://bfg.oxfordjournals.org)

Figure 2:

Modeling protein:DNA complexes. The choice of protocol depends on the structural ‘template’ available for constructing the model. If a bound structure is available for the protein of interest (‘Native complex’, top left), the modeling needed for binding predictions involves primarily base pair mutations (‘Gua→Ade’: template in cyan/dark gray and model in yellow/light gray) and side chain rearrangements (gray arrow). Building a model using a homologous complex as a template will require protein (‘R→A’, ‘E→N’) as well as base pair mutations, and may require protein and DNA backbone relaxation. If the unbound structure of the native protein is known, a DNA-bound model can be constructed by superimposing this unbound structure onto the structure of a homologous factor in a bound structure (bottom left), or by de novo ‘docking’ onto DNA (bottom right, multiple candidate docked conformations shown). (A colour version of this figure is available online at: http://bfg.oxfordjournals.org)

Figure 3:

Water molecules at the protein:DNA interface participate in hydrogen bonding networks. (A) The trp repressor protein achieves recognition of its operator sequence through multiple water-mediated contacts, involving both protein side chain and mainchain atoms. (B) The EcoRI restriction enzyme interacts with its cognate cleavage site with both and water-mediated contacts. Failure to model water molecules explicitly leads to a relaxed DNA specificity profile reminiscent of ‘star activity’, which has been attributed to the loss of bound interfacial water. (A colour version of this figure is available online at: http://bfg.oxfordjournals.org)

Figure 4:

Protein and DNA adopt diverse backbone conformations and orientations in complex. (A) Variation in triplet-docking orientation of the protein backbone for eight zinc finger domains from Zif268 (1AAY), Tramtrack (2DRP) and TFIIIA (1TF6) (B) The recognition element of PurR undergoes substantial deformation from the unbound state (1HQ7, magenta/dark gray) on protein binding in the minor groove (1QPZ, green/light gray). Upper panel: top view. Lower panel: side view. (A colour version of this figure is available online at: http://bfg.oxfordjournals.org)