Statistical analysis of structural determinants for protein-DNA-binding specificity

Abstract

DNA-binding proteins play critical roles in biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific (HS) to nonspecific (NS). Alterations of DNA-binding specificity, due to either genetic variation or somatic mutations, can lead to various diseases. In this study, a comparative analysis of protein-DNA complex structures was carried out to investigate the structural features that contribute to binding specificity. Protein-DNA complexes were grouped into three general classes based on degrees of binding specificity: HS, multispecific (MS), and NS. Our results show a clear trend of structural features among the three classes, including amino acid binding propensities, simple and complex hydrogen bonds, major/minor groove and base contacts, and DNA shape. We found that aspartate is enriched in HS DNA binding proteins and predominately binds to a cytosine through a single hydrogen bond or two consecutive cytosines through bidentate hydrogen bonds. Aromatic residues, histidine and tyrosine, are highly enriched in the HS and MS groups and may contribute to specific binding through different mechanisms. To further investigate the role of protein flexibility in specific protein-DNA recognition, we analyzed the conformational changes between the bound and unbound states of DNA-binding proteins and structural variations. The results indicate that HS and MS DNA-binding domains have larger conformational changes upon DNA-binding and larger degree of flexibility in both bound and unbound states. Proteins 2016; 84:1147-1161. © 2016 Wiley Periodicals, Inc.

Keywords: DNA shape; aromatic residue; aspartate; conformational changes; flexibility; hydrogen bond; structural variations; transcription factor; π-interaction.

Figure 1

Flowchart for compiling the non-redundant datasets of DNA-binding domains.

Figure 2

Residue-base contacts in protein-DNA complexes. (A) Amino acid propensities for DNA base interaction in HS (red), MS (green) and NS (blue) groups; (B) Percentage of major (red) and minor groove (cyan) contacts.

Figure 3

Aspartate forms one bidentate hydrogen bond with two consecutive cytosine bases and one single hydrogen bond with a distant cytosine, via the major groove, in endonuclease NgoMIV (PDB ID: 4abt).

Figure 4

Comparison of protein-DNA interactions. (A) Protein-DNA contact area (PDCA); (B) number of residue-base contacts (NRBC); and (C) NRBC density, NRBC normalized to the total contact area (PDCA). ***p<0.001; **p<0.01; *p<0.05.

Figure 5

Comparison of DNA base/backbone and major/minor groove contacts. (A) Percentage of DNA backbone-only and DNA base contacts; (B) percentage of major and minor groove contacts; (C) number of major groove contacts; and (D) number of minor groove contacts. ***p<0.001; **p<0.01; *p<0.05.

Figure 6

Hydrogen bonds between proteins and DNA. (A) Number of hydrogen bonds between protein side-chains and DNA (PDHB); (B) number of hydrogen bonds between protein side-chains and DNA bases (PBHB); and (C) number of residues that form bidentate hydrogen bonds. ***p<0.001; **p<0.01; *p<0.05.

Figure 7

Comparison of DNA shape features. Median (A) propeller, (B) opening, (C) rise, and (D) roll per structure. The shape features are calculated using 3DNA . ***p<0.001; ** p<0.01; * p<0.05.

Figure 8

Conformational changes upon DNA-binding. C_α RMSD between the bound and unbound structures in the pairNR30 dataset using (A) all residues and (B) binding residues only. Median Δχ₁ (C) and MAD Δχ₁ (D) per domain. *** p<0.001; ** p<0.01; * p<0.05.

Figure 9

Comparison of structural variations in the multiHolo dataset for median RMSD (A) and MAD RMSD (B); in the multiApo dataset for median RMSD (C) and MAD RMSD (D); in the multiApoHolo dataset for median RMSD (E) and MAD RMSD (F). ***p<0.001; ** p<0.01; * p<0.05.