Bioinformatic analysis of the protein/DNA interface

Abstract

To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271–287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690–3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into ‘interaction matrices’ revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.

Local dynamics of proteins and DNA evaluated from crystallographic B-factors

“…This observation is perhaps surprising considering the fact that it was drawn from the structures in the highresolution bin R1, which have the highest ratio between the experimental data (structure factors) and refined parameters (coordinates and B factors) and thus provide the best estimate of the inherent dynamic properties of molecules. The relatively low flexibility of the bridge waters, comparable to that of DNA bases, stresses their importance in protein-DNA recognition and is in agreement with our earlier observation that protein-DNA interfaces formed by direct amino acidnucleotide contacts or via water bridges have similar structural features (Schneider et al, 2014).…”

“…The data set was curated as described in detail previously (Schneider et al, 2014). The original nonredundant data set contained 1018 complexes with crystallographic resolution better than 3.3 Å .…”

“…In our previous work (Schneider et al, 2014), we sorted protein-DNA complexes into various functional groups, and some of the groups contained enough structures in the three resolution bins to be analyzed separately. Of these, the B-factor distributions for DNA complexes of transcription factors and nucleases are shown in Supplementary Figs.…”

“…To determine whether and to what extent they can be used as a realistic gauge of the local molecular dynamics at the subnanometre scale, we decided to analyze their distributions in over 700 crystal structures of protein-DNA complexes selected from a larger well curated data set previously used for the analysis of the structural properties of protein-DNA complexes (Schneider et al, 2014). We were primarily interested in comparing the flexibility of residues of these key biomolecules in different types of molecular environment: exposed to solvent or surrounded by residues from the same or neighbouring biomolecules; we also wanted to juxtapose the flexibility of biopolymer residues and supposedly the least restricted molecules, waters.…”

“…The local molecular dynamics concealed in diffraction images is expressed as socalled B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein-DNA crystal structures were analyzed [Schneider et al (2014), Nucleic Acids Res. 42,[3381][3382][3383][3384][3385][3386][3387][3388][3389][3390][3391][3392][3393][3394].…”