Transcription factor NF-κB is modulated by symbiotic status in a sea anemone model of cnidarian bleaching.

Transcription factor NF-κB plays a central role in immunity from fruit flies to humans, and NF-κB activity is altered in many human diseases. To investigate a role for NF-κB in immunity and disease on a broader evolutionary scale we have characterized NF-κB in a sea anemone (Exaiptasia pallida; called Aiptasia herein) model for cnidarian symbiosis and dysbiosis (i.e.

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

Predicting the binding specificity of transcription factors is a critical step in the characterization and computational identification and of cis-regulatory elements in genomic sequences. Here we use protein-DNA structures to predict binding specificity and consider the possibility of predicting position weight matrices (PWM) for an entire protein family based on the structures of just a few family members. A particular focus is the sensitivity of prediction accuracy to the docking geometry of the structure used.

Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.

A new method is introduced to structurally align interfaces observed in protein--DNA complexes. The method is based on a procedure that describes the interfacial geometry in terms of the spatial relationships between individual amino acid--nucleotide pairs. An amino acid--amino acid similarity matrix, S, is defined that provides a quantitative measure of the geometric relationships of amino acids in different interfaces and the entire stretch of "local" DNA within some distance of each amino acid.