Structural requirements for DNA binding of GCM proteins

Structural requirements for DNA binding of GCM proteins.

Members of the GCM family of transcription factors contain a DNA binding domain unrelated to any other known DNA binding domain and bind to a DNA sequence motif not recognized by any other known transcription factor. Here we show that positions 2, 3, 6 and 7 of the 5'-ATGCGGGT-3' motif are particularly important for DNA binding and that methylation of several G residues on the upper strand, but...

Structural and thermodynamic strategies for site-specific DNA binding proteins.

BACKGROUND Site-specific protein-DNA complexes vary greatly in structural properties and in the thermodynamic strategy for achieving an appropriate binding free energy. A better understanding of the structural and energetic engineering principles might lead to rational methods for modification or design of such proteins. RESULTS A novel analysis of ten site-specific protein-DNA complexes reve...

Prediction of DNA-Binding Proteins from Structural Features

We use logic-based machine learning to distinguish DNAbinding proteins from non-binding proteins. We combine previously suggested coarse-grained features (such as the dipole moment) with automatically constructed structural (spatial) features. Prediction based only on structural features already improves on the state-of-the-art predictive accuracies achieved in previous work with coarse-grained...

Using structural motifs to identify proteins with DNA binding function

This work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix±turn±helix (HTH) motifs comprise a signi®cant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were...

Structural Requirements for Adenovirus DNA Replication