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3.1 Papers
Section Intro | Molecular modeling | Bioinformatics | docking | Methods and algorithms | Applications | Chronological list

3.1.6 Chronological list
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3.1.6.26 Gibson, T.J., Thompson, J.D. and Abagyan, R.A (1993). Proposed structure for the DNA-binding Domain of the Helix-Loop-Helix family of eucaryotic gene regulatory proteins. Protein Engineering, 6, 41-50

A modelled tertiary structure for the dimeric HLH domain of the E47 protein is presented. Structural information was obtained from the aligned sequences of>40 members of the HLH family. The information was used to model each monomer as an alpha-helical hairpin, with knobs-into-holes packing of side-chains as found in antiparallel coiled-coil. The dimer forms a four-helix bundle with additional knobs-into-holes packing at the dimer interface. The size and electrostatic properties of core-forming residues are all accounted for in the model. The model does not violate any known properties of protein structure. The monomers are related by two-fold rotational symmetry, in agreement with the observed DNA-binding sites which are imperfect inverted repeats. The N-terminal basic region, in which DNA binding and base specificity reside, forms the first part of helix 1. A prediction based on the model structure is that the HLH domains do not bind to DNA in its B form but require a partially unwound conformation in order to enter the major groove.