  Homeodomain containing proteins are a broad class of DNA binding proteins
that are believed to primarily function as transcription factors.
Electrostatics interactions have been demonstrated to be critical for the
binding of the homeodomain to DNA. An examination of the electrostatic state of
homeodomain residues involved in DNA phosphate binding has demonstrated the
conserved presence of upward shifted pKa values among the basic residue of
lysine and arginine. It is believed that these pKa perturbations work to
facilitate binding to DNA since they ensure that the basic residues always
retain a positive charge.
