Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding

Abstract

SUMMARY The Gastrulation Brain Homeobox 1 (Gbx1) gene encodes the Gbx1 homeodomain that targets TAATTA motifs in dsDNA. Residues Glu17 and Arg52 in Gbx1 form a salt bridge, which is preserved in crystal structures and MD simulations of homologous homeodomain–DNA complexes. In contrast, our NMR studies show that DNA-binding to Gbx1 induces dynamic local polymorphisms, which include breaking of the Glu17–Arg52 salt bridge. To study this interaction, we produced a variant with Glu17Arg and Arg52Glu mutations, which exhibited the same fold as the wild-type protein, but a two-fold reduction in affinity for dsDNA. Analysis of the NMR structures of the Gbx1 homeodomain in the free form, the Gbx1[E17R,R52E] variant, and a Gbx1 homeodomain–DNA complex showed that stabilizing interactions of the Arg52 side chain with the DNA backbone are facilitated by transient breakage of the Glu17–Arg52 salt bridge in the DNA-bound Gbx1.

The ancestry of Antennapedia-like homeobox genes

“…In the case of loss of proline, Fersht and co-workers have argued that the conformational flexibility of the network of residue interactions centred around L26 is important for induced fit interactions with DNA [56]. Salt bridge polarity can have subtle but unpredictable effects on function - in GBX, inverting the polarity of the 17,52 salt bridge causes a loss of DNA binding affinity through transient molecular interactions [57]. At a similarly subtle level, it is not clear how the precise nature of homeodomain residue 28 affects the biological roles of different ANTP-like homeodomains - and yet the evidence discussed above suggests that it does.…”

Transcriptome and open chromatin analysis reveals the process of myocardial cell development and key pathogenic target proteins in Long QT syndrome type 7

“…MIXL1 is expressed in the early differentiation of human PSCs toward cardiac mesodermal derivatives [ 52 ]. GBX1 is involved in the development of neurons in the dorsal and ventral spinal cord during embryogenesis [ 53 ], and DLX5 is involved in brain development [ 38 ]. High HOXB4 expression can enhance the differentiation of embryonic stem cells [ 54 ], and HOXB4 is an effective differentiation-promoting transcriptional regulator [ 55 ].…”