G. Michel et al., A model for the complex between the hypoxia-inducible factor-1 (HIF-1) andits consensus DNA sequence, J BIO STRUC, 18(2), 2000, pp. 169-179
Hypoxia-inducible factor-1 (HIF-1) is a heterodimeric transcription factor
activated by hypoxia. When activated, HIF-1 mediates the differential expre
ssion of genes such as erythropoietin and Vascular Endothelial Growth Facto
r (VEGF) during hypoxia. It is composed of two different subunits, HIF-1 al
pha and ARNT (Aryl Receptor Nuclear Translocator). These two subunits belon
g to the bHLH (basic Helix-Loop-Helix) PAS (Per, Ahr/ARNT, Sim) family. The
bHLH domain of these factors is responsible for dimerization through the t
wo helices and for DNA binding through their basic domain.
In this work, we used various methods of molecular modeling in order to dev
elop a 3D structure for the HIF-1 bHLH domain bound to its DNA consensus se
quence. Firstly, the 3D structure of the bHLH domain of both subunits based
on their amino acid sequence was defined. Secondly, we compared this model
with data from known crystal structures of basic leucine zipper-DNA and bH
LH-DNA complexes in order to determine a potential canvas for HIF-1. Thirdl
y, we performed a manual approach of the HF-1 bHLH domain onto the DNA reco
gnition site using this canvas. Finally, the protein-DNA complex 3D structu
re was optimized using a Monte Carlo program called MONTY.
The model predicted a pattern of interactions between amino acids and DNA b
ases which reflect for ARNT what is experimentally observed among different
X-ray structures of other bHLH transcription factors possessing the H (His
), E (Glu), R (Arg) triad, as ARNT does. On the other hand, only the Arg re
sidue is conserved in HIF-1 alpha. We propose from this model that a serine
replaces the histidine while an alanine and a lysine also make contacts wi
th DNA. From these results, we postulate that the specificity of HIF-1 towa
rd its DNA sequence could be driven by the HIF-1 alpha subunit. The predict
ed model will be verified by X-Ray currently ongoing.