Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB

Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β-barrel with a unique topology. At the top of the barrel, four loops connect the eight β-strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand-binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.

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Modulation of HIF-2 Function with Small Molecules: Did Nature Beat Us to It?

Blood ◽

10.1182/blood.v118.21.sci-39.sci-39 ◽

2011 ◽

Vol 118 (21) ◽

pp. SCI-39-SCI-39

Author(s):

Richard K. Bruick ◽

Kevin H Gardner ◽

John MacMillan ◽

Uttam Tambar

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Conformational Changes ◽

Conflicts Of Interest ◽

Single Agent ◽

Amino Acid Identity ◽

Ligand Binding Site ◽

Low Oxygen ◽

High Amino Acid

Abstract Abstract SCI-39 Hypoxia inducible factors (HIFs) govern a mammalian cellular hypoxic response, regulating the transcription of hundreds of genes in response to low oxygen levels. Though this pathway performs critical functions under physiological conditions, increased levels of HIFs are also highly correlated with several disease states. As such, the development of artificial compounds that directly and selectively regulate HIF function is of interest. We have used a combination of biophysical, biochemical, and chemical approaches to study the structure and function of the Per-ARNT-Sim (PAS) domains of human HIFs, which serve as critical protein/protein interaction modules in assembling the functional HIF heterodimer. These studies have revealed the presence of a putative ligand-binding site within one of the HIF-2α PAS domains. A series of biased and unbiased approaches were undertaken to identify compounds that bind at this site and trigger conformational changes within the domain, leading to dissociation of the HIF-2 heterodimer in vitro and in living cells. Consequently, the expression of many hypoxia-inducible genes can be coordinately downregulated by a single agent. Despite its high amino acid identity, HIF-1α lacks a comparable ligand-binding site, indicating that these agents will be useful in deciphering differences in the biological roles of the HIF-1 and HIF-2 isoforms. The presence of a preformed cavity within HIF-2α is particularly as exciting as it suggests the potential for direct physiological regulation of HIF-2 by endogenous metabolite(s). Together, these studies offer further insight into HIF function and regulation while providing chemical tools that advance therapeutic applications. Disclosures: No relevant conflicts of interest to declare.

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