Molecular Research Suggest Shift Needed In How Some Drugs Are Created

Reportingin the Oct. 1 issue of the Journal of Immunology, researchers at theUniversity of Illinois at Urbana-Champaign unveiled the crystalstructure of mouse interleukin-1 receptor-associated kinase-4 (IRAK-4).

Theyfound a distinct highly structured loop between two helices that isremarkably different from that found in Pelle, an IRAK-4-like“death-domain” protein from Drosophila melanogaster that was determinednearly a decade ago. The death domain is so-named because of aresemblance to proteins that are involved in programmed cell death.

“Ithas been thought in the field that a death domain is a death domain,and molecular recognition takes place in the same fashion,” said leadauthor Michael V. Lasker, an M.D./Ph.D. student in the College ofMedicine at Urbana-Champaign. “But the crystal structure of our deathdomain clearly shows that indeed this is not the case.”

Thecrystal structure of IRAK-4, as was the case for Pelle, was determinedby X-ray crystallography. Using this technique, X-rays are directedinto molecules of IRAK-4 that have been coaxed to form crystals. Thediffraction data from the experiments allow the structure to bevisualized down to angstrom-level resolution (one hundred-millionth ofa centimeter). The structure of IRAK-4 was determined to a resolutionof 1.7 angstroms.

The molecules in question are part of innateimmune systems – an inherent immune response coded by DNA in all livingthings – that are crucial for survival against pathogens such asbacteria and fungi. Deficiencies in the system or an over-activeresponse can set the stage for various infections, septic shock andnumerous autoimmune disorders.

Since researchers at theUniversity of Texas Southwestern in Dallas and the Howard HughesMedical Institute reported the structure of Pelle bound to the adaptermolecule known as Tube, there has been an effort to target the similarIRAK-4 molecule in mammals, said Satish K. Nair, a U. of I. professorof biochemistry.

The Pelle-Tube complex plays a crucial role inthe innate immune response of fruit flies to fungal infection. IRAK-4plays a similar role in humans and animals.

The hope is thatdrugs can be developed to target the molecule-binding pathway, whichwould be beneficial for treating arthritis and reducing inflammation,said Nair, who also is a researcher in the Center for Biophysics andComputational Biology at Illinois. Signaling in the pathway usesprotein molecules that contain death-domains.

“What our structuretells us is that the particular arrangement that was seen in thestructure that was solved by the researchers at Dallas Southwesterncannot possibly exist in humans, because of bad steric interactionsthat preclude the formation of this particular complex,” Nair said.

Stericinteractions refer to contacts that result when two protein moleculesbind with each other. Bad interactions mean that the proteins cannotline up and connect properly. A tight connection is necessary totrigger an immune response.

A mammalian counterpart forDrosophila’s Tube molecule has not been found, but Lasker and Nairtheorize that adaptors that bind IRAK-4 will either bind at a differentsite, or the adapter molecule will have an interface that can handleIRAK-4’s larger loop.

Researchers in Nair’s lab already are looking at the complex’s structure in humans.

MarkM. Gajjar, an undergraduate student who now works in the department ofbiochemistry and molecular biology at the University of Chicago, alsowas a co-author.

The research was supported through start-upfunds to Nair from the Institute for Genomic Biology at Illinois.Lasker was funded by a National Institutes of Health National ResearchService Award from the NIH Institute of Neurological Disorders andStroke.