PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Drug Discovery: Solving the Structure of an Anti-hypertension Drug Target
July 2015
Retrospective: 7,000 Structures Closer to Understanding Biology
July 2015
Design and Evolution: Bespoke Design of Repeat Proteins
June 2015
Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity
June 2015
Design and Evolution: Tunable Antibody Binders
June 2015
Design and Evolution: Unveiling Translocator Proteins
June 2015
Evolution of Photoconversion
June 2015
Families in Gene Neighborhoods
June 2015
Protein Folding and Misfolding: A TRiC-ster that Follows the Rules
March 2015
Protein Folding and Misfolding: Beneficial Aggregation
March 2015
Peptidyl-carrier Proteins
October 2014
Predicting Protein Crystal Candidates
October 2014
Protein and Peptide Synthesis: Coming Full Circle
October 2014
Protein and Peptide Synthesis: Sensing Energy Balance
October 2014
Mining Protein Dynamics
May 2014
Novel Proteins and Networks: Assigning Function
May 2014
Novel Proteins and Networks: Polysaccharide Metabolism in the Human Gut
May 2014
Design and Discovery: Evolutionary Dynamics
January 2014
Design and Discovery: Identifying New Enzymes and Metabolic Pathways
January 2014
Design and Discovery: Virtual Drug Screening
January 2014
Caught in the Act
December 2013
Microbiome: Insights into Secondary Bile Acid Synthesis
September 2013
Microbiome: Structures from Lactic Acid Bacteria
September 2013
The Immune System: A Brotherhood of Immunoglobulins
June 2013
The Immune System: Super Cytokines
June 2013
Design and Discovery: A Cocktail for Proteins Without ID
February 2013
Design and Discovery: Enzyme Reprogramming
February 2013
Design and Discovery: Extreme Red Shift
February 2013
Design and Discovery: Flexible Backbone Protein Redesign
February 2013
Designer Proteins
February 2013
Membrane Proteome: Sphingolipid Synthesis Selectivity
December 2012
Symmetry from Asymmetry
October 2012
Serum albumin diversity
August 2012
Pocket changes
July 2012
Predictive protein origami
July 2012
Targeting Enzyme Function with Structural Genomics
July 2012
Finding function for enolases
June 2012
Substrate specificity sleuths
April 2012
Disordered Proteins
February 2012
Metal mates
February 2012
Making invisible proteins visible
October 2011
Alpha/Beta Barrels
October 2010
Deducing function from small structural clues
February 2010
Extremely salty
February 2010
Membrane proteins spotted in their native habitat
January 2010
How does Dali work?
December 2009
Secretagogin
December 2009
Designing activity
September 2008

Research Themes Protein design

The Immune System: Super Cytokines

SBKB [doi:10.1038/sbkb.2012.146]
Technical Highlight - June 2013
Short description: Crystal structures of cytokine receptor complexes pinpoint target regions to create 'superkines' with altered cell specificity.

The main receptor binding sites on the D-helices of IL-4 (left) and IL-13 (right). Left, positions randomized in IL-4 site 2 are shown. Right, IL-13 D-helix (purple) is superimposed to that of IL-4 (green); substituted residues are in red. 1

Cytokines orchestrate wide-ranging signaling cascades in cells. Cytokine receptor activation is initiated by interaction with one receptor chain followed by a second. The second interaction is of much lower affinity, so its manipulation is considered promising for potential therapeutic applications; this is the interaction Garcia and colleagues targeted in their study of interleukin-4 (IL-4). IL-4 first binds the receptor IL-4Rα with high affinity; a subsequent interaction with either γc or IL-13Rα1 results in, respectively, type I and type II ternary complexes. Secondary cytokine receptors are expressed at different levels in various cells, thus enabling cell-type specific signaling.

Recently solved crystal structures reveal how γc and IL-13Rα1 bind IL-4. To alter affinity to type II receptors, the authors compared structures of IL-4 and IL-13 bound to IL-13Rα1, which led them to engineer a high-affinity version of IL-4 by substituting three residues from the native high-affinity binder IL-13. With no such information for the type I receptor, the researchers used in vivo evolution. These respective approaches resulted in the development of high-affinity triple mutant 'superkines' KFR and RGA.

In vitro, as measured by surface plasmon resonance (SPR), binding affinity of KFR–IL-4Rα for the type II receptor IL-13Rα1 was 440-fold greater than that of wild-type IL-4–IL-4Rα, and for the type I receptor γc, about twofold lower. In contrast, binding affinity of RGA–IL-4Rα for its destined receptor γc was 3,700-fold greater than that of wild-type cytokine complex, also with a decrease in affinity to IL-13Rα1. Structural analysis of the RGA–γc interface (PDB 3QB7) pinpointed changes responsible for the affinity increase.

This binding specificity was preserved in vivo, in cells that naturally express different amounts of type I and type II receptors. The differences, however, were not as dramatic as those observed by SPR, which the authors attribute to differences in diffusion rates when one of the components is soluble in the latter setup, or to co-localization of receptors in vivo. Nevertheless, this proof-of-principle work suggests the possibility of engineering, for therapeutic applications, superkines with high affinities to target receptors and those with minimal affinity to other receptors, thus limiting side effects.

Irene Kaganman

References

  1. I.S. Junttila et al. Redirecting cell-type specific cytokine responses with engineered interleukin-4 superkines.
    Nat. Chem. Biol. 8, 990-998 (2012). doi:10.1038/nchembio.1096

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health