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

Design and Evolution: Molecular Sleuthing Reveals Drug Selectivity

SBKB [doi:10.1038/sbkb.2015.17]
Featured Article - June 2015
Short description: Reconstructed ancient ancestors of Src and Abl shed light on Gleevec's specificity.


Structures of Gleevec bound to Src (PDB 2OIQ), the ancestral kinase ANC-AS (PDB 4CSV), and Abl (PDB 1OPJ) show how only the P-loop in Abl can lock down the drug. Figure from ref. 1 , reprinted with permission from AAAS.

Kinases have a strongly conserved catalytic domain structure, yet the cancer drug Gleevec shows high selectivity towards Abl kinase, with 103-lower affinity for closely related kinases such as Src. It has been proposed that Gleevec binding induces a global conformational change that differs between Abl and Src, but both modeling- and domain-swapping experiments have failed to identify the basis of specificity.

As protein function reflects not only its sequence and structure but also its energy landscape, Kern and colleagues decided to take an orthogonal approach. Reasoning that both Abl and Src kinases share a common ancestor, they postulated that not just specific residues, but also the surrounding amino acids would be important in sculpting the distinct energy landscapes of the kinases during evolution. They therefore used a Bayesian phylogenetic approach to design four potential ancestral proteins of Abl and Src. These proteins were constructed and shown to have intermediate Gleevec-binding affinities. Overall, the kinetic scheme of the ancestral proteins is the same as that of modern kinases, but the conformational steps (i.e. kinetic parameters) are altered in concert with the affinity changes. This reflects a progressive shift in conformational equilibrium between two bound states; differences in this dynamic process of the kinase/drug complex, but not binding/dissociation rates, are primarily responsible for selectivity.

Structural analysis of the last common ancestor, ANC-AS, helped identify globally distributed amino acid changes responsible for selectivity. In particular, modifying 15 amino acids in the N-terminal domain of ANC-AS (to generate ANC-AS(+15)) increased the Gleevec affinity to equal that of Abl; those amino acid residues underlie most of the change in the equilibrium towards Abl's inhibitor-bound, induced-fit state. Mapping those 15 amino acid changes onto the crystal structure of ANC-AS emphasizes why the basis of selectivity had been so difficult to determine: many of the 15 residues are removed from the binding pocket and form a hydrogen bond network in ANC-AS that cannot occur in ANC-AS(+15) or Abl. The authors speculated that in the absence of this network, the conserved P-loop has mobility and can close over the drug, whereas with the network, the P-loop is stabilized in a different conformation. The concept that the P-loop may be involved in discrimination was previously tested in domain-swapping experiments, but those experiments did not include these 15 residues that were identified from the ancestral reconstruction.

In conclusion, this study illustrates not only the important role that evolutionary reconstruction can offer in identifying key elements that allow for atomistic discrimination of ligands, but also indicates that energy landscapes are a driving force in evolution.

Angela K. Eggleston

References

  1. C. Wilson et al. Using ancient protein kinases to unravel a modern cancer drug's mechanism.
    Science. 347, 882-6 (2015). doi:10.1126/science.aaa1823

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