PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Automating NMR Structures
April 2015
Protein Folding and Misfolding: A TRiC-ster that Follows the Rules
March 2015
Virology: Making Sensitive Magic
March 2014
Microbiome: Solid-State NMR, Crystallized
September 2013
Membrane Proteome: Making DNA Nanotubes for NMR Structure Determination
August 2013
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Cell-Cell Interaction: Magic Structure from Microcrystals
March 2013
Membrane Proteome: Soft Sampling
December 2012
Membrane Proteome: Specific vs. Non-specific weak interactions
November 2012
Automatic NMR
September 2012
NMR structure test
September 2012
To structure, faster
August 2012
S is for solubility
June 2012
Blind faith
April 2012
Follow the RNA leader
December 2011
Making invisible proteins visible
October 2011
A fragmented approach to membrane protein structures
September 2011
Molecular replacement by magnetic resonance
August 2011
Solutions in the solution
June 2011
No more labeled lipids
May 2011
Capsid assembly in motion
April 2011
NMR challenges current protein hydration dogma
March 2011
Solving homodimeric structures with NMR
November 2010
CASD-NMR: assessing automated structure determination by NMR
June 2010
Peptidoglycan binding: Calcium-free killing
June 2010
Removing the NMR bottleneck
April 2010
NMR has its wiki way
March 2010
Extremely salty
February 2010
The future of NMR
September 2009
Tips for crystallizing membrane proteins
June 2009
Faster solid-state NMR
May 2009
Powerful NMR
April 2009
Activating BAX
December 2008

Protein-Nucleic Acid Interaction: Inhibition Through Allostery

SBKB [doi:10.1038/sbkb.2012.151]
Technical Highlight - July 2013
Short description: NMR studies highlight the importance of investigating transitional species to fully understand protein function.

Energy landscape of mutant CAP showing the two states, inactive (I) and active (A), and their fractional populations. DNA binding selects the active conformation in a population shift mechanism. 1

Small molecule inhibitors often compete directly with native enzyme substrates or binding partners. However, because these sites are frequently conserved among similar proteins, allosteric inhibitors, which exert their activity by binding at a site distal to the active or partner interaction site, may offer increased specificity.

Kalodimos and Tzeng investigated the mechanism behind the allosteric inhibition of catabolite activator protein (CAP) by cyclic guanosine monophosphate (cGMP). Normally, the binding of cyclic adenosine monophosphate (cAMP) to the cyclic nucleotide-binding domain (CBD) of CAP induces an allosteric change in the DNA-binding domain (DBD) and promotes DNA binding. The authors used a previously identified mutant of CAP in which the ability of the DBD to bind to DNA is reduced upon binding of cGMP to the CBD. NMR analyses did not reveal major structural differences between the wild-type and mutant CAP DBDs, indicating that both should adopt the inactive conformation. However, the mutant CAP DBD was able to bind DNA, whereas the wild-type DBD was not.

Speculating that the mutant DBD may be able to transiently adopt an active conformation not accessible to the wild-type species, the authors used an NMR technique called relaxation dispersion, which can provide information on lowly populated species. In fact, NMR is unique in that it can provide information on both the ground state, or most populated species, as well as higher-energy intermediate states that are transient and less populated. It is these higher-energy states that are often responsible for protein activity.

The relaxation dispersion results revealed a transient intermediate state in the mutant CAP that was not detected in the wild-type protein. While this transient state is a minor species, accounting for 7% of the total protein population, it is the conformation that is able to bind DNA.

While binding of cGMP did not alter the structure of the DBD, it did prevent the formation of the intermediate state in the mutant CAP. Further structural analysis of the mutant CAP revealed that the mutation promotes a coil-to-helix transition, which is disrupted upon cGMP binding. These results demonstrate the utility of investigating lowly populated, transitional species to better understand, and perhaps better manipulate, protein function.

Jennifer Cable


  1. S.-R. Tzeng and C.G. Kalodimos. Allosteric inhibition through suppression of transient conformational states.
    Nat Chem Bio. (5 May 2013). doi:10.1038/nchembio.1250

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