PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Cas4 Nuclease and Bacterial Immunity
February 2014
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Stabilizing DNA Single Strands
July 2013
AlkB Homologs
August 2012
Methyl maintenance
May 2012
Follow the RNA leader
December 2011
RNA Chaperone NMB1681
July 2011
Seeing HetR
July 2011
Structure from sequence
July 2011
Added benefits
April 2011
Nitrile Reductase QueF
March 2011
Inhibiting factor
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
tRNA Isopentenyltransferase MiaA
August 2010
Mre11 Nuclease
May 2010
Seek and destroy 8-oxoguanine
May 2010
Antibiotics and Ribosome Function
March 2010
Pseudouridine Synthase TruA
November 2009
Get3 into the groove
October 2009
Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1
October 2009
Proofreading RNA
July 2009
Hda and DNA Replication
June 2009
The elusive helicase
April 2009
Poly(A) RNA recognition
January 2009
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
RNase T
July 2008
SARS Coronavirus Nonstructural Protein 1
June 2008

Research Themes DNA and RNA

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

References

  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