Question

“Lactose repressor protein (LacI) utilizes an allosteric mechanism to regulate transcription in E. coli, and the transition between inducer- and operator-bound states has been simulated by targeted molecular dynamics (TMD). The side chains of amino acids 149 and 193 interact and were predicted by TMD simulation to play a critical role in the early stages of the LacI conformational change. D149 contacts IPTG directly, and variations at this site provide the opportunity to dissect its role in inducer binding and signal transduction. Single mutants at D149 or S193 exhibit minimal change in operator binding, and alterations in inducer binding parallel changes in operator release, indicating normal allosteric response. The observation that the double mutant D149A/S193A exhibits wild-type properties excludes the requirement for inter-residue hydrogen bond formation in the allosteric response. The double mutant D149C/S193C purified from cell extracts shows decreased sensitivity to inducer binding, while retaining wild-type binding affinities and kinetic constants for both operator and inducer. By manipulating cysteine oxidation, we show that the more reduced state of D149C/ S193C responds to inducer more similarly to wild-type protein, whereas the more oxidized state displays diminished inducer sensitivity. These features of D149C/S193C indicate that the novel disulfide bond formed in this mutant impedes the allosteric transition, consistent with the role of this

region predicted by TMD simulation. Together, these results establish the requirement for flexibility of spatial relationship between D149 and S193 rather than a specific D149-S193 interaction in the LacI allosteric response to inducer.” Biochemistry 48:4988.

(4 points) What is allosteric regulation?

(4 points) How does the lactose repressor protein (LacI) use an allosteric mechanism to regulate transcription?

(6 points) How do the side chains of amino acids 149 and 193, of the lactose repressor protein, play a role in the LacI conformational change.

(6 points) What would you predict would happen if either amino acid 149 or 193 were mutated?

Answer 1

What is allosteric regulation?

Regulation of enzyme activity or metabolic pathway by binding of effector molecule at a site other than the active site of enzyme or protein is known as allosteric regulation and the effector binding site knowns as the allosteric site. Generally, it is present in multi-subunit proteins. The binding of the effector molecule to the allosteric site leads to the conformation change and that enhances the binding of the effector molecule to the other subunits leads to allosteric regulation.

How does the lactose repressor protein (LacI) use an allosteric mechanism to regulate transcription?

The binding of two molecules lactose/allolactose/IPTG to its Lac repressor (tetramer) at allosteric site in regulatory domain leads conformational change in DNA binding domain (N-helix-turn-helix) the leads to loss of affinity towards the operator region of DNA and slowly repressor will be removed from the DNA leads to activation of transcription (means the RNA polymerase can further move towards the structural genes and able to synthesize the functional mRNA.

How do the side chains of amino acids 149 and 193, of the lactose repressor protein, play a role in the LacI conformational change.

These two amino acids located near to induced binding site nothing but the allosteric site (IPTC or allolactose binding site). The binding of IPTG to the allosteric site leads to the shift of side chains at D149 (4 Aº) and S193 and movement of the backbone of D149 when the IPTC present (the bound state). The D149 act as a flexible loop (from 149 to 156 and D149) and involved in the formation of two hydrogen bonds to the S193 side chain in each monomer. The author suggests that the D149 and S193 might be participants in determining the distinct conformational states of the repressor.

What would you predict would happen if either amino acid 149 or 193 were mutated?

The mutational studies indicate that the substitutions with N, S, and A at residue D149 decreased IPTG binding affinity only slightly. The data in the paper suggest that substitutions at residue 149 do not significantly impact LacI allostery and even if the inducer binding affinity is affected.

And similar with S193 mutant as stated that minimal effect on LacI binding properties like alter both inducer binding affinity and operator release but there is no change in allosteric transition and the double mutant D149C/S193C has operator binding affinity comparable to wild-type LacI in the absence of IPTG and whereas in the presence of 1 mM IPTG, this mutant still binds to operator means it has decreased sensitivity to inducer binding.