Engineering allosteric transcription factors guided by the LacI topology

Hersey, Ashley N; Kay, Valerie E; Lee, Siow Ming; Park, Jongwoo; Wilson, Clive

doi:10.1016/j.cels.2023.04.008

Cited by 7 publications

(6 citation statements)

References 49 publications

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“…This realization offers insights into how distal mutations might affect inhibitor potency in the context of drug resistance development . Moreover, it also highlights additional flexibility in the strategies that can be used to fine-tune the various properties relevant to the allostery function, including effector specificity …”

Section: Discussionmentioning

confidence: 99%

“…6 Moreover, it also highlights additional flexibility in the strategies that can be used to finetune the various properties relevant to the allostery function, including effector specificity. 44 ■ CONCLUSIONS For many biomedical and biotechnological applications, modulating allosteric coupling offers unique opportunities. Such efforts can largely benefit from the efficient prediction and evaluation of allostery hotspot residues that dictate the degree of cooperativity between distant sites.…”

Section: Doubly Bound States Are Better Stabilized Inmentioning

confidence: 99%

“…43 This feature makes allostery highly adaptable during evolution and ensures robustness of functionally essential cooperativities; 37 it can also facilitate rewiring of allostery communication pathways in engineering applications. 12,44 Nevertheless, these compensatory effects have major implications to the design of allosteric inhibitors, as the effect of design might be easily abolished by additional mutations. 4,6 Therefore, robust designs should target allostery communications that, once disrupted, are difficult to restore.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Another feature that is commonly observed in allosteric systems is the network of compensatory interactions, which leads to near-degenerate allosteric communication pathways . This feature makes allostery highly adaptable during evolution and ensures robustness of functionally essential cooperativities; it can also facilitate rewiring of allostery communication pathways in engineering applications. , Nevertheless, these compensatory effects have major implications to the design of allosteric inhibitors, as the effect of design might be easily abolished by additional mutations. , Therefore, robust designs should target allostery communications that, once disrupted, are difficult to restore. Such properties are costly to evaluate using experiments due to the need for sampling a large number of sequences.…”

Section: Introductionmentioning

confidence: 99%

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Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR

Deng,

Yuan,

Cui

2024

J. Am. Chem. Soc.

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Modulating allosteric coupling offers unique opportunities for biomedical applications. Such efforts can benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of cooperativity between distant sites. We demonstrate that effects of allostery hotspot mutations can be evaluated qualitatively and semiquantitatively by molecular dynamics simulations in a bacterial tetracycline repressor (TetR). The simulations recapitulate the effects of these mutations on abolishing the induction function of TetR and provide a rationale for the different rescuabilities observed to restore allosteric coupling of the hotspot mutations. We demonstrate that the same noninducible phenotype could be the result of perturbations in distinct structural and energetic properties of TetR. Our work underscores the value of explicitly computing the functional free energy landscapes to effectively evaluate and rank hotspot mutations despite the prevalence of compensatory interactions and therefore provides quantitative guidance to allostery modulation for therapeutic and engineering applications.

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Section: Discussionmentioning

confidence: 99%

Section: Doubly Bound States Are Better Stabilized Inmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR

Deng,

Yuan,

Cui

2024

J. Am. Chem. Soc.

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“…43 This feature makes allostery highly adaptable during evolution and ensures robustness of functionally essential co-operativities; 37 it can also facilitate re-wiring of allostery communication pathways in engineering applications. 12,44 Nevertheless, these compensatory effects have major implications to the design of allosteric inhibitors, as the effect of design might be easily abolished by additional mutations. 4,6 Therefore, robust designs should target allostery communications that, once disrupted, are difficult to restore.…”

Section: Introductionmentioning

confidence: 99%

Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR

Deng,

Yuan,

Cui

2023

Preprint

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For many biomedical and biotechnological applications, modulating allosteric coupling offers unique opportunities. Such efforts can largely benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of co-operativity between distant sites. In several hotspot mutants revealed by recent deep mutational scanning (DMS) experiments of a bacterial transcription factor, tetracycline repressor (TetR), we demonstrate that effects of allostery hotspot mutations can be evaluated by judiciously combining extensive unbiased and enhanced sampling molecular dynamics simulations. The results recapitulate the qualitative effects of these mutations on abolishing the induction function of TetR and provide a semi-quantitative rationale for the different degrees of rescuability to restore allosteric coupling of the hotspot mutations observed in the DMS analysis. Free energy landscapes and variations of structural and energetic properties of different functional states of the mutants show that the hotspot mutations perturb inter-domain coupling and/or intra-domain conformational properties relative to the wild type. Several mutations clearly perturb multiple properties, also highlighting the complexity of realistic situations. Thus, the results support our mechanistic model that hotspot residues contribute to allostery through distinct molecular mechanisms, a feature that we propose to be broadly applicable to many allosteric systems. Overall, our study provides general computational strategies for the identification and evaluation of hotspot mutations modulating allostery in proteins.

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