Analysis of Allostery in a Transcription Factor Using Molecular Simulations and Machine Learning 

 Abstract:                                                                                      

While allostery has been a topic of intense interest for the past several decades, our understanding of the underlying mechanism at the molecular level continues to be challenged by new experimental observations. Specifically, a recent deep mutational scanning study of a bacterial transcription factor TetR found that allostery hotspot residues are broadly distributed over a major portion of the protein structure, rather than being clustered near the ligand-binding and DNA-binding domain interfaces as often discussed in structure-based studies. Similarly, loss of inducibility due to mutation of hotspots could be rescued by additional mutations that were also broadly distributed throughout the protein. These findings suggest that the contributions of hotspot residues are unlikely explained by a single mechanism, thus calling for different analysis strategies compared to previous computational studies.   

In this seminar, I’ll discuss our recent efforts that integrated atomistic simulations, machine learning analysis and a thermodynamic (MWC like) model to explain the various aspects of the experimental findings. The key realization from these analyses is that allostery hotspots may contribute by either mediating inter-domain communications or intra-domain energetics. The mechanistic insights we gleaned for TetR might be broadly applicable to allosteric systems with the similar structural topology.  

 Relevant references: 

A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery, Z. Liu, T. Gillis, S. Raman, Q. Cui*, eLife, 12, RP92262 (2024)  

Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR, J. Deng*, Y. Yuan and Q. Cui*, J. Am. Chem. Soc. 146, 2757-2768 (2024)  

Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins, M. Leander‡, Z. Liu‡, Q. Cui* and S. Raman*, eLife, 11, e79932 (2022)  

Molecular Dynamics Simulations Establish the Molecular Basis for the Broad Allostery Hotspots Distribution in the Tetracycline Repressor,  Y. Yuan‡, J. Deng‡ and Q. Cui*, J. Am. Chem. Soc., 144, 10870-10887 (2022) 

Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation, M. Leander, Y. C. Yuan, A. Meger, Q. Cui and S. Raman*, Proc. Natl. Acad. Sci. USA, 117, 25445-25454 (2020)