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CD Spectroscopy to Study DNA-Protein Interactions

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Published on: February 10, 2022

Disordered Tails Shape DNA Specificity of Myc:Max via Transient Competition.

Shira Peer¹, Yaakov Levy¹

¹Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

Journal of Molecular Biology

|June 3, 2026

Summary

This summary is machine-generated.

Negatively charged intrinsically disordered regions (IDRs) in transcription factors accelerate DNA binding by promoting hopping diffusion. These charged tails act as kinetic gatekeepers, enhancing target search speed and specificity.

Keywords:

coarse-grained simulations conformational changes intrinsically disordered regions negatively charged tails protein-DNA interactions

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Area of Science:

Molecular Biology
Biophysics
Genomics

Background:

Intrinsically disordered regions (IDRs) are common in transcription factors but their negative charge poses a paradox for DNA binding.
The Myc:Max transcription factor complex features negatively charged terminal tails proposed to influence DNA binding dynamics.

Purpose of the Study:

To investigate the molecular mechanism by which negatively charged tails modulate DNA recognition kinetics, thermodynamics, and specificity in the Myc:Max complex.
To elucidate the role of these tails in optimizing the balance between rapid genomic search and high-fidelity discrimination.

Main Methods:

Coarse-grained molecular dynamics simulations were employed to study the Myc:Max transcription factor complex.
Analysis focused on diffusion modes, electrostatic interactions, and binding kinetics.

Main Results:

The negatively charged tail of the Max monomer accelerates target search by promoting hopping over sliding diffusion.
This acceleration is mediated by a dynamic autoinhibitory mechanism where tails compete with DNA for binding.
Negative tails enhance specificity by acting as a kinetic filter, reducing off-target binding.
Phosphorylation amplifies acceleration but reduces binding stability; heterodimerization attenuates acceleration.

Conclusions:

Negatively charged IDRs in transcription factors act as dynamic kinetic gatekeepers, optimizing DNA search speed and specificity.
These tails regulate transcription factor function through electrostatic interactions and dynamic mechanisms, rather than direct base-specific contacts.