Thermodynamic restrictions on evolutionary optimization of transcription factor proteins

Abstract

Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can be minimized, under selective pressure, by adjusting the spectrum of conformational states so that the fraction of time spent in more mobile conformations is matched with the target recognition rate. The associated optimal binding time is then within an order of magnitude of the limiting binding time imposed by thermodynamics, corresponding to an idealized protein with instant target recognition. Numerical estimates suggest that typical bacteria operate in this regime of optimized conformational fluctuations.

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Cited by in corpus (7)

• Intermittent search strategies
• First passages for a search by a swarm of independent random searchers
• Classes of fast and specific search mechanisms for proteins on DNA
• Searching fast for a target on a DNA without falling to traps
• Narrow-escape times for diffusion in microdomains with a particle-surface affinity: Mean-field results
• Transcription factor search for a DNA promoter in a three-states model
• Facilitated diffusion framework for transcription factor search with conformational changes