Allostery and Kinetic Proofreading.

Rob Phillips,Vahe Galstyan

doi:10.1021/acs.jpcb.9b08380

Rob Phillips, Vahe Galstyan

Open Access

https://doi.org/10.1021/acs.jpcb.9b08380

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Abstract

Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many biological proofreading schemes are known, our understanding of how energy consumption is managed to promote fidelity remains incomplete. In our work, we introduce an alternative conceptual scheme called "the piston model of proofreading" in which enzyme activation through hydrolysis is replaced with allosteric activation achieved through mechanical work performed by a piston on regulatory ligands. Inspired by Feynman's ratchet and pawl mechanism, we consider a mechanical engine designed to drive the piston actions powered by a lowering weight, whose function is analogous to that of ATP synthase in cells. Thanks to its mechanical design, the piston model allows us to tune the "knobs" of the driving engine and probe the graded changes and trade-offs between speed, fidelity, and energy dissipation. It provides an intuitive explanation of the conditions necessary for optimal proofreading and reveals the unexpected capability of allosteric molecules to beat the Hopfield limit of fidelity by leveraging the diversity of states available to them. The framework that we have built for the piston model can also serve as a basis for additional studies of driven biochemical systems.

Highlights

Many enzymatic processes in biology need to operate with very high fidelities in order to ensure the physiological well-being of the cell
The conceptual answer to this challenge was provided more than 40 years ago in the work of John Hopfield 9 and Jacques Ninio 10 and was coined “kinetic proofreading” in Hopfield’s elegant paper entitled “Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity.” 9 The key idea behind kinetic proofreading is to introduce a delay between substrate binding and turnover steps, effectively giving the enzyme more than one chance to release the incorrect substrate
The sequential application of substrate filters on the way to product formation gives directionality to the flow of time and is necessarily accompanied by the expenditure of free energy, making kinetic proofreading an intrinsically nonequilibrium phenomenon. This free energy is typically supplied to proofreading pathways through the hydrolysis of energy-rich nucleotides, whose chemical potential is maintained at large out-of-equilibrium values through the constant operation of the cell’s metabolic machinery

Summary

Introduction

Many enzymatic processes in biology need to operate with very high fidelities in order to ensure the physiological well-being of the cell. This requirement of having a large free energy difference between the compressed and expanded piston states (β∆F = ln(f ) 1) can be paralleled with a similar condition in Hopfield’s model where for optimal proofreading the energy of the activated enzyme-substrate complex needs to be much larger than that of the inactive complex.

Results

Conclusion