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Updated: Dec 25, 2025

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
Published on: June 19, 2018
The guiding role of dissipation in kinetic proofreading networks: Implications for protein synthesis
Kinshuk Banerjee1, Biswajit Das2, Gautam Gangopadhyay2
1Department of Chemistry, Acharya Jagadish Chandra Bose College, Kolkata 700 020, India.
Abstract:
Major biological polymerization processes achieve remarkable accuracy while operating out of thermodynamic equilibrium by utilizing the mechanism known as kinetic proofreading. Here, we study the interplay of the thermodynamic and kinetic aspects of proofreading by exploring the dissipation and catalytic rate, respectively, under the realistic constraint of fixed chemical potential difference. Theoretical analyses reveal no-monotonic variations of the catalytic rate and total entropy production rate (EPR), the latter quantifying the dissipation, at steady state. Applying this finding to a tRNA selection network in protein synthesis, we observe that the network tends to maximize both the EPR and catalytic rate, but not the accuracy. Simultaneously, the system tries to minimize the ratio of the EPRs due to the proofreading steps and the catalytic steps. Therefore, dissipation plays a guiding role in the optimization of the catalytic rate in the tRNA selection network of protein synthesis.
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