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Research Article

Elucidating interplay of speed and accuracy in biological error correction

Kinshuk Banerjee, Anatoly B. Kolomeisky, and Oleg A. Igoshin
PNAS first published May 2, 2017; https://doi.org/10.1073/pnas.1614838114
Kinshuk Banerjee
aCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005;
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Anatoly B. Kolomeisky
aCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005;
bDepartment of Chemistry, Rice University, Houston, TX 77005;
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  • For correspondence: tolya@rice.edu igoshin@rice.edu
Oleg A. Igoshin
aCenter for Theoretical Biological Physics, Rice University, Houston, TX 77005;
cDepartment of Bioengineering, Rice University, Houston, TX 77005
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  • For correspondence: tolya@rice.edu igoshin@rice.edu
  1. Edited by William Bialek, Princeton University, Princeton, NJ, and approved April 7, 2017 (received for review September 4, 2016)

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Significance

Biological processes are unique in showing a remarkable level of accuracy in discriminating between similar molecules. This characteristic is attributed to an error-correcting mechanism known as kinetic proofreading. It is widely believed that the enhancement of the accuracy in biological processes always slows them down. By analyzing the fundamental processes of DNA replication and protein translation, we established that these systems maximize speed rather than accuracy with additional energetic constraints. Our theoretical study further indicates that both speed and accuracy can be enhanced in certain parameter regimes. The resulting findings provide a microscopic picture of how complex biological processes can be accomplished so quickly with minimal errors.

Abstract

One of the most fascinating features of biological systems is the ability to sustain high accuracy of all major cellular processes despite the stochastic nature of underlying chemical processes. It is widely believed that such low error values are the result of the error-correcting mechanism known as kinetic proofreading. However, it is usually argued that enhancing the accuracy should result in slowing down the process, leading to the so-called speed–accuracy trade-off. We developed a discrete-state stochastic framework that allowed us to investigate the mechanisms of the proofreading using the method of first-passage processes. With this framework, we simultaneously analyzed the speed and accuracy of the two fundamental biological processes, DNA replication and tRNA selection during the translation. The results indicate that these systems tend to optimize speed rather than accuracy, as long as the error level is tolerable. Interestingly, for these processes, certain kinetic parameters lay in the suboptimal region where their perturbations can improve both speed and accuracy. Additional constraints due to the energetic cost of proofreading also play a role in the error correcting process. Our theoretical findings provide a microscopic picture of how complex biological processes are able to function so fast with high accuracy.

  • kinetic proofreading mechanisms
  • stochastic models
  • first-passage processes

Footnotes

  • ↵1O.A.I. and A.B.K. contributed equally to this work.

  • ↵2To whom correspondence may be addressed. Email: tolya{at}rice.edu or igoshin{at}rice.edu.
  • Author contributions: A.B.K. and O.A.I. designed research; K.B., A.B.K., and O.A.I. performed research; and K.B., A.B.K., and O.A.I. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1614838114/-/DCSupplemental.

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Trade-off in biological error correction
Kinshuk Banerjee, Anatoly B. Kolomeisky, Oleg A. Igoshin
Proceedings of the National Academy of Sciences May 2017, 201614838; DOI: 10.1073/pnas.1614838114

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Trade-off in biological error correction
Kinshuk Banerjee, Anatoly B. Kolomeisky, Oleg A. Igoshin
Proceedings of the National Academy of Sciences May 2017, 201614838; DOI: 10.1073/pnas.1614838114
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