Signaling cascades: Escape from kinetic proofreading

MacGlashan, Donald

doi:10.1073/pnas.131215498

Cited by 7 publications

(4 citation statements)

References 13 publications

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“…utilizing energy from ATP hydrolysis and other sources achieves biologically acceptable specificity at a physiologically relevant rate. It is an essential specificity determinant in replication (28), recombination (29), transcription (30), splicing (31), translation (32)(33)(34)(35)(36)(37), T cell receptor signaling (38,39), microtubule and actin filament formation (40), and anaphasepromoting complex-mediated cell cycle control (41) and excision repair (15,(42)(43)(44).…”

Section: Minireview: Mechanisms and Maps Of Dna Excision Repairmentioning

confidence: 99%

Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans

Selby

Adar

et al. 2017

Journal of Biological Chemistry

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Nucleotide excision repair is a major DNA repair mechanism in all cellular organisms. In this repair system, the DNA damage is removed by concerted dual incisions bracketing the damage and at a precise distance from the damage. Here, we review the basic mechanisms of excision repair in and humans and the recent genome-wide mapping of DNA damage and repair in these organisms at single-nucleotide resolution.

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Section: Minireview: Mechanisms and Maps Of Dna Excision Repairmentioning

confidence: 99%

Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans

Selby

Adar

et al. 2017

Journal of Biological Chemistry

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“…[16][17] When applied to specific biological systems there are variations on the original scheme. [18][19] However, for a particular cellular response to occur, kinetic proofreading in general requires that the enzyme-substrate (or DNA-protein) complex complete a series of irreversible reactions (such as ATP hydrolysis or protein phosphorylation) while a moderate-specificity ligand is bound; this temporally separates the binding step from the effector step. If the ligand dissociates before the full set of modifications is completed, the reaction is aborted and must restart at the beginning.…”

Section: Macromolecular Recognition Mechanismsmentioning

confidence: 99%

Thermodynamic Cooperativity and Kinetic Proofreading in DNA Damage Recognition and Repair

Reardon¹,

Sancar²

2004

Cell Cycle

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In humans UV-induced cyclobutane thymine dimers are excised by the joint action of six repair factors, RPA, XPA, XPC, TFIIH, XPG, and XPF•ERCC1. Yet, in vitro assays show that none of these six factors is capable of detectably discriminating thymine dimer-containing DNA from undamaged DNA. We show how two elementary principles in macromolecular recognition, (1) cooperativity and (2) kinetic proofreading, are utilized to confer specificity to the repair system where none exists at the individual repair factor level and enable human cells to excise thymine dimers with a physiologically relevant specificity and at a biologically acceptable rate.

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“…1A. Such models [16][17][18][19][28][29][30][31][32] have attracted bulk of the attention, partly owing to early applications to immunology. It must be emphasized that while these models are easiest to analyze, there is little experimental evidence to favor these models over those with the possibility of rescue.…”

Section: A) No Rescues: the Network Of Fig 3a Not Allowmentioning

confidence: 99%

Biological Implications of Dynamical Phases in Non-equilibrium Networks

Murugan

Vaikuntanathan

2016

J Stat Phys

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Biology achieves novel functions like error correction, ultra-sensitivity and accurate concentration measurement at the expense of free energy through Maxwell Demon-like mechanisms. The design principles and free energy trade-offs have been studied for a variety of such mechanisms. In this review, we emphasize a perspective based on dynamical phases that can explain commonalities shared by these mechanisms. Dynamical phases are defined by typical trajectories executed by nonequilibrium systems in the space of internal states. We find that coexistence of dynamical phases can have dramatic consequences for function vs free energy cost trade-offs. Dynamical phases can also provide an intuitive picture of the design principles behind such biological Maxwell Demons.

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Signaling cascades: Escape from kinetic proofreading

Cited by 7 publications

References 13 publications

Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans

Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans

Thermodynamic Cooperativity and Kinetic Proofreading in DNA Damage Recognition and Repair

Biological Implications of Dynamical Phases in Non-equilibrium Networks

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