Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium

Debashish Sahu, Junji Iwahara

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

In the target DNA search process, sequence-specific DNA-binding proteins first nonspecifically bind to DNA and stochastically move from one site to another before reaching their targets. To rigorously assess how the translocation process influences NMR signals from proteins interacting with nonspecific DNA, we incorporated a discrete-state kinetic model for protein translocation on DNA into the McConnell equation. Using this equation, we simulated line shapes of NMR signals from proteins undergoing translocations on DNA through sliding, dissociation/reassociation, and intersegment transfer. Through this analysis, we validated an existing NMR approach for kinetic investigations of protein translocation on DNA, which utilizes NMR line shapes of two nonspecific DNA-protein complexes and their mixture. We found that, despite its use of simplistic two-state approximation neglecting the presence of many microscopic states, the previously proposed NMR approach provides accurate kinetic information on the intermolecular translocations of proteins between two DNA molecules. Interestingly, our results suggest that the same NMR approach can also provide qualitative information about the one-dimensional diffusion coefficient for proteins sliding on DNA.

Original languageEnglish (US)
Pages (from-to)9548-9556
Number of pages9
JournalJournal of Physical Chemistry B
Volume121
Issue number41
DOIs
StatePublished - Oct 19 2017

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Protein Transport
DNA
deoxyribonucleic acid
Nuclear magnetic resonance
proteins
Proteins
nuclear magnetic resonance
Kinetics
kinetics
line shape
sliding
DNA-Binding Proteins
Complex Mixtures
diffusion coefficient
dissociation
Molecules

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium. / Sahu, Debashish; Iwahara, Junji.

In: Journal of Physical Chemistry B, Vol. 121, No. 41, 19.10.2017, p. 9548-9556.

Research output: Contribution to journalArticle

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