OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities

Haji Abdolvahab, R ; Sharif University of Technology | 2016

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  1. Type of Document: Article
  2. DOI: 10.1016/j.physa.2016.03.031
  3. Publisher: Elsevier B.V , 2016
  4. Abstract:
  5. The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage sensitivity of channel at different concentrations and membrane potentials. The amplitude and frequency of ion current fluctuation increased in the presence of Adenine more than Cytosine and Thymine in milli-molar (0.5mM) concentrations. The variance of the current TS at various applied voltages showed a non-monotonic trend whose initial increasing slope in the presence of Thymine changed to a decreasing one in the second phase and was different from that of Adenine and Cytosine; e.g., by increasing the voltage from 40 to 140 mV in the 0.5mM concentration of Adenine or Cytosine, the variance decreased by one third while for the case of Thymine it was doubled. Moreover, according to the structure function of TS, the fractality of current TS differed as a function of varying membrane potentials (pd) and nucleotide concentrations. Accordingly, the calculated permutation entropy of the TS, validated the biophysical approach defined for the recognition of different nucleotides at various concentrations, pd's and polarities. Thus, the promising outcomes of the combined experimental and theoretical methodologies presented here can be implemented as a complementary means in pore-based nucleotide recognition approaches
  6. Keywords:
  7. Entropy ; Fractals ; Molecular biology ; Spectral density ; Time series ; Computational evaluation ; Fractality ; Ion channel ; Membrane potentials ; Molecular biophysics ; Permutation entropy ; Structure functions ; Voltage sensitivity ; Nucleotides
  8. Source: Physica A: Statistical Mechanics and its Applications ; Volume 457 , 2016 , Pages 215-224 ; 03784371 (ISSN)
  9. URL: http://www.sciencedirect.com/science/article/pii/S0378437116300292