Mechanisms Regulating Escherichia Coli dps Gene Expression under Stress: Reconstruction on Kinetic Data

Khlebodarova, T. M.

doi:10.17537/2015.10.1

Math.Biol.Bioinf.

2015

DOI: 10.17537/2015.10.1

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Mechanisms Regulating Escherichia Coli dps Gene Expression under Stress: Reconstruction on Kinetic Data

T. M. Khlebodarova¹

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Cited by 2 publications

References 24 publications

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Mask-based approach to phasing of single-particle diffraction data

Lunin

Lunina

Petrova

et al. 2016

Acta Cryst Sect D Struct Biol

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A Monte Carlo-type approach for low- and medium-resolution phasing of single-particle diffraction data is suggested. Firstly, the single-particle phase problem is substituted with the phase problem for an imaginary crystal. A unit cell of this crystal contains a single isolated particle surrounded by a large volume of bulk solvent. The developed phasing procedure then generates a large number of connected and finite molecular masks, calculates their Fourier coefficients, selects the sets with magnitudes that are highly correlated with the experimental values and finally aligns the selected phase sets and calculates the averaged phase values. A test with the known structure of monomeric photosystem II resulted in phases that have 97% correlation with the exact phases in the full 25 Å resolution shell (1054 structure factors) and correlations of 99, 94, 81 and 79% for the resolution shells ∞-60, 60-40, 40-30 and 30-25 Å, respectively. The same procedure may be used for crystallographic ab initio phasing.

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Mask-based approach to phasing of single-particle diffraction data

Lunin

Lunina

Petrova

et al. 2016

Acta Cryst Sect D Struct Biol

View full text Add to dashboard Cite

show abstract

Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation

et al. 2022

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Transcription regulation plays an important role in bacterial activity. The operon concept coined by François Jacob and Jacques Monod has had a considerable effect on investigations into gene expression regulation, including modeling. However, most such studies have considered the regulation models devised manually for one or several operons. For that reason, the objective of the present study was automated genome model reconstruction for different bacteria. The suggested algorithm accounted for all possible interactions of transcription factors and their binding sites in an operon’s promoter region. Transcription factor enumeration was performed using the deep-first search technique. The obtained models are of interest for those involved in the research of transcription factor regulatory effects on bacterial gene expression in microbiology and biotechnology.

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Mechanisms Regulating Escherichia Coli dps Gene Expression under Stress: Reconstruction on Kinetic Data

Cited by 2 publications

References 24 publications

Mask-based approach to phasing of single-particle diffraction data

Mask-based approach to phasing of single-particle diffraction data

Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation

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