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Addressing the role of centromere sites in activation of ParB proteins for partition complex assembly.
PLoS One
August 2020
Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), CBI, CNRS, UPS, Toulouse, France.
The ParB-parS partition complexes that bacterial replicons use to ensure their faithful inheritance also find employment in visualization of DNA loci, as less intrusive alternatives to fluorescent repressor-operator systems. The ability of ParB molecules to interact via their N-terminal domains and to bind to non-specific DNA enables expansion of the initial complex to a size both functional in partition and, via fusion to fluorescent peptides, visible by light microscopy. We have investigated whether it is possible to dispense with the need to insert parS in the genomic locus of interest, by determining whether ParB fused to proteins that bind specifically to natural DNA sequences can still assemble visible complexes.
View Article and Find Full Text PDFThe aqueous environment as an active participant in the protein folding process.
J Mol Graph Model
March 2019
Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Łazarza 16, 31-530, Kraków, Poland. Electronic address:
Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of HO molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution.
View Article and Find Full Text PDFChromatin imaging and new technologies for imaging the nucleome.
Wiley Interdiscip Rev Syst Biol Med
May 2019
Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois.
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores.
View Article and Find Full Text PDFSynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins.
ACS Omega
July 2018
Centre for Discovery Brain Sciences, Deanery for Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, U.K.
A major challenge in synthetic biology, particularly for mammalian systems, is the inclusion of adequate external control for the synthetic system activities. Control at the transcriptional level can be achieved by adaptation of bacterial repressor-operator systems (e.g.
View Article and Find Full Text PDFTethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.
Methods Mol Biol
May 2018
Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA, 30322, USA.
Tethered Particle Motion (TPM) is a versatile in vitro technique for monitoring the conformations a linear macromolecule, such as DNA, can exhibit. The technique involves monitoring the diffusive motion of a particle anchored to a fixed point via the macromolecule of interest, which acts as a tether. In this chapter, we provide an overview of TPM, review the fundamental principles that determine the accuracy with which effective tether lengths can be used to distinguish different tether conformations, present software tools that assist in capturing and analyzing TPM data, and provide a protocol which uses TPM to characterize lac repressor-induced DNA looping.
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