Chromosome segregation in Escherichia coli division: A free energy-driven string model

2007-08-01
Fan, J.
Tuncay, Kağan
Ortoleva, P. J.
Show full item record
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
170
views
0
downloads
Although the mechanisms of eukaryotic chromosome segregation and cell division have been elucidated to a certain extent, those for bacteria remain largely unknown. Here we present a computational string model for simulating the dynamics of Escherichia coli chromosome segregation. A novel thermal-average force field accounting for stretching, bending, volume exclusion, friction and random fluctuation is introduced. A Langevin equation is used to simulate the chromosome structural changes. The mechanism of chromosome segregation is thereby postulated as a result of free energy-driven structural optimization with replication introduced chromosomal mass increase. Predictions of the model agree well with observations of fluorescence labeled chromosome loci movement in living cells. The results demonstrate the possibility of a mechanism of chromosome segregation that does not involve cytoskeletal guidance or advanced apparatus in an E. coli cell. The model also shows that DNA condensation of locally compacted domains is a requirement for successful chromosome segregation. Simulations also imply that the shape-determining protein MreB may play a role in the segregation via modification of the membrane pressure. Published by Elsevier Ltd.
Organic Chemistry, Biochemistry, Structural Biology, Computational Mathematics
https://hdl.handle.net/11511/35152
COMPUTATIONAL BIOLOGY AND CHEMISTRY
Department of Civil Engineering, Article

Suggestions

ImaGene: a convolutional neural network to quantify natural selection from genomic data
Torada, Luis; Lorenzon, Lucrezia; Beddis, Alice; Isildak, Ulas; Pattini, Linda; Mathieson, Sara; Fumagalli, Matteo (Springer Science and Business Media LLC, 2019-11-22)
Background: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms...
DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles
Hoffmann, Thomas; Marıon, Antoıne; Antes, Iris (Springer Science and Business Media LLC, 2017-02-02)
Background: T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Va/V beta) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly...
Immune modulatory effects of pediococcus pentosaceus derived membrane vesicles: mechanism of action and therapeutic applications
Alpdündar Bulut, Esin; Gürsel, Mayda; Department of Biology (2018)
In our previous studies, we characterized 5 different human gram positive commensal bacteria derived membrane vesicles (MVs) and compared their activity with non-pathogenic E.coli derived membrane vesicles. Results showed that commensal bacteria derived MVs had immunomodulatory properties whereas non-pathogenic E.coli derived membrane vesicles had immune stimulatory properties. In this thesis, we aimed to focus our attention to Pediococcus pentosaceus-derived MVs that displayed the highest immunomodulatory ...
Discovering functional interaction patterns in protein-protein interaction networks
Turanalp, Mehmet E.; Can, Tolga (Springer Science and Business Media LLC, 2008-06-11)
Background: In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution...
Epigenetic Mechanisms Underlying the Dynamic Expression of Cancer-Testis Genes, PAGE2, -2B and SPANX-B, during Mesenchymal-to-Epithelial Transition
Yilmaz-Ozcan, Sinem; Sade, Asli; Kucukkaraduman, Baris; Kaygusuz, Yasemin; Senses, Kerem Mert; Banerjee, Sreeparna; GÜRE, ALİ OSMAY (Public Library of Science (PLoS), 2014-09-17)
Cancer-testis (CT) genes are expressed in various cancers but not in normal tissues other than in cells of the germline. Although DNA demethylation of promoter-proximal CpGs of CT genes is linked to their expression in cancer, the mechanisms leading to demethylation are unknown. To elucidate such mechanisms we chose to study the Caco-2 colorectal cancer cell line during the course of its spontaneous differentiation in vitro, as we found CT genes, in particular PAGE2, -2B and SPANX-B, to be up-regulated duri...
Citation Formats
J. Fan, K. Tuncay, and P. J. Ortoleva, “Chromosome segregation in Escherichia coli division: A free energy-driven string model,” COMPUTATIONAL BIOLOGY AND CHEMISTRY, pp. 257–264, 2007, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/35152.
METU IIS - Integrated Information Service open@metu.edu.tr