A Non-equilibrium model of the ParBS bacterial system
Andrea Salati
A Non-equilibrium model of the ParBS bacterial system.
Rel. Andrea Pagnani. Politecnico di Torino, Corso di laurea magistrale in Physics Of Complex Systems (Fisica Dei Sistemi Complessi), 2022
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Abstract
ParABS systems are a tripartite mechanism that ensure chromosome and low- copy-number plasmid separation in most bacterial species. This thesis focuses on the interaction of two of these elements: centromere DNA sequence ParS and the DNA-binding protein ParB. A new analytical coarse-grained model for the diffusion of ParB dimers on DNA is proposed. A first diffusive model was introduced in recent article but it ignores both the structural transitions of the dimer and the change of nucleotide it is bound to (either CDP or CTP). This model distinguishes between the open and closed states of the protein, therefore taking also in account the transition between these two conformations.
Adding this feature in the model is crucial for a more faithful description of the ParBS interaction
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