title: Intracellular crowding effects on the self-association of the bacterial cell division protein FtsZ.
abstract: The dimerization rate of the bacterial cell division protein FtsZ is strongly affected by the intracellular crowding. Yet the complexity of the intracellular environment makes it difficult to investigate via all-atom molecular dynamics or other detailed theoretical methods. We study the crowding effect on FtsZ dimerization which is the first step of an oligomerization process that results in more elaborate supramolecular structures. In particular, we consider the effect of intracellular crowding on the reaction rates, and their dependence on the different concentrations of crowding agents. We achieved this goal by using Brownian dynamics (BD) simulation techniques and a modified post-processing approach in which we decompose the rate constant in crowded media as a product of the rate constant in the dilute solution times a factor that incorporates the crowding effect. The latter factor accounts for the diffusion reduction and crowder induced energy. In addition we include the crowding effects on water viscosity in the BD simulations of crowded media. We finally show that biomolecular crowding has a considerable effect on the FtsZ dimerization by increasing the dimerization rate constant from 2.6×10(7)M(-1)s(-1) in the absence of crowders to 1.0×10(8)M(-1)s(-1) at crowding level of 0.30.
authors.affiliation: Department of Physics, Birzeit University, Birzeit, Palestine.
authors.forename: Lamis
authors.initials: L
authors.lastname: Naddaf
authors.affiliation: Department of Physics, Birzeit University, Birzeit, Palestine. Electronic address: asayyeda@birzeit.edu.
authors.forename: Abdallah
authors.initials: A
authors.lastname: Sayyed-Ahmad
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D003598:Cytoskeletal Proteins / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D055503:Protein Multimerization; D014783:Viscosity
chemical_list: D001426:Bacterial Proteins; D003598:Cytoskeletal Proteins; C071525:FtsZ protein, Bacteria
keywords: Brownian dynamics; FtsZ protein; Macromolecular crowding; Protein–protein interaction