title: A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion.
abstract: A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Sabeeha
authors.initials: S
authors.lastname: Hasnain
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, United States of America.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: McClendon
authors.affiliation: Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Monica T
authors.initials: MT
authors.lastname: Hsu
authors.affiliation: Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Jacobson
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Pradipta
authors.initials: P
authors.lastname: Bandyopadhyay
mesh_terms: D003593:Cytoplasm / Q000378:metabolism*; D004058:Diffusion; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D049452:Green Fluorescent Proteins / Q000378:metabolism; D057446:Hydrodynamics; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D013997:Time Factors
chemical_list: D029968:Escherichia coli Proteins; D049452:Green Fluorescent Proteins