1. Center for Functional Nanomaterials Seminar

    "BIOLOGISTICS : mobility of ligands, proteins and plasmids in cytoplasm of the eukaryotic and prokaryotic cells"

    Presented by Robert Hołyst, Institute of Physical Chemistry PAS, Warsaw, Poland

    Monday, September 23, 2013, 10 am
    CFN, Bldg. 735, Conference Room B

    Hosted by: Oleg Gang

    Biologistics and biochemistry in a crowded environment are two emerging interdisciplinary fields of science. They provide quantitative analysis of transport of proteins and their interactions involved in gene expression and regulation. These processes inside living cells strongly depend on the physics of liquids at the nanoscale. As I will try to convince you during my talk the length-scale dependent nanoviscosity [1-4] characterizing motion of proteins at the nanoscale is a key to quantitative analysis of biochemical reactions in living cells[5]. Genes are activated and repressed by proteins referred to as transcription factors (TF). The binding of TFs to the operator region on DNA is believed to be diffusion limited. TFs search for operators by performing a combination of three-dimensional (3D) diffusion in a defined volume and one-dimensional (1D) diffusion along DNA molecule. The diffusion coefficients for 3D diffusion, D, and 1D diffusion, D1, are inversely proportional to the viscosity. For the model Gram-negative bacterium Escherichia coli, the nanoviscosity of the cytoplasm depends on the size of diffusing objects. This length scale dependent nanoviscosity changes by a factor of >104 between 0.001 Pas for water molecules (size 0.14 nm) and 18 Pas for large plasmids (size 300 nm). Accordingly D for biomolecules in E. coli varies[4] by a factor of ~108; representative diffusion coefficients for biomolecules in E. coli at temperature 310 K, include: D= 474 μm2/s for arginine (radius rp= 0.34 nm); D=80.4 μm2/s for protein TrpL (rp=1.1 nm); D=0.23 μm2/s for protein IbpB (oligomer 100 subunits rp=10.3 nm); and D=0.5–10-5 μm2/s for plasmids (rp=210 nm). Reaction rates of biomolecules are proportional to D, and therefore they are sensitive to diffusion that arises with substrate size. An understanding of how D, D1 and the reaction rates for gene expression depend on the length-scale dependent nanoviscosity and non-specific interactions between DNA