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Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects
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10.1063/1.2789434
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    Affiliations:
    1 Department of Physiology and Biophysics, Weill Medical College, Cornell University, 1300 York Avenue, New York, New York 10021, USA
    2 Department of Physiology and Biophysics, Weill Medical College, Cornell University, 1300 York Avenue, New York, New York 10021, USA and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, 1305 York Avenue, New York, New York 10021, USA
    a) Electronic mail: haw2002@med.cornell.edu
    J. Chem. Phys. 127, 155105 (2007); http://dx.doi.org/10.1063/1.2789434
/content/aip/journal/jcp/127/15/10.1063/1.2789434
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2789434

Figures

Image of FIG. 1.
FIG. 1.

Effect of time-step length on the calculation of the diffusion constant. Time is expressed as , where , and is plotted vs (in unit of ) for three different values of the volume fractions of the crowding molecules (0.10, 0.20, and 0.30). The is varied by keeping the number of hard sphere with radius of at 1001 and changing the edge length of the simulation box from 69 to 55 and , respectively. The dashed lines show results for a time step of 0.001, and the symbols are for 0.01.

Image of FIG. 2.
FIG. 2.

Volume fraction dependence of the diffusion constant and association rate for a monodisperse hard sphere system. The number of hard spheres is 1001 and the simulation box size varies to achieve the required volume fraction. (a) was calculated according to Eq. (5) and from Eq. (8). The results for are shown by the symbols representing different methods: squares for our BD simulation, triangles for Cichocki and Hinsen (Ref. 34), and stars for Tokuyama (Ref. 49). The two lines represent corresponding theoretical predictions: continuous line from Tokuyama and Oppenheim (Ref. 42) and dashed line from Medina-Noyola (Ref. 48). (b) The mean value of at each volume fraction was obtained for all collision times, while the standard deviation was obtained from the distribution of the calculated rate based on 1000 reaction events. The circles are for , the squares for the corresponding , and the long dashed line is the fitted dependence of .

Image of FIG. 3.
FIG. 3.

Survival probability for reacting molecules obtained from the BD simulations. was calculated according to Eq. (7) and plotted vs simulation time (in milliseconds). For both and , the edge length of the simulation box was . For free association there are no crowding molecules, while for there are 999 spheres of the same size as the reacting particles.

Image of FIG. 4.
FIG. 4.

Effect of simulation box size on the calculated diffusion constant and association rate in the monodisperse hard sphere suspension. All spheres have a radius of . The open symbols indicate values for and closed symbols for . Squares, ; triangles, ; diamonds, .

Image of FIG. 5.
FIG. 5.

Effect of crowding molecule size on the diffusion constant and association rate of the interacting spheres. The open symbols indicate values for and closed symbols for . Squares, crowding molecule (including data from , 501, and 251); diamonds, (, 500, and 250); triangles, (, 500, and 250). All lines are fitted to the data to show the dependence for (solid) and (dashed).

Image of FIG. 6.
FIG. 6.

Effect of hydrodynamic interactions. (a) The diffusion constant calculated from BD simulation with HI correction for monodisperse system with sphere radius of is shown in comparison with results from other methods: Solid line, Tokuyama and Oppenheim (Ref. 42); dashed line, Medina-Noyola (Ref. 48); squares, our BD simulation with HI correction. (b) Dependence on volume fraction of the effective diffusion constant and association rate calculated with the HI contribution. Diamonds, crowding sphere ; squares, ; triangles, . The open symbols represent the diffusion constant values and closed symbols show the association rate values. Lines are fitted to represent the dependence of (dashed) and (solid).

Image of FIG. 7.
FIG. 7.

(Color online) Effect of electrostatic attraction between reacting molecules on the association rate with neutral and charged crowding molecules. Squares, ; diamonds, ; triangles, , all for the neutral crowding environment. Circles are for in the charged crowding environment (half with positive charge and the other half with negative charge); time step is . Open symbols are for calculations without the HI component and closed ones are for values calculated with HI.

Tables

Generic image for table
Table I.

Relative contribution to the crowding effect on diffusion and association in a monodisperse hard sphere system from HS (the excluded volume) and HI (the hydrodynamic interactions).

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/content/aip/journal/jcp/127/15/10.1063/1.2789434
2007-10-18
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2789434
10.1063/1.2789434
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