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Monte Carlo simulations of single- and multistep enzyme-catalyzed reaction sequences: Effects of diffusion, cell size, enzyme fluctuations, colocalization, and segregation
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10.1063/1.3459111
/content/aip/journal/jcp/133/3/10.1063/1.3459111
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/3/10.1063/1.3459111

Figures

Image of FIG. 1.
FIG. 1.

Variation of reaction rate with the number of A reactant molecules for a single-step reaction with diffusion effects, .

Image of FIG. 2.
FIG. 2.

Effect of varying diffusion coefficient for a single-step reaction . The dashed line indicates the rate for complete rapid mixing.

Image of FIG. 3.
FIG. 3.

Effect of varying rate constant for a single-step reaction . Reaction-limited for low , diffusion-limited for high .

Image of FIG. 4.
FIG. 4.

Effect of varying size of reaction zone on reaction rate for a single-step reaction with diffusion. Diffusion limited for small , reaction-limited for large .

Image of FIG. 5.
FIG. 5.

Variation of rate with number of A molecules in cell for a simple enzyme-catalyzed reaction with diffusion effects .

Image of FIG. 6.
FIG. 6.

Effect of varying diffusion coefficient on rates for the reaction .

Image of FIG. 7.
FIG. 7.

Lineweaver–Burk plot for the reaction with diffusion effects.

Image of FIG. 8.
FIG. 8.

Geometry of cubic cell with segregation of enzymes and catalyzing the reactions .

Image of FIG. 9.
FIG. 9.

Effects of enzyme fluctuations on a sequential reaction, R1234, with colocalized enzymes and (see Table VI).

Tables

Generic image for table
Table I.

Rate constants for reactions R1–R4.

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Table II.

Effects of diffusion for a sequential reaction, R1234, , steady state. Number of A held constant, C removed, values are averages with uncertainties about 1%.

Generic image for table
Table III.

Effects of enzyme distribution for a sequential reaction, R1234, , steady-state. Number of A held constant, C removed, 512 and 512 . Average values with uncertainties of about 1%.

Generic image for table
Table IV.

Effects of enzyme segregation for a sequential reaction, R1234, , steady-state. Number of A held constant, C removed, 4096 and 4096 segregated left and right. Average values with uncertainties of about 1%.

Generic image for table
Table V.

Effects of colocalization of enzymes and for a sequential reaction, R1234, , steady-state. Number of A held constant, C removed, 512 and 512 with placed on a regular grid and placed adjacent at varied distances. Average values with uncertainties of about 1%.

Generic image for table
Table VI.

Effects of enzyme fluctuations on a sequential reaction, R1234, with colocalized enzymes and . Random phases for each enzyme, Number of A held constant, C removed, 512 and 512 with placed on a regular grid and placed adjacent at varied distances. Average values with uncertainties of about 1%.

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/content/aip/journal/jcp/133/3/10.1063/1.3459111
2010-07-15
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Monte Carlo simulations of single- and multistep enzyme-catalyzed reaction sequences: Effects of diffusion, cell size, enzyme fluctuations, colocalization, and segregation
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/3/10.1063/1.3459111
10.1063/1.3459111
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