Biology Reference
In-Depth Information
Fig. 12.27 A simplified diagram indicating the interactions between
transcriptosome
(T) and
degradosome
(D) that together determine the trajectory of an RNA molecules, X or Y. Steps 1 and
4
¼
transcription; Steps 2 and 5
¼
transcript degradation; Steps 3 and 6
¼
translation; Steps 7
and 8
functional coupling between the transcriptosome and degradosome associated with
mRNA
X
and mRNA
Y
; Steps 9
¼
the functional coupling between the two transcriptosome/
degradosome complexes, (T
X
D
X
) and (T
Y
D
Y
), that determine the trajectories of the difference
([mRNA]
X
- [mRNA]
Y
). [RNA]
X
and [RNA]
Y
refer to the intracellular concentrations of
mRNA
X
and mRNA
Y
, respectively
¼
intracellular “crowding” (Goodsell 1991; Minton 2001; McGuffee and Elcock 2010).
A more realistic model of the cytoplasm of the living cell is shown in Fig.
12.28
which was computationally constructed by McGuffee and Elcock (2010) utilizing
quantitative proteomic data (Link et al. 1997) and atomic-level structural data of
protein molecules ranging in size from 7,000 to 1,350,000 Daltons (Berman et al.
2000). The McGuffee and Elcock model of the cytoplasm shown in Fig.
12.28
incorporates steric (i.e., molecular shape), electrostatic and short-range attractive
hydrophobic interactions but does not yet include water, hydrodynamic interactions,
and protein flexibility (and hence the role of conformons; Chap.
8
). The maximum
average distances moved by each molecule type during 15
m
s of simulation decreases
nonlinearly with molecular weights, ranging from 12 molecular diameters for
5,000 Da molecules to 1 molecular dimension for 1,000,000 Da molecules.
The average number of neighbors possessed by a molecular type increases nonlinearly
with molecular weights. Thus, the immediate neighborhood of a GFP molecule
