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Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.

Hall D, Hoshino M - Biophys Rev (2010)

Bottom Line: Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts.Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments.We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.

View Article: PubMed Central - PubMed

ABSTRACT
Compared to biochemical reactions taking place in relatively well-defined aqueous solutions in vitro, the corresponding reactions happening in vivo occur in extremely complex environments containing only 60-70% water by volume, with the remainder consisting of an undefined array of bio-molecules. In a biological setting, such extremely complex and volume-occupied solution environments are termed 'crowded'. Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts. In this review, we seek to highlight how the complex background environment of the cell can affect the diffusion of substances within it. Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments. We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.

No MeSH data available.


Pair potential functions useful for describing particle interactions at the coarse grained level. a Free overlap, b hard particle, c square well, d saw tooth, e soft sphere, f Lennard Jones. The associated mathematical descriptions are included in Table 1
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Fig5: Pair potential functions useful for describing particle interactions at the coarse grained level. a Free overlap, b hard particle, c square well, d saw tooth, e soft sphere, f Lennard Jones. The associated mathematical descriptions are included in Table 1

Mentions: The types of potential specified depend upon the level of detail included in the description of tracer and background molecules (Elimelech et al. 1995; Leach 2001; Elcock 2003; McGuffee and Elcock 2006; Qin and Zhou 2009). Figure 5 and Table 1 describe six simple interparticle potentials commonly used in polymer and colloidal physical chemistry (Minton 1989; Elimelech et al. 1995; Doi and Edwards 1999; Zhou et al 2008) to account for the effects of concentrated solution environments. In this review, we regard the tracer particle (particle i) and crowding background molecule (particle j) as spheres of respective radii Ri and Rj. In general, the intermolecular potentials all feature some form of repulsive interaction at short range that physically arises from electronic repulsion. At longer distances, the interaction may take on attractive or repulsive characteristics empirically defined in terms of a potential energy depth ε and a screening length, Lij. The potentials described in Fig. 5 and Table 1 are assumed to have spherical symmetry and hence are functions of intermolecular distance, dij, only .Fig. 5


Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.

Hall D, Hoshino M - Biophys Rev (2010)

Pair potential functions useful for describing particle interactions at the coarse grained level. a Free overlap, b hard particle, c square well, d saw tooth, e soft sphere, f Lennard Jones. The associated mathematical descriptions are included in Table 1
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2957576&req=5

Fig5: Pair potential functions useful for describing particle interactions at the coarse grained level. a Free overlap, b hard particle, c square well, d saw tooth, e soft sphere, f Lennard Jones. The associated mathematical descriptions are included in Table 1
Mentions: The types of potential specified depend upon the level of detail included in the description of tracer and background molecules (Elimelech et al. 1995; Leach 2001; Elcock 2003; McGuffee and Elcock 2006; Qin and Zhou 2009). Figure 5 and Table 1 describe six simple interparticle potentials commonly used in polymer and colloidal physical chemistry (Minton 1989; Elimelech et al. 1995; Doi and Edwards 1999; Zhou et al 2008) to account for the effects of concentrated solution environments. In this review, we regard the tracer particle (particle i) and crowding background molecule (particle j) as spheres of respective radii Ri and Rj. In general, the intermolecular potentials all feature some form of repulsive interaction at short range that physically arises from electronic repulsion. At longer distances, the interaction may take on attractive or repulsive characteristics empirically defined in terms of a potential energy depth ε and a screening length, Lij. The potentials described in Fig. 5 and Table 1 are assumed to have spherical symmetry and hence are functions of intermolecular distance, dij, only .Fig. 5

Bottom Line: Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts.Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments.We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.

View Article: PubMed Central - PubMed

ABSTRACT
Compared to biochemical reactions taking place in relatively well-defined aqueous solutions in vitro, the corresponding reactions happening in vivo occur in extremely complex environments containing only 60-70% water by volume, with the remainder consisting of an undefined array of bio-molecules. In a biological setting, such extremely complex and volume-occupied solution environments are termed 'crowded'. Through a range of intermolecular forces and pseudo-forces, this complex background environment may cause biochemical reactions to behave differently to their in vitro counterparts. In this review, we seek to highlight how the complex background environment of the cell can affect the diffusion of substances within it. Engaging the subject from the perspective of a single particle's motion, we place the focus of our review on two areas: (1) experimental procedures for conducting single particle tracking experiments within cells along with methods for extracting information from these experiments; (2) theoretical factors affecting the translational diffusion of single molecules within crowded two-dimensional membrane and three-dimensional solution environments. We conclude by discussing a number of recent publications relating to intracellular diffusion in light of the reviewed material.

No MeSH data available.