Life in a crowded world

@article{Rivas2004LifeIA,
  title={Life in a crowded world},
  author={G. Rivas and F. Ferrone and J. Herzfeld},
  journal={EMBO reports},
  year={2004},
  volume={5}
}
This workshop took place at the Palacio de Magalia (Las Navas del Marques, Avila, Spain), between 14 and 18 June 2003, and was organized by J. Ellis, A. Minton and G. Rivas. Further details on the workshop can be found at http://www.cib.csic.es/~revers/embo2003/index.htm ![][1] Macromolecules are present as soluble species and/or structural arrays at total concentrations of up to several hundred grams per litre in essentially all physiological compartments. Although local composition varies… Expand
Complexity of molecular crowding in cell-free enzymatic reaction networks.
TLDR
The effects of crowding are interpreted using a model based on experimentally determined activity coefficients of crowded protein solutions, instead of introducing power-law scaling parameters with no direct link to chemical processes. Expand
Molecular Crowding: A Way to Deal with Crowding in Photosynthetic Membranes
TLDR
Molecular crowding is an important but underestimated phenomenon that is worth to be investigated in more detail already because of its omnipresence. Expand
Effects of macromolecular crowding agents on protein folding in vitro and in silico
TLDR
Synthetic macromolecular crowding agents are used in combination with strategically selected proteins and a range of equilibrium and time-resolved biophysical methods to address excluded volume effects of protein folding. Expand
A natural and readily available crowding agent: NMR studies of proteins in hen egg white
TLDR
This work proposes the use of hen egg white (HEW) as a simple natural medium, with all features of the media of crowded cells, that could be used by any researcher without difficulty and inexpensively, and presents a study of the stability and dynamics behavior of model proteins in HEW. Expand
Isolation of Cell Nuclei Using Inert Macromolecules to Mimic the Crowded Cytoplasm
TLDR
Immunofluorescence labelling and experiments using cells expressing GFP-fusion proteins showed that internal compartments were conserved in these nuclei, and nascent RNA transcripts could be elongated, consistent with the hypothesis that crowding by diffusible cytoplasmic macromolecules is a crucial but overlooked factor which supports the nucleus in vivo by equilibrating the opposing osmotic pressure cause by the high concentration of macromolescules in the nucleus. Expand
What Macromolecular Crowding Can Do to a Protein
TLDR
The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule to represent one of the most comprehensive compendia of the current knowledge in this exciting area. Expand
Crowding induces complex ergodic diffusion and dynamic elongation of large DNA molecules.
TLDR
Results collectively show that mobility reduction and coil elongation of large crowded DNAs are due to a complex interplay between entropic effects and crowder mobility. Expand
Crowding Induces Entropically-Driven Changes to DNA Dynamics That Depend on Crowder Structure and Ionic Conditions
TLDR
It is shown that both DNA diffusion and conformational size exhibit an emergent non-monotonic dependence on salt concentration that is not seen in the absence of crowders, and the extent to which DNA mobility is reduced by increasing crowder concentrations appears largely insensitive to crowder structure. Expand
Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.
TLDR
It is proposed that the anomality of the diffusion can be used as a quantifiable measure for the crowdedness of the cytoplasm at the molecular scale. Expand
Crowding versus molecular seeding: NMR studies of protein aggregation in hen egg white.
TLDR
It is shown that HEW can increase dramatically the aggregation kinetics of proteins with an in-built tendency to associate, and a role of glycosylated proteins in aggregation is suggested. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 48 REFERENCES
The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media*
  • A. Minton
  • Chemistry, Medicine
  • The Journal of Biological Chemistry
  • 2001
TLDR
To properly assess the physiological role of a particular reaction or set of reactions characterized in vitro, it is important to consider the possible influence of crowding and/or confinement upon the reaction in its physiological milieu. Expand
Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding.
TLDR
Electron cryotomography offers an incisive probe to examine crowding in different cellular compartments and should be more easily identifiable in tomograms of eukaryotic cytoplasm, which is found to be markedly less crowded than in the prokaryotes previously studied. Expand
Bacterial chemotaxis and the question of gain
  • D. Bray
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2002
TLDR
The devil was always in the details, but as the authors accumulate more and more quantitative data on living cells, those diabolical details become increasingly finicky and numerical and the nub of debate if not controversy. Expand
Confinement as a determinant of macromolecular structure and reactivity.
  • A. Minton
  • Chemistry, Medicine
  • Biophysical journal
  • 1992
TLDR
Calculations indicate that the equilibrium constants of reactions that result in significant change in macromolecular size, shape, and/or mobility may be altered within pores by as much as several orders of magnitude relative to the value in the unbounded or bulk phase. Expand
Direct observation of the enhancement of noncooperative protein self-assembly by macromolecular crowding: Indefinite linear self-association of bacterial cell division protein FtsZ
TLDR
The functional dependence of the sedimentation of FtsZ on the concentrations of FTSZ and either crowder indicates that, in the presence of high concentrations of crowder, both the weight-average degree of FttZ self-association and the range of FtZ oligomer sizes present in significant abundance are increased substantially. Expand
Direct observation of the self-association of dilute proteins in the presence of inert macromolecules at high concentration via tracer sedimentation equilibrium: theory, experiment, and biological significance.
TLDR
It is found that in the absence of the divalent cations, the large dependence of the thermodynamic activity of fibrinogen on BSA concentration is well accounted for by a simple model for steric repulsion. Expand
Macromolecular crowding: obvious but underappreciated.
  • R. Ellis
  • Biology, Medicine
  • Trends in biochemical sciences
  • 2001
TLDR
Positive results of crowding include enhancing the collapse of polypeptide chains into functional proteins, the assembly of oligomeric structures and the efficiency of action of some molecular chaperones and metabolic pathways. Expand
Volume Exclusion Effect as a Driving Force for Reverse Proteolysis
TLDR
It is shown that proteosynthesis of a polypeptide product with an interacting folding motif such as coiled coil is facilitated in crowded media as a consequence of the volume exclusion effect, and that crowding could also effect the conversion of a noncovalent protein complex obtained by limited proteolysis to the native covalent form. Expand
Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges.
The concept of excluded volume and the theory of effects of excluded volume on the equilibria and rates of macromolecular reactions in fluid media containing high total concentrations ofExpand
Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell
TLDR
The results can be explained by preferential excluded volume stabilization of compact states relative to more unfolded states, and suggest that the rates of many protein folding processes are likely to be altered under conditions that more closely resemble the intracellular environment. Expand
...
1
2
3
4
5
...