Electrochemical structure of the crowded cytoplasm

Spitzer, Jan J.; Poolman, Bert

doi:10.1016/j.tibs.2005.08.002

Cited by 89 publications

(115 citation statements)

References 48 publications

(78 reference statements)

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“…These findings as well as those of Chu et al (22) that PABPs have common sites for nonspecific interactions suggest that such interactions are of functional importance in a cell. A similar view has been proposed recently in which electrolyte pathways and pools "wire" the cytoplasm and organize the crowded environment of the cell (59). In this work, however, we suggest a different "wiring" system in which the cellular polyanions provide a matrix within which some of the functional activity of the cell occurs.…”

supporting

confidence: 74%

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays

Salamat‐Miller

Fang

Seidel

et al. 2006

Molecular & Cellular Proteomics

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The high affinity of certain cellular polyanions for many proteins (polyanion-binding proteins (PABPs)) has been demonstrated previously. It has been hypothesized that such polyanions may be involved in protein structure stabilization, stimulation of folding through chaperone-like activity, and intra-and extracellular protein transport as well as intracellular organization. The purpose of the proteomics studies reported here was to seek evidence for the idea that the nonspecific but high affinity interactions of PABPs with polyanions have a functional role in intracellular processes. Utilizing yeast protein arrays and five biotinylated cellular polyanion probes (actin, tubulin, heparin, heparan sulfate, and DNA), we identified proteins that interact with these probes and analyzed their structural and amino acid sequence requirements as well as their predicted functions in the yeast proteome. A living cell consists of a number of only partially defined compartments in constant communication. Both the interior and exterior of a cell and its compartments possess regions of high negative charge density. Exterior negatively charged entities such as phospholipids, proteoglycans, and polysialic acids as well as intracellular components including inositol phosphates, nucleotides, actin and tubulin microfilaments, DNA, RNA, and ribosomes render cells an ultimately highly crowded and extremely polyanionic environment. Considering the nature of this environment, it seems reasonable to postulate that numerous nonspecific interactions between cellular polyanions and proteins can take place. Cellular polyanions are of important functional significance to cells because at a minimum they (a) perform regulatory functions (e.g. binding of growth factors to proteoglycans) (1, 2), (b) transfer genetic information (RNA/DNA), (c) play a multitude of roles in cell structure and dynamics (actin and tubulin), (d) potentially serve as chaperones for protein folding (3-5), (e) stabilize proteins (6 -8), and (f) perhaps facilitate non-classical transport of proteins into and out of the cell (9 -11). In a recent exploration of the nonspecificity of polyanion-protein interactions, two-dimensional gels of proteins from cellular extracts in the presence and absence of matrix-bound polyanions were compared (12). It was demonstrated that hundreds to thousands of COS-7 proteins interacted with polyanions under the experimental conditions used. The polyanion with the greatest extent of interaction was heparin, binding 944 of 1,751 proteins resolved. It was observed that no direct relationship apparently exists between the overall net charge of the identified proteins and their binding potential to polyanions. This presumably reflects the presence of highly localized regions of positive charge in PABPs 1 and negates any requirement for an overall positive charge for protein-polyanion interaction (12). It was also observed that certain proteins in COS-7 cell extracts bound to actin, tubulin, and DNA with little obvious preference for any specific po...

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supporting

confidence: 74%

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays

Salamat‐Miller

Fang

Seidel

et al. 2006

Molecular & Cellular Proteomics

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“…Specific interaction aside, altering the salt concentration will result in an alteration in the ionic strength of the buffer, unless controlled for. An alteration in the ionic strength could affect interactions between amino acids residues in a protein by electrostatic screening [21] [22] leading to changes in the structural properties of the protein [23]. Therefore, an attempt was made to determine the role of Na + ions on the structure of the cGMP-binding GAFa domain of PDE5.…”

Section: Resultsmentioning

confidence: 99%

Buffer NaCl concentration regulates Renilla luciferase activity and ligand-induced conformational changes in the BRET-based PDE5 sensor

Biswas

Visweswariah

2017

Matters

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“…However, based on studies primarily of bacteria, it is first and foremost, neither a dilute aqueous solution nor a sack of enzymes and metabolites interacting by random diffusion. It is, instead, highly crowded (Verkman 2002;Spitzer and Poolman 2005;van den Bogaart et al 2007;Spitzer and Poolman 2009). When biomacromolecules occupy 20-30% of the cytoplasmic volume (the normal situation) it becomes highly structured with spatially and temporally self-constructing molecular devices.…”

Section: Sodium Toxicity Cellular Water and Cytosolic Conditionsmentioning

confidence: 99%

The integration of activity in saline environments: problems and perspectives

Cheeseman

2013

Functional Plant Biol.

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Abstract. The successful integration of activity in saline environments requires flexibility of responses at all levels, from genes to life cycles. Because plants are complex systems, there is no 'best' or 'optimal' solution and with respect to salt, glycophytes and halophytes are only the ends of a continuum of responses and possibilities. In this review, I briefly examine seven major aspects of plant function and their responses to salinity including transporters, secondary stresses, carbon acquisition and allocation, water and transpiration, growth and development, reproduction, and cytosolic function and 'integrity'. I conclude that new approaches are needed to move towards understanding either organismal integration or 'salt tolerance', especially cessation of protocols dependent on sudden, often lethal, shock treatments and the embracing of systems level resources. Some of the tools needed to understand the integration of activity and even 'salt stress' are already in hand, such as those for whole-transcriptome analysis. Others, ranging from discovery studies of the nature of the cytosol to expanded tool kits for proteomic, metabolomic and epigenomic studies, still need to be further developed. After resurrecting the distinction between applied stress and the resultant strain and noting that with respect to salinity, the strain is manifest in changes at all -omic levels, I conclude that it should be possible to model and quantify stress responses.

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Electrochemical structure of the crowded cytoplasm

Cited by 89 publications

References 48 publications

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays

A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays

Buffer NaCl concentration regulates Renilla luciferase activity and ligand-induced conformational changes in the BRET-based PDE5 sensor

The integration of activity in saline environments: problems and perspectives

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