The physical chemistry of cytoplasm and its influence on cell function: An update

Molecular Biology of the Cell

Volumn 24, Issue 17, 2013, Pages 2593-2596

  Luby Phelps, Kate ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEURAL WISKOTT ALDRICH SYNDROME PROTEIN;

CELL COMPARTMENTALIZATION; CELL FUNCTION; CELL INCLUSION; CELL WATER; CELLULAR PARAMETERS; CYTOPLASM; DIFFUSION; HUMAN; INTRACELLULAR MEMBRANE; LIPID METABOLISM; MEDICAL LITERATURE; METABOLISM; MOLECULAR INTERACTION; NONHUMAN; PHASE SEPARATION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; REVIEW;

CELL PHYSIOLOGICAL PROCESSES; CELL SIZE; CYTOPLASM; DIFFUSION; MACROMOLECULAR SUBSTANCES; PHYSICOCHEMICAL PHENOMENA; SIGNAL TRANSDUCTION;

EID: 84883390305     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E12-08-0617     Document Type: Review

References (32)

1. Dix JA, Verkman AS (2008). Crowding effects on diffusion in solutions and cells. Annu Rev Biophys 37, 247-263.
2. Elcock AH (2010). Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 20, 196-206.
3. Goychuk I (2012). Fractional-time random walk subdiffusion and anomalous transport with finite mean residence times: faster, not slower. Phys Rev E Stat Nonlin Soft Matter Phys 86, 021113.
4. Hancock R (2012). Structure of metaphase chromosomes: a role for effects of macromolecular crowding. PloS One 7, e36045.
5. Hong J, Gierasch LM (2010). Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state. J Am Chem Soc 132, 10445-10452.
6. Hyman AA, Simons K (2012). Beyond oil and water - phase transitions in cells. Science 337, 1047-1049.
7. Inomata K et al. (2009). High-resolution multi-dimensional NMR spectroscopy of proteins in human cells. Nature 458, 106-109.
8. Jasnin M, Moulin M, Haertlein M, Zaccai G, Tehei M (2008). Down to atomic-scale intracellular water dynamics. EMBO Rep 9, 543-547.
9. Jo Y, Hartman IZ, DeBose-Boyd RA (2013). Ancient ubiquitous protein-1 mediates sterol-induced ubiquitination of 3-hydroxy-3-methylglutaryl CoA reductase in lipid droplet-associated endoplasmic reticulum membranes. Mol Biol Cell 24, 169-183.
10. Kato M et al. (2012). Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753-767.
11. Li P et al. (2012). Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336-340.
12. Long MS, Jones CD, Helfrich MR, Mangeney-Slavin LK, Keating CD (2005). Dynamic microcompartmentation in synthetic cells. Proc Nat Acad Sci USA 102, 5920-5925.
13. Luby-Phelps K (2000). Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int Rev Cytol 192, 189-221.
14. Nenninger A, Mastroianni G, Mullineaux CW (2010). Size dependence of protein diffusion in the cytoplasm of Escherichia coli. J Bacteriol 192, 4535-4540.
15. Nevo-Dinur K, Govindarajan S, Amster-Choder O (2012). Subcellular localization of RNA and proteins in prokaryotes. Trends Genet 28, 314-322.
16. Norris MG, Malys N (2011). What is the true enzyme kinetics in the biological system? An investigation of macromolecular crowding effect upon enzyme kinetics of glucose-6-phosphate dehydrogenase. Biochem Biophys Res Commun 405, 388-392.
17. O'Connell JD, Zhao A, Ellington AD, Marcotte EM (2012). Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu Rev Cell Dev Biol 28, 89-111.
18. Persson E, Halle B (2008). Cell water dynamics on multiple time scales. Proc Natl Acad Sci USA 105, 6266-6271.
19. Potma EO, de Boeij WP, Wiersma DA (2001). Femtosecond dynamics of intracellular water probed with nonlinear optical Kerr effect microspectroscopy. Biophys J 80, 3019-3024.
20. Saxton MJ (2012). Wanted: a positive control for anomalous subdiffusion. Biophys J 103, 2411-2422.
21. Schlesinger AP, Wang Y, Tadeo X, Millet O, Pielak GJ (2011). Macromolecular crowding fails to fold a globular protein in cells. J Am Chem Soc 133, 8082-8085.
22. Stadler AM, Embs JP, Digel I, Artmann GM, Unruh T, Buldt G, Zaccai G (2008). Cytoplasmic water and hydration layer dynamics in human red blood cells. J Am Chem Soc 130, 16852-16853.
23. Stagg L, Christiansen A, Wittung-Stafshede P (2011). Macromolecular crowding tunes folding landscape of parallel alpha/beta protein, apoflavodoxin. J Am Chem Soc 133, 646-648.
24. Walther TC, Farese RV (2012). Lipid droplets and cellular lipid metabolism. Annu Rev Biochem 81, 687-714.
25. Wang Q, Zhuravleva A, Gierasch LM (2011). Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy. Biochemistry 50, 9225-9236.
26. Wang Y, Sarkar M, Smith AE, Krois AS, Pielak GJ (2012). Macromolecular crowding and protein stability. J Am Chem Soc 134, 16614-16618.
27. Weber SC, Brangwynne CP (2012). Getting RNA and protein in phase. Cell 149, 1188-1191.
28. Welch GR, Clegg JS (2010). From protoplasmic theory to cellular systems biology: a 150-year reflection. Am J Physiol Cell Physiol 298, C1280-C1290.
29. Wilson EB (1899). The structure of protoplasm. Science 10, 33-45.
30. Yeates TO, Thompson MC, Bobik TA (2011). The protein shells of bacterial microcompartment organelles. Curr Opin Struct Biol 21, 223-231.
31. Zhang DL, Wu LJ, Chen J, Liang Y (2012). Effects of macromolecular crowding on the structural stability of human alpha-lactalbumin. Acta Biochim Biophys Sin (Shanghai) 44, 703-711.
32. Zhou HX, Rivas G, Minton AP (2008). Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37, 375-397.