165:
17:
384:. The underlying physical mechanism by which macromolecular crowding helps to stabilize proteins in their folded state is often explained in terms of excluded volume - the volume inaccessible to the proteins due to their interaction with macromolecular crowders. This notion goes back to Asakura and Oosawa, who have described
350:
performed in dilute solution may fail to reflect the actual process and its kinetics taking place in the cytosol. One approach to produce more accurate measurements would be to use highly concentrated extracts of cells, to try to maintain the cell contents in a more natural state. However, such
283:
in the cell, which could counteract this reduction in folding efficiency. It has also been shown that macromolecular crowding affects protein-folding dynamics as well as overall protein shape where distinct conformational changes are accompanied by secondary structure alterations implying that
219:
and shape of the molecule involved, although mass seems to be the major factor – with the effect being stronger with larger molecules. Notably, the size of the effect is non-linear, so macromolecules are much more strongly affected than are small molecules such as
393:, which are preferentially excluded from proteins, also shift the protein folding equilibrium towards the folded state. However, it has been shown by various methods, both experimental and theoretical, that depletion forces are not always entropic in nature.
307:. Crystallins are present in the lens at extremely high concentrations, over 500 mg/ml, and at these levels crowding effects are very strong. The large crowding effect adds to the thermal stability of the crystallins, increasing their resistance to
388:
induced by steric, hard-core, interactions. A hallmark of the mechanism inferred from the above is that the effect is completely a-thermal, and thus completely entropic. These ideas were also proposed to explain why small cosolutes, namely protective
371:
to experimental media. However, using such artificial crowding agents can be complicated, as these crowding molecules can sometimes interact in other ways with the process being examined, such as by binding weakly to one of the components.
113:). The study of biochemical processes under realistically crowded conditions is very important, since these conditions are a ubiquitous property of all cells and crowding may be essential for the efficient operation of metabolism. Indeed,
271:. Here, the crowding effect can accelerate the folding process, since a compact folded protein will occupy less volume than an unfolded protein chain. However, crowding can reduce the yield of correctly folded protein by increasing
1521:
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".
180:
These high concentrations of macromolecules occupy a large proportion of the volume of the cell, which reduces the volume of solvent that is available for other macromolecules. This
141:
can contain up to 4,288 different types of proteins, and about 1,000 of these types are produced at a high enough level to be easily detected. Added to this mix are various forms of
1464:
Hochmair J, Exner C, Franck M, Dominguez-Baquero A, Diez L, Brognaro H, Kraushar ML, Mielke T, Radbruch H, Kaniyappan S, Falke S, Mandelkow E, Betzel C, Wegmann S (June 2022).
2106:
351:
extracts contain many kinds of biologically active molecules, which can interfere with the phenomena being studied. Consequently, crowding effects are mimicked
93:
This crowding effect can make molecules in cells behave in radically different ways than in test-tube assays. Consequently, measurements of the properties of
244:. For example, the increase in the strength of interactions between proteins and DNA produced by crowding may be of key importance in processes such as
82:
available for other molecules in the solution, which has the result of increasing their effective concentrations. Crowding can promote formation of a
2114:
Satyam A; et al. (May 2014). "Macromolecular
Crowding Meets Tissue Engineering by Self-Assembly: A Paradigm Shift in Regenerative Medicine".
1388:
Steadman BL, Trautman PA, Lawson EQ, et al. (December 1989). "A differential scanning calorimetric study of the bovine lens crystallins".
1274:
212:. Crowding may also affect enzyme reactions involving small molecules if the reaction involves a large change in the shape of the enzyme.
1657:
168:
The volume of accessible solvent (red) for two molecules of widely different sizes (black circles) at high concentrations of
2019:
Sapir, L; Harries, D. (2015). "Macromolecular
Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions".
1466:"Molecular crowding and RNA synergize to promote phase separation, microtubule interaction, and seeding of Tau condensates"
796:
863:"The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media"
1701:
Asakura, Sho; Oosawa, F (1 January 1954). "On
Interaction between Two Bodies Immersed in a Solution of Macromolecules".
228:. Macromolecular crowding is therefore an effect exerted by large molecules on the properties of other large molecules.
311:. This effect may partly explain the extraordinary resistance shown by the lens to damage caused by high temperatures.
2183:
2178:
308:
953:"Macromolecular crowding effects on macromolecular interactions: some implications for genome structure and function"
1992:
Sapir, L; Harries, D. (2015). "Is the depletion force entropic? Molecular crowding beyond steric interactions".
2188:
1298:
Dirar Homouz; Michael Perham; Antonios
Samiotakis; Margaret S. Cheung & Pernilla Wittung-Stafshede (2008).
245:
509:"Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli"
107:) in dilute solutions may be different by many orders of magnitude from the true values seen in living cells (
904:"Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences"
83:
1736:
Asakura, Sho; Oosawa, F. (1958). "Interaction between
Particles Suspended in Solutions of Macromolecules".
410:
347:
331:
323:
78:
of macromolecules. Crowding occurs since these high concentrations of macromolecules reduce the volume of
2100:
296:
197:
1051:"Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell"
551:
Minton AP (July 2006). "How can biochemical reactions within cells differ from those in test tubes?".
2123:
1838:
Politi, R; Harries, D. (2010). "Enthalpically Driven
Peptide Stabilization by Protective Osmolytes".
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1745:
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by favoring the association of macromolecules, such as when multiple proteins come together to form
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356:
276:
272:
257:
205:
1912:
Sukenik, S; Sapir, L.; Harries, D. (2013). "Balance of enthalpy and entropy in depletion forces".
1605:
Minton, A. (1981). "Excluded Volume as a
Determinant of Macromolecular Structure and Reactivity".
2157:
1939:
1921:
1675:
1622:
1503:
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576:
315:
252:. Crowding has also been suggested to be involved in processes as diverse as the aggregation of
1771:
Stagg, Loren; Zhang, Shao-Qing; Cheung, Margaret S.; Wittung-Stafshede, Pernilla (2007-11-27).
601:"DNA binding proteins explore multiple local configurations during docking via rapid rebinding"
599:
Ganji, Mahipal; Docter, Margreet; Le Grice, Stuart F. J.; Abbondanzieri, Elio A. (2016-09-30).
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284:
crowding-induced shape changes may be important for protein function and malfunction in vivo.
2059:"Life in a crowded world: Workshop on the Biological Implications of Macromolecular Crowding"
919:
380:
A major importance of macromolecular crowding to biological systems stems from its effect on
2139:
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2001:
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chromosome, giving a total concentration of macromolecules of between 300 and 400 mg/ml. In
129:
66:
1687:
381:
264:
249:
201:
181:
119:
studies have shown that crowding greatly influences binding stability of proteins to DNA.
2127:
1788:
1749:
1714:
1315:
1207:
1007:
992:"Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect"
812:
164:
2083:
2058:
1874:
1815:
1772:
1582:
1557:
1490:
1465:
1423:
Bloemendal H, de Jong W, Jaenicke R, Lubsen NH, Slingsby C, Tardieu A (November 2004).
1334:
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903:
829:
772:
747:
633:
600:
405:
295:. These proteins have to remain stable and in solution for the lens to be transparent;
292:
225:
216:
57:
1773:"Molecular crowding enhances native structure and stability of Îą/Îē protein flavodoxin"
1649:
1075:
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991:
820:
682:
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482:
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368:
189:
169:
49:
25:
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1943:
1626:
580:
314:
Crowding may also play a role in diseases that involve protein aggregation, such as
1176:
343:
287:
A particularly striking example of the importance of crowding effects involves the
241:
237:
158:
33:
723:
706:
469:
Ellis RJ (October 2001). "Macromolecular crowding: obvious but underappreciated".
673:
184:
effect increases the effective concentration of macromolecules (increasing their
2005:
1935:
1757:
1266:
842:
327:
1777:
Proceedings of the
National Academy of Sciences of the United States of America
1618:
1534:
1147:
Ellis RJ, Minton AP (May 2006). "Protein aggregation in crowded environments".
1115:
1066:
137:(Ξm) long and 0.5 Ξm in diameter, with a cell volume of 0.6 - 0.7 Ξm. However,
1877:(2012). "Unexpected Effects of Macromolecular Crowding on Protein Stability".
1192:"The effect of macromolecular crowding on chaperonin-mediated protein folding"
319:
288:
268:
253:
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134:
98:
75:
16:
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1806:
1481:
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1324:
1300:"Crowded, cell-like environment induces shape changes in aspherical protein"
1253:
Molecular
Aspects of the Stress Response: Chaperones, Membranes and Networks
390:
150:
71:
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1016:
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642:
572:
490:
1425:"Ageing and vision: structure, stability and function of lens crystallins"
1409:
1374:
1235:
1035:
976:
838:
763:
732:
691:
532:
450:
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797:"Confinement as a determinant of macromolecular structure and reactivity"
616:
304:
115:
103:
1573:
1401:
1160:
2144:
1851:
1100:"Effects of macromolecular crowding on protein folding and aggregation"
658:"Cell volume increase in Escherichia coli after shifts to richer media"
364:
109:
87:
79:
61:
53:
29:
21:
1970:
1957:
Sapir, L; Harries, D. (2014). "Origin of
Enthalpic Depletion Forces".
1890:
1722:
564:
360:
209:
94:
952:
748:"The Escherichia coli proteome: past, present, and future prospects"
508:
355:
by adding high concentrations of relatively inert molecules such as
161:, this meshwork divides the cytosol into a network of narrow pores.
1926:
1644:. International Review of Cytology. Vol. 215. pp. 1â31.
280:
163:
15:
1359:"Cataract as a protein condensation disease: the Proctor Lecture"
705:
Blattner FR, Plunkett G, Bloch CA, et al. (September 1997).
127:
The interior of cells is a crowded environment. For example, an
146:
142:
172:(grey circles). Reducing the available volume increases the
1558:"Protein folding by the effects of macromolecular crowding"
1049:
van den Berg B, Wain R, Dobson CM, Ellis RJ (August 2000).
1556:
Tokuriki N, Kinjo M, Negi S, et al. (January 2004).
260:, and the responses of cells to changes in their volume.
707:"The complete genome sequence of Escherichia coli K-12"
56:
are present. Such conditions occur routinely in living
1098:
van den Berg B, Ellis RJ, Dobson CM (December 1999).
196:
of their reactions. In particular this effect alters
215:
The size of the crowding effect depends on both the
2057:Rivas G, Ferrone, F, Hertzfeld J. (December 2003).
1250:
275:. Crowding may also increase the effectiveness of
236:Macromolecular crowding is an important effect in
153:the cell's interior is further crowded by the
8:
2105:: CS1 maint: multiple names: authors list (
429:Goodsell DS (1991). "Inside a living cell".
502:
500:
376:Macromolecular crowding and protein folding
2143:
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1814:
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681:
632:
546:
544:
542:
334:under crowded conditions within neurons.
1873:Benton, L.A.; Smith, A.E.; Young, G.B.;
1249:Ellis RJ (2007). "Protein Misassembly".
920:10.1146/annurev.biophys.37.032807.125817
507:Zimmerman SB, Trach SO (December 1991).
44:alters the properties of molecules in a
990:Zimmerman SB, Harrison B (April 1987).
464:
462:
460:
421:
2098:
1683:
1673:
7:
1190:Martin J, Hartl FU (February 1997).
902:Zhou HX, Rivas G, Minton AP (2008).
594:
592:
590:
24:of cells alters the properties of
14:
1994:Curr. Opin. Colloid Interface Sci
1914:Curr. Opin. Colloid Interface Sci
101:that are made in the laboratory (
1442:10.1016/j.pbiomolbio.2003.11.012
656:Kubitschek HE (1 January 1990).
342:Due to macromolecular crowding,
1703:The Journal of Chemical Physics
1357:Benedek GB (1 September 1997).
20:Macromolecular crowding in the
951:Zimmerman SB (November 1993).
291:that fill the interior of the
263:The importance of crowding in
1:
1650:10.1016/S0074-7696(02)15003-0
1523:Biochem. Biophys. Res. Commun
821:10.1016/S0006-3495(92)81663-6
724:10.1126/science.277.5331.1453
483:10.1016/S0968-0004(01)01938-7
267:is of particular interest in
208:bind to their targets in the
1363:Invest. Ophthalmol. Vis. Sci
1304:Proc. Natl. Acad. Sci. U.S.A
1196:Proc. Natl. Acad. Sci. U.S.A
996:Proc. Natl. Acad. Sci. U.S.A
969:10.1016/0167-4781(93)90142-Z
746:Han MJ, Lee SY (June 2006).
674:10.1128/jb.172.1.94-101.1990
525:10.1016/0022-2836(91)90499-V
443:10.1016/0968-0004(91)90083-8
188:), which in turn alters the
70:contains about 300â400
48:when high concentrations of
2006:10.1016/j.cocis.2014.12.003
1936:10.1016/j.cocis.2013.10.002
1758:10.1002/pol.1958.1203312618
1267:10.1007/978-0-387-39975-1_1
2210:
1738:Journal of Polymer Science
1642:Protein-water interactions
1619:10.1002/bip.1981.360201006
1535:10.1016/j.bbrc.2011.01.037
795:Minton AP (October 1992).
752:Microbiol. Mol. Biol. Rev
2075:10.1038/sj.embor.7400056
2033:10.1021/acs.jctc.5b00258
1482:10.15252/embj.2021108882
1429:Prog. Biophys. Mol. Biol
1116:10.1093/emboj/18.24.6927
1067:10.1093/emboj/19.15.3870
348:biophysical measurements
1798:10.1073/pnas.0705127104
1640:Parsegian, VA. (2002).
1325:10.1073/pnas.0803672105
332:neurofibrillary tangles
174:effective concentration
84:biomolecular condensate
42:macromolecular crowding
2136:10.1002/adma.201304428
2021:J. Chem. Theory Comput
1217:10.1073/pnas.94.4.1107
1017:10.1073/pnas.84.7.1871
957:Biochim. Biophys. Acta
880:10.1074/jbc.R100005200
605:Nucleic Acids Research
411:Colligative properties
303:of crystallins causes
198:dissociation constants
177:
37:
764:10.1128/MMBR.00036-05
322:forms aggregates and
194:equilibrium constants
167:
133:cell is only about 2
19:
206:DNA-binding proteins
60:; for instance, the
2128:2014AdM....26.3024S
1959:J. Phys. Chem. Lett
1789:2007PNAS..10418976S
1783:(48): 18976â18981.
1750:1958JPoSc..33..183A
1715:1954JChPh..22.1255A
1574:10.1110/ps.03288104
1402:10.1021/bi00451a017
1316:2008PNAS..10511754H
1310:(33): 11754â11759.
1208:1997PNAS...94.1107M
1161:10.1515/BC.2006.064
1008:1987PNAS...84.1871Z
813:1992BpJ....63.1090M
471:Trends Biochem. Sci
431:Trends Biochem. Sci
357:polyethylene glycol
324:alzheimer's disease
273:protein aggregation
258:sickle-cell disease
2184:Tissue engineering
2179:Physical chemistry
2116:Advanced Materials
1852:10.1039/c0cc01763a
861:Minton AP (2001).
617:10.1093/nar/gkw666
316:sickle cell anemia
277:chaperone proteins
178:
176:of macromolecules.
90:phase separation.
40:The phenomenon of
38:
2122:(19): 3024â3034.
1971:10.1021/jz5002715
1891:10.1021/bi300909q
1885:(49): 9773â9775.
1846:(35): 6449â6451.
1723:10.1063/1.1740347
1613:(10): 2093â2120.
1276:978-0-387-39974-4
717:(5331): 1453â74.
611:(17): 8376â8384.
565:10.1242/jcs.03063
559:(Pt 14): 2863â9.
202:protein complexes
186:chemical activity
157:that make up the
155:protein filaments
123:Cause and effects
2201:
2165:
2147:
2110:
2104:
2096:
2086:
2045:
2044:
2027:(7): 3478â3490.
2016:
2010:
2009:
1989:
1983:
1982:
1965:(7): 1061â1065.
1954:
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1864:
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1835:
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1744:(126): 183â192.
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908:Annu Rev Biophys
899:
893:
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873:(14): 10577â80.
858:
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846:
841:. Archived from
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504:
495:
494:
466:
455:
454:
426:
386:depletion forces
130:Escherichia coli
97:or processes in
67:Escherichia coli
2209:
2208:
2204:
2203:
2202:
2200:
2199:
2198:
2189:Protein methods
2169:
2168:
2113:
2097:
2056:
2053:
2048:
2018:
2017:
2013:
1991:
1990:
1986:
1956:
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1911:
1910:
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1476:(11): e108882.
1463:
1462:
1458:
1422:
1421:
1417:
1387:
1386:
1382:
1369:(10): 1911â21.
1356:
1355:
1351:
1297:
1296:
1292:
1277:
1248:
1247:
1243:
1189:
1188:
1184:
1146:
1145:
1141:
1110:(24): 6927â33.
1097:
1096:
1092:
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1043:
989:
988:
984:
950:
949:
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901:
900:
896:
860:
859:
850:
807:(4): 1090â100.
794:
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789:
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744:
740:
704:
703:
699:
655:
654:
650:
598:
597:
588:
550:
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506:
505:
498:
477:(10): 597â604.
468:
467:
458:
428:
427:
423:
419:
402:
396:
382:protein folding
378:
340:
265:protein folding
250:DNA replication
234:
182:excluded volume
145:and the cell's
125:
12:
11:
5:
2207:
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2186:
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2171:
2170:
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2052:
2051:External links
2049:
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1920:(6): 495â501.
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1684:|journal=
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1061:(15): 3870â5.
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894:
848:
845:on 2008-09-07.
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758:(2): 362â439.
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170:macromolecules
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