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Volumn 5, Issue 2, 2013, Pages 187-194

Soft interactions and crowding

Author keywords

Crowding; Excluded volume; Osmolytes; Protein stability; Second virial coefficient; Synthetic polymers

Indexed keywords


EID: 84877014249     PISSN: 18672450     EISSN: 18672469     Source Type: Journal    
DOI: 10.1007/s12551-013-0104-4     Document Type: Review
Times cited : (210)

References (66)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 3
    • 79551565926 scopus 로고    scopus 로고
    • Internal and global protein motion assessed with a fusion construct and in-cell NMR spectroscopy
    • Barnes CO, Monteith WB, Pielak GJ (2011) Internal and global protein motion assessed with a fusion construct and in-cell NMR spectroscopy. ChemBioChem 12: 390-391.
    • (2011) ChemBioChem , vol.12 , pp. 390-391
    • Barnes, C.O.1    Monteith, W.B.2    Pielak, G.J.3
  • 4
    • 84870899331 scopus 로고    scopus 로고
    • Unexpected effects of macromolecular crowding on protein stability
    • Benton LA, Smith AE, Young GB, Pielak GJ (2012) Unexpected effects of macromolecular crowding on protein stability. Biochemistry 51: 9773-9775.
    • (2012) Biochemistry , vol.51 , pp. 9773-9775
    • Benton, L.A.1    Smith, A.E.2    Young, G.B.3    Pielak, G.J.4
  • 5
    • 0025608495 scopus 로고
    • The influence of macromolecular crowding on thermodynamic activity: solubility and dimerization constants for spherical and dumbbell-shaped molecules in a hard-sphere mixture
    • Berg OG (1990) The influence of macromolecular crowding on thermodynamic activity: solubility and dimerization constants for spherical and dumbbell-shaped molecules in a hard-sphere mixture. Biopolymers 30: 1027-1037.
    • (1990) Biopolymers , vol.30 , pp. 1027-1037
    • Berg, O.G.1
  • 6
    • 44349088135 scopus 로고    scopus 로고
    • Residue-level interrogation of macromolecular crowding effects on protein stability
    • Charlton LM, Barnes CO, Li C, Orans J, Young GB, Pielak GJ (2008) Residue-level interrogation of macromolecular crowding effects on protein stability. J Am Chem Soc 130: 6826-6830.
    • (2008) J Am Chem Soc , vol.130 , pp. 6826-6830
    • Charlton, L.M.1    Barnes, C.O.2    Li, C.3    Orans, J.4    Young, G.B.5    Pielak, G.J.6
  • 7
    • 77955249021 scopus 로고    scopus 로고
    • Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome C
    • Christiansen A, Wang Q, Samiotakis A, Cheung MS, Wittung-Stafshede P (2010) Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome C. Biochemistry 49: 6519-6530.
    • (2010) Biochemistry , vol.49 , pp. 6519-6530
    • Christiansen, A.1    Wang, Q.2    Samiotakis, A.3    Cheung, M.S.4    Wittung-Stafshede, P.5
  • 8
    • 0034681955 scopus 로고    scopus 로고
    • Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro
    • Courtenay ES, Capp MW, Anderson CF, Record MTJ (2000) Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro. Biochemistry 39: 4455-4471.
    • (2000) Biochemistry , vol.39 , pp. 4455-4471
    • Courtenay, E.S.1    Capp, M.W.2    Anderson, C.F.3    Record, M.T.J.4
  • 10
    • 43149125445 scopus 로고    scopus 로고
    • NMR spectroscopy reveals cytochrome C-poly(ethylene glycol) interactions
    • Crowley PB, Brett K, Muldoon J (2008) NMR spectroscopy reveals cytochrome C-poly(ethylene glycol) interactions. ChemBioChem 9: 685-688.
    • (2008) ChemBioChem , vol.9 , pp. 685-688
    • Crowley, P.B.1    Brett, K.2    Muldoon, J.3
  • 11
    • 79955024130 scopus 로고    scopus 로고
    • Protein interactions in the Escherichia coli cytosol: an impediment to in-cell NMR spectroscopy
    • Crowley PB, Chow E, Papkovskaia T (2011) Protein interactions in the Escherichia coli cytosol: an impediment to in-cell NMR spectroscopy. ChemBioChem 12: 1043-1048.
    • (2011) ChemBioChem , vol.12 , pp. 1043-1048
    • Crowley, P.B.1    Chow, E.2    Papkovskaia, T.3
  • 14
    • 80052479046 scopus 로고    scopus 로고
    • Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells
    • Dhar A, Girdhar K, Singh D, Gelman H, Ebbinghaus S, Gruebele M (2011) Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells. Biophys J 101: 421-430.
    • (2011) Biophys J , vol.101 , pp. 421-430
    • Dhar, A.1    Girdhar, K.2    Singh, D.3    Gelman, H.4    Ebbinghaus, S.5    Gruebele, M.6
  • 15
    • 77951643591 scopus 로고    scopus 로고
    • Protein folding stability and dynamics imaged in a living cell
    • Ebbinghaus S, Dhar A, McDonald JD, Gruebele M (2010) Protein folding stability and dynamics imaged in a living cell. Nat Methods 7: 319-323.
    • (2010) Nat Methods , vol.7 , pp. 319-323
    • Ebbinghaus, S.1    Dhar, A.2    McDonald, J.D.3    Gruebele, M.4
  • 16
    • 84855848788 scopus 로고    scopus 로고
    • Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding
    • Feig M, Sugita Y (2012) Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding. J Phys Chem B 116: 599-605.
    • (2012) J Phys Chem B , vol.116 , pp. 599-605
    • Feig, M.1    Sugita, Y.2
  • 18
    • 0034814860 scopus 로고    scopus 로고
    • Quantitative protein stability measurement in vivo
    • Ghaemmaghami S, Oas TG (2001) Quantitative protein stability measurement in vivo. Nat Struct Biol 8: 879-882.
    • (2001) Nat Struct Biol , vol.8 , pp. 879-882
    • Ghaemmaghami, S.1    Oas, T.G.2
  • 19
    • 84868130708 scopus 로고    scopus 로고
    • Temperature dependence of protein folding kinetics in living cells
    • Guo M, Xu Y, Gruebele M (2012) Temperature dependence of protein folding kinetics in living cells. Proc Natl Acad Sci USA 109: 17863-17867.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 17863-17867
    • Guo, M.1    Xu, Y.2    Gruebele, M.3
  • 20
    • 84858198890 scopus 로고    scopus 로고
    • Protein crowding affects hydration structure and dynamics
    • Harada R, Sugita Y, Feig M (2012) Protein crowding affects hydration structure and dynamics. J Am Chem Soc 134: 4842-4849.
    • (2012) J Am Chem Soc , vol.134 , pp. 4842-4849
    • Harada, R.1    Sugita, Y.2    Feig, M.3
  • 21
    • 0000469960 scopus 로고
    • Excluded volume theory of polymer-protein interactions based on polymer chain statistics
    • Hermans J (1982) Excluded volume theory of polymer-protein interactions based on polymer chain statistics. J Chem Phys 77: 2193-2203.
    • (1982) J Chem Phys , vol.77 , pp. 2193-2203
    • Hermans, J.1
  • 24
    • 0347004717 scopus 로고    scopus 로고
    • Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling
    • Ignatova Z, Gierasch LM (2004) Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling. Proc Natl Acad Sci USA 101: 523-528.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 523-528
    • Ignatova, Z.1    Gierasch, L.M.2
  • 27
    • 77955699308 scopus 로고    scopus 로고
    • Attractive protein-polymer interactions markedly alter the effect of macromolecular crowding on protein association equilibria
    • Jiao M, Li HT, Chen J, Minton AP, Liang Y (2010) Attractive protein-polymer interactions markedly alter the effect of macromolecular crowding on protein association equilibria. Biophys J 99: 914-923.
    • (2010) Biophys J , vol.99 , pp. 914-923
    • Jiao, M.1    Li, H.T.2    Chen, J.3    Minton, A.P.4    Liang, Y.5
  • 29
    • 63149177937 scopus 로고    scopus 로고
    • Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions
    • Li C, Pielak GJ (2009) Using NMR to distinguish viscosity effects from nonspecific protein binding under crowded conditions. J Am Chem Soc 131: 1368-1369.
    • (2009) J Am Chem Soc , vol.131 , pp. 1368-1369
    • Li, C.1    Pielak, G.J.2
  • 30
    • 43949111008 scopus 로고    scopus 로고
    • Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy
    • Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, Young GB, Macdonald JM, Pielak GJ (2008) Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy. J Am Chem Soc 130: 6310-6311.
    • (2008) J Am Chem Soc , vol.130 , pp. 6310-6311
    • Li, C.1    Charlton, L.M.2    Lakkavaram, A.3    Seagle, C.4    Wang, G.5    Young, G.B.6    Macdonald, J.M.7    Pielak, G.J.8
  • 31
    • 84876695491 scopus 로고    scopus 로고
    • NMR studies of weak protein-protein interactions
    • (in press)
    • Lian L-Y (2013) NMR studies of weak protein-protein interactions. Prog Nucl Magn Reson Spectrosc (in press).
    • (2013) Prog Nucl Magn Reson Spectrosc
    • Lian, L.-Y.1
  • 32
    • 0026729426 scopus 로고
    • Protein interactions with urea and guanidinium chloride: a calorimetric study
    • Makhatadze GI, Privalov PL (1992) Protein interactions with urea and guanidinium chloride: a calorimetric study. J Mol Biol 226: 491-505.
    • (1992) J Mol Biol , vol.226 , pp. 491-505
    • Makhatadze, G.I.1    Privalov, P.L.2
  • 33
    • 0343764928 scopus 로고
    • Contribution to statistical mechanics
    • Mayer JE (1942) Contribution to statistical mechanics. J Chem Phys 10: 629-643.
    • (1942) J Chem Phys , vol.10 , pp. 629-643
    • Mayer, J.E.1
  • 34
    • 77950792003 scopus 로고    scopus 로고
    • Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm
    • McGuffee SR, Elcock AH (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 6: e1000694.
    • (2010) PLoS Comput Biol , vol.6
    • McGuffee, S.R.1    Elcock, A.H.2
  • 35
    • 23544458810 scopus 로고
    • The statistical thermodynamics of multicomponent systems
    • McMillan WG, Mayer JE (1945) The statistical thermodynamics of multicomponent systems. J Chem Phys 13: 276-305.
    • (1945) J Chem Phys , vol.13 , pp. 276-305
    • McMillan, W.G.1    Mayer, J.E.2
  • 36
    • 77955707910 scopus 로고    scopus 로고
    • Volume exclusion and soft interaction effects on protein stability under crowded conditions
    • Miklos AC, Li C, Sharaf NG, Pielak GJ (2010) Volume exclusion and soft interaction effects on protein stability under crowded conditions. Biochemistry 49: 6984-6991.
    • (2010) Biochemistry , vol.49 , pp. 6984-6991
    • Miklos, A.C.1    Li, C.2    Sharaf, N.G.3    Pielak, G.J.4
  • 38
    • 84985735713 scopus 로고
    • Excluded volume as a determinant of macromolecular structure and reactivity
    • Minton AP (1981) Excluded volume as a determinant of macromolecular structure and reactivity. Biopolymers 20: 2093-2120.
    • (1981) Biopolymers , vol.20 , pp. 2093-2120
    • Minton, A.P.1
  • 39
    • 0028822574 scopus 로고
    • A molecular model for the dependence of the osmotic pressure of bovine serum albumin upon concentration and pH
    • Minton AP (1995) A molecular model for the dependence of the osmotic pressure of bovine serum albumin upon concentration and pH. Biophys Chem 57: 65-70.
    • (1995) Biophys Chem , vol.57 , pp. 65-70
    • Minton, A.P.1
  • 40
    • 84872904773 scopus 로고    scopus 로고
    • Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding
    • Minton AP (2013) Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding. Biopolymers 99: 239-244.
    • (2013) Biopolymers , vol.99 , pp. 239-244
    • Minton, A.P.1
  • 43
    • 77956022419 scopus 로고    scopus 로고
    • Enthalpically driven peptide stabilization by protective osmolytes
    • Politi R, Harries D (2010) Enthalpically driven peptide stabilization by protective osmolytes. Chem Commun (Camb) 46: 6449-6451.
    • (2010) Chem Commun (Camb) , vol.46 , pp. 6449-6451
    • Politi, R.1    Harries, D.2
  • 44
    • 0002278843 scopus 로고
    • Scaled particle methods in the statistical thermodynamics of fluids
    • Reiss H (1966) Scaled particle methods in the statistical thermodynamics of fluids. Adv Chem Phys 9: 1-84.
    • (1966) Adv Chem Phys , vol.9 , pp. 1-84
    • Reiss, H.1
  • 45
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • Richards FM (1977) Areas, volumes, packing, and protein structure. Annu Rev Biophys Bioeng 6: 151-176.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 46
    • 0035853141 scopus 로고    scopus 로고
    • Direct observation of the enhancement of noncooperative protein self-assembly by macromolecular crowding: indefinite linear self-association of bacterial cell division protein Ftsz
    • Rivas G, Fernandez JA, Minton AP (2001) Direct observation of the enhancement of noncooperative protein self-assembly by macromolecular crowding: indefinite linear self-association of bacterial cell division protein Ftsz. Proc Natl Acad Sci USA 98: 3150-3155.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 3150-3155
    • Rivas, G.1    Fernandez, J.A.2    Minton, A.P.3
  • 49
    • 0037470574 scopus 로고    scopus 로고
    • Effect of dextran on protein stability and conformation attributed to macromolecular crowding
    • Sasahara K, McPhie P, Minton AP (2003) Effect of dextran on protein stability and conformation attributed to macromolecular crowding. J Mol Biol 326: 1227-1237.
    • (2003) J Mol Biol , vol.326 , pp. 1227-1237
    • Sasahara, K.1    McPhie, P.2    Minton, A.P.3
  • 50
    • 33947437221 scopus 로고
    • Physical chemistry of protein solutions; derivation of the equations for the osmotic pressure
    • Scatchard G (1946) Physical chemistry of protein solutions; derivation of the equations for the osmotic pressure. J Am Chem Soc 68: 2315-2319.
    • (1946) J Am Chem Soc , vol.68 , pp. 2315-2319
    • Scatchard, G.1
  • 51
    • 0038311869 scopus 로고    scopus 로고
    • Protein stability in mixed solvents: a balance of contact interactions and excluded volume
    • Schellman J (2003) Protein stability in mixed solvents: a balance of contact interactions and excluded volume. Biophys J 85: 108-125.
    • (2003) Biophys J , vol.85 , pp. 108-125
    • Schellman, J.1
  • 53
    • 66749128608 scopus 로고    scopus 로고
    • The role of biomacromolecular crowding, ionic strength, and physicochemical gradients in the complexities of life's emergence
    • Spitzer J, Poolman B (2009) The role of biomacromolecular crowding, ionic strength, and physicochemical gradients in the complexities of life's emergence. Microbiol Mol Biol Rev 73: 371-388.
    • (2009) Microbiol Mol Biol Rev , vol.73 , pp. 371-388
    • Spitzer, J.1    Poolman, B.2
  • 54
    • 37649016316 scopus 로고    scopus 로고
    • Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin
    • Stagg L, Zhang SQ, Cheung MS, Wittung-Stafshede P (2007) Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin. Proc Natl Acad Sci USA 104: 18976-18981.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 18976-18981
    • Stagg, L.1    Zhang, S.Q.2    Cheung, M.S.3    Wittung-Stafshede, P.4
  • 55
    • 33749365298 scopus 로고    scopus 로고
    • A molecular mechanism for osmolyte-induced protein stability
    • Street TO, Bolen DW, Rose GD (2006) A molecular mechanism for osmolyte-induced protein stability. Proc Natl Acad Sci USA 103: 13997-14002.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 13997-14002
    • Street, T.O.1    Bolen, D.W.2    Rose, G.D.3
  • 56
    • 84870931817 scopus 로고    scopus 로고
    • Diversity in the mechanisms of cosolute action on biomolecular processes
    • Sukenik S, Liel S, Gilman-Polit R, Harries D (2012) Diversity in the mechanisms of cosolute action on biomolecular processes. Faraday Discuss 160: 1-13.
    • (2012) Faraday Discuss , vol.160 , pp. 1-13
    • Sukenik, S.1    Liel, S.2    Gilman-Polit, R.3    Harries, D.4
  • 58
    • 0027310845 scopus 로고
    • The control of protein stability and association by weak interactions with water: how do solvents control these processes?
    • Timasheff SN (1993) The control of protein stability and association by weak interactions with water: how do solvents control these processes? Annu Rev Biophys Biomol Struct 22: 67-97.
    • (1993) Annu Rev Biophys Biomol Struct , vol.22 , pp. 67-97
    • Timasheff, S.N.1
  • 59
    • 77955686807 scopus 로고    scopus 로고
    • Effects of proteins on protein diffusion
    • Wang Y, Li C, Pielak GJ (2010) Effects of proteins on protein diffusion. J Am Chem Soc 132: 9392-9397.
    • (2010) J Am Chem Soc , vol.132 , pp. 9392-9397
    • Wang, Y.1    Li, C.2    Pielak, G.J.3
  • 60
    • 80055013471 scopus 로고    scopus 로고
    • Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy
    • 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.
    • (2011) Biochemistry , vol.50 , pp. 9225-9236
    • Wang, Q.1    Zhuravleva, A.2    Gierasch, L.M.3
  • 62
    • 0034745484 scopus 로고    scopus 로고
    • Second virial coefficients as a measure of protein-osmolyte interactions
    • Weatherly GT, Pielak GJ (2001) Second virial coefficients as a measure of protein-osmolyte interactions. Protein Sci 10: 12-16.
    • (2001) Protein Sci , vol.10 , pp. 12-16
    • Weatherly, G.T.1    Pielak, G.J.2
  • 63
    • 0004154123 scopus 로고
    • Thermodynamic non-ideality and protein interactions
    • R. B. Gregory (Ed.), New York: Marcel Dekker
    • Winzor DJ, Wills PR (1995) Thermodynamic non-ideality and protein interactions. In: Gregory RB (ed) Protein-solvent interactions. Marcel Dekker, New York.
    • (1995) Protein-Solvent Interactions
    • Winzor, D.J.1    Wills, P.R.2
  • 64
    • 84864479275 scopus 로고    scopus 로고
    • Effects of macromolecular crowding on the structural stability of human alpha-lactalbumin
    • 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.
    • (2012) Acta Biochim Biophys Sin (Shanghai) , vol.44 , pp. 703-711
    • Zhang, D.L.1    Wu, L.J.2    Chen, J.3    Liang, Y.4
  • 65
    • 41049090929 scopus 로고    scopus 로고
    • Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences
    • Zhou HX, Rivas G, Minton AP (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37: 375-397.
    • (2008) Annu Rev Biophys , vol.37 , pp. 375-397
    • Zhou, H.X.1    Rivas, G.2    Minton, A.P.3
  • 66
    • 0026344818 scopus 로고
    • Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli
    • Zimmerman SB, Trach SO (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol 222: 599-620.
    • (1991) J Mol Biol , vol.222 , pp. 599-620
    • Zimmerman, S.B.1    Trach, S.O.2


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