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Volumn 397, Issue 5, 2010, Pages 1329-1338

Protein folding requires crowd control in a simulated cell

Author keywords

Macromolecular crowding; Protein aggregation; Protein expression; Protein misfolding; Protein structure prediction

Indexed keywords

ARTICLE; CROWDING; HYDROPHOBICITY; PREDICTION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; PROTEIN TERTIARY STRUCTURE;

EID: 77950518894     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.01.074     Document Type: Article
Times cited : (78)

References (49)
  • 1
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
    • Liwo A., Khalili M., Scheraga H.A. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl Acad. Sci. USA 2005, 102:2362-2367.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Scheraga, H.A.3
  • 3
    • 64549115839 scopus 로고    scopus 로고
    • Protein structure prediction: when is it useful?
    • Zhang Y. Protein structure prediction: when is it useful?. Curr. Opin. Struct. Biol. 2009, 19:145-155.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 145-155
    • Zhang, Y.1
  • 4
    • 36749055649 scopus 로고    scopus 로고
    • Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
    • Das R., Qian B., Raman S., Vernon R., Thompson J., Bradley P., et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 2007, 69:118-128.
    • (2007) Proteins , vol.69 , pp. 118-128
    • Das, R.1    Qian, B.2    Raman, S.3    Vernon, R.4    Thompson, J.5    Bradley, P.6
  • 5
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
    • (2008) BMC Bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 6
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: a case study using the Phyre server
    • Kelley L.A., Sternberg M.J.E. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4:363-371.
    • (2009) Nat. Protoc. , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.E.2
  • 7
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soeding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33:W244-W248.
    • (2005) Nucleic Acids Res. , vol.33
    • Soeding, J.1    Biegert, A.2    Lupas, A.N.3
  • 8
    • 34547496252 scopus 로고    scopus 로고
    • Protein folding under confinement: a role for solvent
    • Lucent D., Vishal V., Pande V.S. Protein folding under confinement: a role for solvent. Proc. Natl Acad. Sci. USA 2007, 104:10430-10434.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 10430-10434
    • Lucent, D.1    Vishal, V.2    Pande, V.S.3
  • 9
    • 61549140397 scopus 로고    scopus 로고
    • Blind test of physics-based prediction of protein structures
    • Shell M.S., Ozkan S.B., Voelz V., Wu G.A., Dill K.A. Blind test of physics-based prediction of protein structures. Biophys. J. 2009, 96:917-924.
    • (2009) Biophys. J. , vol.96 , pp. 917-924
    • Shell, M.S.1    Ozkan, S.B.2    Voelz, V.3    Wu, G.A.4    Dill, K.A.5
  • 11
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt M., Warshel A. Computer simulation of protein folding. Nature 1975, 253:694-698.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 12
    • 0035253217 scopus 로고    scopus 로고
    • Macromolecular crowding: an important but neglected aspect of the intracellular environment
    • Ellis R.J. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr. Opin. Struct. Biol. 2001, 11:114-119.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 114-119
    • Ellis, R.J.1
  • 14
    • 17844393334 scopus 로고    scopus 로고
    • A model of intracellular organization
    • Pielak G.J. A model of intracellular organization. Proc. Natl Acad. Sci. USA 2005, 102:5901-5902.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 5901-5902
    • Pielak, G.J.1
  • 16
    • 25444487734 scopus 로고    scopus 로고
    • Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations
    • Minton A.P. Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations. J. Pharm. Sci. 2005, 94:1668-1675.
    • (2005) J. Pharm. Sci. , vol.94 , pp. 1668-1675
    • Minton, A.P.1
  • 17
    • 0033572725 scopus 로고    scopus 로고
    • Effects of macromolecular crowding on protein folding and aggregation
    • van den Berg B., Ellis R.J., Dobson C.M. Effects of macromolecular crowding on protein folding and aggregation. EMBO J. 1999, 18:6927-6933.
    • (1999) EMBO J. , vol.18 , pp. 6927-6933
    • van den Berg, B.1    Ellis, R.J.2    Dobson, C.M.3
  • 18
    • 0034254189 scopus 로고    scopus 로고
    • Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell
    • van den Berg B., Wain R., Dobson C.M., Ellis R.J. Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell. EMBO J. 2000, 19:3870-3875.
    • (2000) EMBO J. , vol.19 , pp. 3870-3875
    • van den Berg, B.1    Wain, R.2    Dobson, C.M.3    Ellis, R.J.4
  • 19
    • 16344389134 scopus 로고    scopus 로고
    • Molecular crowding enhances native state stability and refolding rates of globular proteins
    • Cheung M.S., Klimov D., Thirumalai D. Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc. Natl Acad. Sci. USA 2005, 102:4753-4758.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 4753-4758
    • Cheung, M.S.1    Klimov, D.2    Thirumalai, D.3
  • 20
    • 33645454904 scopus 로고    scopus 로고
    • 15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions
    • 15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions. J. Am. Chem. Soc. 2006, 128:3916-3917.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 3916-3917
    • Ai, X.1    Zhou, Z.2    Bai, Y.3    Choy, W.Y.4
  • 21
    • 33646155113 scopus 로고    scopus 로고
    • Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation
    • Lu D., Liu Z., Wu J. Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation. Biophys. J. 2006, 90:3224-3238.
    • (2006) Biophys. J. , vol.90 , pp. 3224-3238
    • Lu, D.1    Liu, Z.2    Wu, J.3
  • 22
    • 37649016316 scopus 로고    scopus 로고
    • Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin
    • Stagg L., Zhang S.Q., Cheung M.S., Wittung-Stafshede P. Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin. Proc. Natl Acad. Sci. USA 2007, 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
  • 23
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation: I. The effect of specific amino acid sequence represented by specific inter-unit interactions
    • Taketomi H., Ueda Y., Go N. Studies on protein folding, unfolding and fluctuations by computer simulation: I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int. J. Pept. Protein Res. 1975, 7:445-459.
    • (1975) Int. J. Pept. Protein Res. , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 24
    • 61449196621 scopus 로고    scopus 로고
    • Folding, stability and shape of proteins in crowded environments: experimental and computational approaches
    • Samiotakis A., Wittung-Stafshede P., Cheung M.S. Folding, stability and shape of proteins in crowded environments: experimental and computational approaches. Int. J. Mol. Sci. 2009, 10:572-588.
    • (2009) Int. J. Mol. Sci. , vol.10 , pp. 572-588
    • Samiotakis, A.1    Wittung-Stafshede, P.2    Cheung, M.S.3
  • 25
    • 0034112774 scopus 로고    scopus 로고
    • Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
    • Li L., Mirny L.A., Shakhnovich E.I. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat. Struct. Biol. 2000, 7:336-342.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 336-342
    • Li, L.1    Mirny, L.A.2    Shakhnovich, E.I.3
  • 26
    • 0025033667 scopus 로고
    • Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels
    • Sikorski A., Skolnick J. Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels. J. Mol. Biol. 1990, 215:183-198.
    • (1990) J. Mol. Biol. , vol.215 , pp. 183-198
    • Sikorski, A.1    Skolnick, J.2
  • 27
    • 84975889264 scopus 로고    scopus 로고
    • Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome
    • Elcock A.H. Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS Comput. Biol. 2006, e98:2.
    • (2006) PLoS Comput. Biol. , vol.e98 , pp. 2
    • Elcock, A.H.1
  • 28
    • 33748796668 scopus 로고    scopus 로고
    • Topological accessibility shows a distinct asymmetry in the folds of betaalpha proteins
    • Taylor W.R. Topological accessibility shows a distinct asymmetry in the folds of betaalpha proteins. FEBS Lett. 2006, 580:5263-5267.
    • (2006) FEBS Lett. , vol.580 , pp. 5263-5267
    • Taylor, W.R.1
  • 30
    • 0029053552 scopus 로고
    • Folding of a nascent polypeptide chain in vitro: cooperative formation of structure in a protein module
    • Gay G.D.P., Ruiz-Sanz J., Neira J.L., Itzhaki L.S., Fersht A.R. Folding of a nascent polypeptide chain in vitro: cooperative formation of structure in a protein module. Proc. Natl Acad. Sci. USA 1995, 92:3683-3686.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 3683-3686
    • Gay, G.D.P.1    Ruiz-Sanz, J.2    Neira, J.L.3    Itzhaki, L.S.4    Fersht, A.R.5
  • 31
    • 0031468437 scopus 로고    scopus 로고
    • Cotranslational protein folding
    • Fedorov A.N., Baldwin T.O. Cotranslational protein folding. J. Biol. Chem. 1997, 272:32715-32718.
    • (1997) J. Biol. Chem. , vol.272 , pp. 32715-32718
    • Fedorov, A.N.1    Baldwin, T.O.2
  • 32
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 1999, 292:195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 33
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y., Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57:702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 34
    • 36749086922 scopus 로고    scopus 로고
    • Assessment of CASP7 structure predictions for template free targets
    • Jauch R., Yeo H.C., Kolatkar P.R., Clarke N.D. Assessment of CASP7 structure predictions for template free targets. Proteins 2007, 69:57-67.
    • (2007) Proteins , vol.69 , pp. 57-67
    • Jauch, R.1    Yeo, H.C.2    Kolatkar, P.R.3    Clarke, N.D.4
  • 35
    • 0037181497 scopus 로고    scopus 로고
    • Accelerated alpha-synuclein fibrillation in crowded milieu
    • Uversky V.N., Cooper E.M., Bower K.S., Li J., Fink A.L. Accelerated alpha-synuclein fibrillation in crowded milieu. FEBS Lett. 2002, 515:99-103.
    • (2002) FEBS Lett. , vol.515 , pp. 99-103
    • Uversky, V.N.1    Cooper, E.M.2    Bower, K.S.3    Li, J.4    Fink, A.L.5
  • 36
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995, 23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 37
    • 22044441063 scopus 로고    scopus 로고
    • A proof of the Kepler conjecture
    • Hales T.C. A proof of the Kepler conjecture. Ann. Math. 2005, 162:1063-1183.
    • (2005) Ann. Math. , vol.162 , pp. 1063-1183
    • Hales, T.C.1
  • 38
    • 34547631623 scopus 로고    scopus 로고
    • Prevention of amyloid-like aggregation as a driving force of protein evolution
    • Monsellier E., Chiti F. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep. 2007, 8:737-742.
    • (2007) EMBO Rep. , vol.8 , pp. 737-742
    • Monsellier, E.1    Chiti, F.2
  • 39
    • 0034653294 scopus 로고    scopus 로고
    • Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins
    • Jansen R., Gerstein M. Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res. 2000, 28:1481-1488.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1481-1488
    • Jansen, R.1    Gerstein, M.2
  • 40
    • 0034666040 scopus 로고    scopus 로고
    • Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
    • Coghlan A., Wolfe K.H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 2000, 16:1131-1145.
    • (2000) Yeast , vol.16 , pp. 1131-1145
    • Coghlan, A.1    Wolfe, K.H.2
  • 41
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu P., Vogel C., Wang R., Yao X., Marcotte E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25:117-124.
    • (2007) Nat. Biotechnol. , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 42
    • 34247882072 scopus 로고    scopus 로고
    • Life on the edge: a link between gene expression levels and aggregation rates of human proteins
    • Tartaglia G.G., Pechmann S., Dobson C.M., Vendruscolo M. Life on the edge: a link between gene expression levels and aggregation rates of human proteins. Trends Biochem. Sci. 2007, 32:204-206.
    • (2007) Trends Biochem. Sci. , vol.32 , pp. 204-206
    • Tartaglia, G.G.1    Pechmann, S.2    Dobson, C.M.3    Vendruscolo, M.4
  • 43
    • 29444444251 scopus 로고    scopus 로고
    • How evolutionary pressure against protein aggregation shaped chaperone specificity
    • Rousseau F., Serrano L., Schymkowitz J.W.H. How evolutionary pressure against protein aggregation shaped chaperone specificity. J. Mol. Biol. 2006, 355:1037-1047.
    • (2006) J. Mol. Biol. , vol.355 , pp. 1037-1047
    • Rousseau, F.1    Serrano, L.2    Schymkowitz, J.W.H.3
  • 44
    • 0033032592 scopus 로고    scopus 로고
    • Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains
    • Teter S.A., Houry W.A., Ang D., Tradler T., Rockabrand D., Fischer G., et al. Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains. Cell 1999, 97:755-765.
    • (1999) Cell , vol.97 , pp. 755-765
    • Teter, S.A.1    Houry, W.A.2    Ang, D.3    Tradler, T.4    Rockabrand, D.5    Fischer, G.6
  • 45
    • 0034646515 scopus 로고    scopus 로고
    • Getting newly synthesized proteins into shape
    • Bukau B., Deuerling E., Pfund C., Craig E.A. Getting newly synthesized proteins into shape. Cell 2000, 101:119-122.
    • (2000) Cell , vol.101 , pp. 119-122
    • Bukau, B.1    Deuerling, E.2    Pfund, C.3    Craig, E.A.4
  • 46
    • 0037040541 scopus 로고    scopus 로고
    • Molecular chaperones in the cytosol: from nascent chain to folded protein
    • Hartl F.U., Hayer-Hartl M. Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 2002, 295:1852-1858.
    • (2002) Science , vol.295 , pp. 1852-1858
    • Hartl, F.U.1    Hayer-Hartl, M.2
  • 49
    • 0037406141 scopus 로고    scopus 로고
    • Can correct protein models be identified?
    • Wallner B., Elofsson A. Can correct protein models be identified?. Protein Sci. 2003, 12:1073-1086.
    • (2003) Protein Sci. , vol.12 , pp. 1073-1086
    • Wallner, B.1    Elofsson, A.2


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