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Volumn 108, Issue 44, 2011, Pages 17876-17882

Physical limits of cells and proteomes

Author keywords

Cell biophysics; Diffusion and folding; Protein dynamics; Protein stability; Proteome modeling

Indexed keywords

PROTEOME;

EID: 81055141521     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1114477108     Document Type: Article
Times cited : (232)

References (72)
  • 5
    • 0000159569 scopus 로고    scopus 로고
    • Protein structure and the energetics of protein stability
    • Robertson AD, Murphy KP (1997) Protein structure and the energetics of protein stability. Chem Rev 97:1251-1267. (Pubitemid 127659597)
    • (1997) Chemical Reviews , vol.97 , Issue.5 , pp. 1251-1267
    • Robertson, A.D.1    Murphy, K.P.2
  • 6
    • 67649774570 scopus 로고    scopus 로고
    • Computing protein stabilities from their chain lengths
    • Ghosh K, Dill KA (2009) Computing protein stabilities from their chain lengths. Proc Natl Acad Sci USA 106:10649-10654.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10649-10654
    • Ghosh, K.1    Dill, K.A.2
  • 7
    • 80052449370 scopus 로고    scopus 로고
    • How do thermophilic proteins and proteomes withstand high temperature?
    • Sawle L, Ghosh K (2011) How do thermophilic proteins and proteomes withstand high temperature ? Biophys J 101:217-227.
    • (2011) Biophys J , vol.101 , pp. 217-227
    • Sawle, L.1    Ghosh, K.2
  • 8
    • 0034161476 scopus 로고    scopus 로고
    • Protein-length distributions for the three domains of life
    • Zhang JZ (2000) Protein-length distributions for the three domains of life. Trends Genet 16:107-109.
    • (2000) Trends Genet , vol.16 , pp. 107-109
    • Zhang, J.Z.1
  • 9
    • 11844304103 scopus 로고    scopus 로고
    • Measurement of protein stability and protein denaturation in cells using differential scanning calorimetry
    • Lepock JR (2005) Measurement of protein stability and protein denaturation in cells using differential scanning calorimetry. Methods 35:117-125.
    • (2005) Methods , vol.35 , pp. 117-125
    • Lepock, J.R.1
  • 10
    • 0015000275 scopus 로고
    • Variation in sensitivity to heat shock during cell-cycle of chinese hamster cells in-vitro
    • Westra A, Dewey WC (1971) Variation in sensitivity to heat shock during cell-cycle of chinese hamster cells in-vitro. Int J Radiat Biol 19:467-477.
    • (1971) Int J Radiat Biol , vol.19 , pp. 467-477
    • Westra, A.1    Dewey, W.C.2
  • 11
    • 78650217130 scopus 로고    scopus 로고
    • Cellular proteomes have broad distributions of protein stability
    • Ghosh K, Dill KA (2010) Cellular proteomes have broad distributions of protein stability. Biophys J 99:3996-4002.
    • (2010) Biophys J , vol.99 , pp. 3996-4002
    • Ghosh, K.1    Dill, K.A.2
  • 13
    • 0034814860 scopus 로고    scopus 로고
    • Quantitative protein stability measurement in vivo
    • DOI 10.1038/nsb1001-879
    • Ghaemmaghami S, Oas TG (2001) Quantitative protein stability measurement in vivo. Nat Struct Biol 8:879-882. (Pubitemid 32923608)
    • (2001) Nature Structural Biology , vol.8 , Issue.10 , pp. 879-882
    • Ghaemmaghami, S.1    Oas, T.G.2
  • 15
    • 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
  • 16
    • 0026276974 scopus 로고
    • Abrupt deep-sea warming, palaeoceanographic changes and benthic extinctions at the end of the Palaeocene
    • Kennett JP, Stott LD (1991) Abrupt deep-sea warming, palaeoceanographic changes and benthic extinctions at the end of the Palaeocene. Nature 353:225-229. (Pubitemid 21896755)
    • (1991) Nature , vol.353 , Issue.6341 , pp. 225-229
    • Kennett, J.P.1    Stott, L.D.2
  • 17
    • 0034687413 scopus 로고    scopus 로고
    • Cooler winters as a possible cause of mass extinctions at the Eocene/Oligocene boundary
    • Ivany LC, PattersonWP, Lohmann KC (2000) Cooler winters as a possible cause of mass extinctions at the Eocene/Oligocene boundary. Nature 407:887-890.
    • (2000) Nature , vol.407 , pp. 887-890
    • Ivany, L.C.1    Patterson, W.P.2    Lohmann, K.C.3
  • 19
    • 0019974904 scopus 로고
    • Temperature of egg incubation determines sex in Alligator mississippiensis
    • DOI 10.1038/296850a0
    • Ferguson MWJ, Joanen T (1982) Temperature of egg incubation determines sex in Alligator mississippiensis. Nature 296:850-853. (Pubitemid 12096591)
    • (1982) Nature , vol.296 , Issue.5860 , pp. 850-853
    • Ferguson, M.W.J.1    Joanen, T.2
  • 20
    • 77957213888 scopus 로고
    • Effects of incubation temperature on crocodiles and the evolution of reptilian oviparity
    • Webb GJW, Cooper-Preston H (1989) Effects of incubation temperature on crocodiles and the evolution of reptilian oviparity. Am Zool 29:953-971.
    • (1989) Am Zool , vol.29 , pp. 953-971
    • Webb, G.J.W.1    Cooper-Preston, H.2
  • 22
    • 33746456976 scopus 로고    scopus 로고
    • Hyperthermic biology and cancer therapies: A hypothesis for the "Lance Armstrong effect"
    • DOI 10.1001/jama.296.4.445
    • Coffey DS, Getzenberg RH, DeWeese TL (2006) Hyperthermic biology and cancer therapies: A hypothesis for the "Lance Armstrong Effect". JAMA 296:445-448. (Pubitemid 44127529)
    • (2006) Journal of the American Medical Association , vol.296 , Issue.4 , pp. 445-448
    • Coffey, D.S.1    Getzenberg, R.H.2    Deweese, T.L.3
  • 23
    • 0033937892 scopus 로고    scopus 로고
    • Oncogenic ras results in increased cell kill due to defective thermoprotection in lung cancer cells
    • DOI 10.1016/S0003-4975(00)01421-1, PII S0003497500014211
    • Vertrees RA, Zwischenberger JB, Boor PJ, Pencil SD (2000) Oncogenic ras results in increased cell kill due to defective thermoprotection in lung cancer cells. Ann Thorac Surg 69:1675-1680. (Pubitemid 30445504)
    • (2000) Annals of Thoracic Surgery , vol.69 , Issue.6 , pp. 1675-1680
    • Vertrees, R.A.1    Zwischenberger, J.B.2    Boor, P.J.3    Pencil, S.D.4
  • 24
    • 39349083915 scopus 로고    scopus 로고
    • Adapting proteostasis for disease intervention
    • DOI 10.1126/science.1141448
    • Balch WE, Morimoto RI, Dillin A, Kelly JW (2008) Adapting proteostasis for disease intervention. Science 319:916-919. (Pubitemid 351263754)
    • (2008) Science , vol.319 , Issue.5865 , pp. 916-919
    • Balch, W.E.1    Morimoto, R.I.2    Dillin, A.3    Kelly, J.W.4
  • 25
    • 0347357617 scopus 로고    scopus 로고
    • Protein folding and misfolding
    • Dobson CM (2003) Protein folding and misfolding. Nature 426:884-890.
    • (2003) Nature , vol.426 , pp. 884-890
    • Dobson, C.M.1
  • 26
    • 1942521649 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of non-native interactions in protein folding: A single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state
    • DOI 10.1016/j.jmb.2004.02.073, PII S0022283604002918
    • Cho JH, Sato S, Raleigh DP (2004) Thermodynamics and kinetics of non-native interactions in protein folding: A single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state. J Mol Biol 338:827-837. (Pubitemid 38507425)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.4 , pp. 827-837
    • Cho, J.-H.1    Sato, S.2    Raleigh, D.P.3
  • 27
    • 57649136399 scopus 로고    scopus 로고
    • Salt bridges in the hyperthermophilic protein Ssh10b are resilient to temperature increases
    • Ge M, Xia, X-Y, Pan X-M (2008) Salt bridges in the hyperthermophilic protein Ssh10b are resilient to temperature increases. J Biol Chem 283:31690-31696.
    • (2008) J Biol Chem , vol.283 , pp. 31690-31696
    • Ge, M.1    Xia, X.-Y.2    Pan, X.-M.3
  • 28
    • 0036606927 scopus 로고    scopus 로고
    • Evidence for cysteine clustering in thermophilic proteomes
    • DOI 10.1016/S0168-9525(02)02691-4, PII S0168952502026914
    • Rosato V, Pucello N, Giuliano G (2002) Evidence for cysteine clustering in thermophilic proteomes. Trends Genet 18:278-281. (Pubitemid 34607109)
    • (2002) Trends in Genetics , vol.18 , Issue.6 , pp. 278-281
    • Rosato, V.1    Pucello, N.2    Giuliano, G.3
  • 29
    • 0034491013 scopus 로고    scopus 로고
    • The effects of disulfide bonds on the denatured state of barnase
    • Clarke J, Hounslow AM, Bond CJ, Fersht AR, Daggett V (2000) The effects of disulfide bonds on the denatured state of barnase. Protein Sci 9:2394-2404. (Pubitemid 32105722)
    • (2000) Protein Science , vol.9 , Issue.12 , pp. 2394-2404
    • Clarke, J.1    Hounslow, A.M.2    Bond, C.J.3    Fersht, A.R.4    Daggett, V.5
  • 30
    • 0033852796 scopus 로고    scopus 로고
    • Charge-charge interactions influence the denatured state ensemble and contribute to protein stability
    • Pace CN, Alston RW, Shaw KL (2000) Charge-charge interactions influence the denatured state ensemble and contribute to protein stability. Protein Sci 9:1395-1398. (Pubitemid 30602294)
    • (2000) Protein Science , vol.9 , Issue.7 , pp. 1395-1398
    • Pace, C.N.1    Alston, R.W.2    Shaw, K.L.3
  • 31
    • 0032573431 scopus 로고    scopus 로고
    • The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins
    • Elcock AH (1998) The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins. J Mol Biol 284:489-502.
    • (1998) J Mol Biol , vol.284 , pp. 489-502
    • Elcock, A.H.1
  • 32
    • 0034017055 scopus 로고    scopus 로고
    • Factors enhancing protein thermostability
    • Kumar S, Tsai C, Nussinov R (2000) Factors enhancing protein thermostability. Protein Eng 13:179-191. (Pubitemid 30237592)
    • (2000) Protein Engineering , vol.13 , Issue.3 , pp. 179-191
    • Kumar, S.1    Tsai, C.-J.2    Nussinov, R.3
  • 33
    • 0033994586 scopus 로고    scopus 로고
    • Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers
    • DOI 10.1002/(SICI)1097-0134(20000301)38:4<368::AID-PROT3>3.0.CO;2-R
    • Kumar S, Ma B, Tsai C, Nussinov R (2000) Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers. Proteins 38:368-383. (Pubitemid 30112440)
    • (2000) Proteins: Structure, Function and Genetics , vol.38 , Issue.4 , pp. 368-383
    • Kumar, S.1    Ma, B.2    Tsai, C.-J.3    Nussinov, R.4
  • 35
    • 0037380834 scopus 로고    scopus 로고
    • Electrostatic contributions to the stability of a thermophilic cold shock protein
    • Zhou HX, Dong F (2003) Electrostatic contributions to the stability of a thermophilic cold shock protein. Biophys J 84:2216-2222.
    • (2003) Biophys J , vol.84 , pp. 2216-2222
    • Zhou, H.X.1    Dong, F.2
  • 36
    • 16244366490 scopus 로고    scopus 로고
    • Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein L30e
    • DOI 10.1016/j.jmb.2005.02.052
    • Lee C, Allen M, Bycroft M, Wong K (2005) Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein 130 e. J Mol Biol 348:419-431. (Pubitemid 40462106)
    • (2005) Journal of Molecular Biology , vol.348 , Issue.2 , pp. 419-431
    • Lee, C.-F.1    Allen, M.D.2    Bycroft, M.3    Wong, K.-B.4
  • 37
    • 0023430560 scopus 로고
    • Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding
    • Matthews BW, Nicholson H, Becktel WJ (1987) Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc Natl Acad Sci USA 84:6663-6667.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6663-6667
    • Matthews, B.W.1    Nicholson, H.2    Becktel, W.J.3
  • 40
    • 0032516409 scopus 로고    scopus 로고
    • Protein thermostabilization by proline substitutions
    • DOI 10.1016/S1381-1177(97)00031-3, PII S1381117797000313
    • Watanabe K, Suzuki Y (1998) Protein thermostabilization by proline substitutions. J Mol Catal B Enzym 4:167-180. (Pubitemid 28303932)
    • (1998) Journal of Molecular Catalysis - B Enzymatic , vol.4 , Issue.4 , pp. 167-180
    • Watanabe, K.1    Suzuki, Y.2
  • 41
    • 34548567337 scopus 로고    scopus 로고
    • Increasing Protein Conformational Stability by Optimizing β-Turn Sequence
    • DOI 10.1016/j.jmb.2007.07.061, PII S0022283607010261
    • Trevino SR, Schaefer S, Scholtz JM, Pace CN (2007) Increasing protein conformational stability by optimizing beta-turn sequence. J Mol Biol 373:211-218. (Pubitemid 47390718)
    • (2007) Journal of Molecular Biology , vol.373 , Issue.1 , pp. 211-218
    • Trevino, S.R.1    Schaefer, S.2    Scholtz, J.M.3    Pace, C.N.4
  • 42
    • 0033538553 scopus 로고    scopus 로고
    • Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability
    • DOI 10.1006/jmbi.1999.2889
    • Thompson MJ, Eisenberg D (1999) Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol 290:595-604. (Pubitemid 29324842)
    • (1999) Journal of Molecular Biology , vol.290 , Issue.2 , pp. 595-604
    • Thompson, M.J.1    Eisenberg, D.2
  • 43
    • 77950605529 scopus 로고    scopus 로고
    • Thermal adaptation of viruses and bacteria
    • Chen P, Shakhnovich EI (2010) Thermal adaptation of viruses and bacteria. Biophys J 98:1109-1118.
    • (2010) Biophys J , vol.98 , pp. 1109-1118
    • Chen, P.1    Shakhnovich, E.I.2
  • 44
    • 0023274170 scopus 로고
    • The Rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias
    • Sharp PM, Li WH (1987) The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol Biol Evol 4:222-230. (Pubitemid 17116760)
    • (1987) Molecular Biology and Evolution , vol.4 , Issue.3 , pp. 222-230
    • Sharp, P.M.1    Li, W.-H.2
  • 45
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pal C, Papp B, Hurst LD (2001) Highly expressed genes in yeast evolve slowly. Genetics 158:927-931. (Pubitemid 32552328)
    • (2001) Genetics , vol.158 , Issue.2 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 47
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
    • DOI 10.1016/j.cell.2008.05.042, PII S0092867408007058
    • Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
    • (2008) Cell , vol.134 , Issue.2 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 50
    • 1842857771 scopus 로고    scopus 로고
    • Asymmetry in the shapes of folded and denatured states of proteins
    • Dima RI, Thirumalai D (2004) Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B 108:6564-6570.
    • (2004) J Phys Chem B , vol.108 , pp. 6564-6570
    • Dima, R.I.1    Thirumalai, D.2
  • 51
    • 58449084188 scopus 로고    scopus 로고
    • Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity
    • Hong L, Lei J (2009) Scaling law for the radius of gyration of proteins and its dependence on hydrophobicity. J Poly Sci B 47:207-214.
    • (2009) J Poly Sci B , vol.47 , pp. 207-214
    • Hong, L.1    Lei, J.2
  • 52
    • 0025388039 scopus 로고
    • Prediction of diffusion coefficients of proteins
    • Tyn MT, Gusek TW (1990) Prediction of diffusion coefficients of proteins. Biotechnol Bioeng 35:327-338. (Pubitemid 20137339)
    • (1990) Biotechnology and Bioengineering , vol.35 , Issue.4 , pp. 327-338
    • Tyn, M.T.1    Gusek, T.W.2
  • 53
    • 0001808747 scopus 로고
    • On the theory of concentrated hard-sphere suspensions
    • Tokuyama M, Oppenheim I (1995) On the theory of concentrated hard-sphere suspensions. Physica A 216:85-119.
    • (1995) Physica A , vol.216 , pp. 85-119
    • Tokuyama, M.1    Oppenheim, I.2
  • 54
    • 0034723445 scopus 로고    scopus 로고
    • Three-dimensional direct imaging of structural relaxation near the colloidal glass transition
    • DOI 10.1126/science.287.5453.627
    • Weeks ER, Crocker JC, Levitt AC, Schofield A, Weitz DA (2000) Three-dimensional direct imaging of structural relaxation near the colloidal glass transition. Science 287:627-631. (Pubitemid 30070905)
    • (2000) Science , vol.287 , Issue.5453 , pp. 627-631
    • Weeks, E.R.1    Crocker, J.C.2    Levitt, A.C.3    Schofield, A.4    Weitz, D.A.5
  • 55
    • 0020184671 scopus 로고
    • How crowded is the cytoplasm?
    • Fulton AB (1982) How crowded is the cytoplasm? Cell 30:345-347.
    • (1982) Cell , vol.30 , pp. 345-347
    • Fulton, A.B.1
  • 56
    • 0026344818 scopus 로고
    • Estimation of macromolecular concentration and excluded volume effects for the cytoplasm of Escherichia coli
    • Zimmerman SB, Trach SO (1991) Estimation of macromolecular concentration 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
  • 57
    • 0035478585 scopus 로고    scopus 로고
    • Macromolecular crowding: Obvious but underappreciated
    • Ellis RJ (2001) Macromolecular crowding: Obvious but underappreciated. Trends Biochem Sci 26:597-604.
    • (2001) Trends Biochem Sci , vol.26 , pp. 597-604
    • Ellis, R.J.1
  • 58
    • 78649876151 scopus 로고    scopus 로고
    • Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
    • Ando T, Skolnick J (2010) Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci USA 107:18457-18462.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 18457-18462
    • Ando, T.1    Skolnick, J.2
  • 59
    • 66049098939 scopus 로고    scopus 로고
    • Lattice model of diffusion-limited bimolecular chemical reactions in confined environments
    • Schmit JD, Kamber E, Kondev J (2009) Lattice model of diffusion-limited bimolecular chemical reactions in confined environments. Phys Rev Lett 102:218302.
    • (2009) Phys Rev Lett , vol.102 , pp. 218302
    • Schmit, J.D.1    Kamber, E.2    Kondev, J.3
  • 60
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • DOI 10.1006/jmbi.1998.1645
    • Plaxco KW, Simons KT, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277:985-994. (Pubitemid 28195995)
    • (1998) Journal of Molecular Biology , vol.277 , Issue.4 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 61
    • 0000050196 scopus 로고
    • From minimal models to real proteins: Time scales for protein folding kinetics
    • Thirumalai D (1995) From minimal models to real proteins: Time scales for protein folding kinetics. J Phys I France 5:1457-1467.
    • (1995) J Phys I France , vol.5 , pp. 1457-1467
    • Thirumalai, D.1
  • 62
    • 46449120907 scopus 로고    scopus 로고
    • Predicting protein folding rates from geometric contact and amino acid sequence
    • DOI 10.1110/ps.034660.108
    • Ouyang Z, Liang J (2008) Predicting protein folding rates from geometric contact and amino acid sequence. Protein Sci 17:1256-1263. (Pubitemid 351930923)
    • (2008) Protein Science , vol.17 , Issue.7 , pp. 1256-1263
    • Ouyang, Z.1    Liang, J.2
  • 64
    • 0030623529 scopus 로고    scopus 로고
    • Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
    • Finkelstein AV, Badretdinov AYA (1997) Rate of protein folding near the point of thermodynamics equilibrium between the coil and the most stable chain fold. Fold Des 2:115-121. (Pubitemid 127740460)
    • (1997) Folding and Design , vol.2 , Issue.2 , pp. 115-121
    • Finkelstein, A.V.1    Badretdinov, A.Ya.2
  • 65
    • 0035850732 scopus 로고    scopus 로고
    • Roles of native topology and chain-length scaling in protein folding: A simulation study with a go-like model
    • DOI 10.1006/jmbi.2001.5037
    • Koga N, Takada S (2001) Role of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model. J Mol Biol 313:171-180. (Pubitemid 33001173)
    • (2001) Journal of Molecular Biology , vol.313 , Issue.1 , pp. 171-180
    • Koga, N.1    Takada, S.2
  • 70
    • 0017105938 scopus 로고
    • Polypeptide-chain-elongation rate in Escherichia coliB/r as a function of growth rate
    • Young R, Bremer H (1976) Polypeptide-chain-elongation rate in Escherichia coliB/r as a function of growth rate. Biochem J 160:185-194.
    • (1976) Biochem J , vol.160 , pp. 185-194
    • Young, R.1    Bremer, H.2
  • 72


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