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Volumn 5, Issue 2, 2013, Pages 109-119

Computer simulations of the bacterial cytoplasm

Author keywords

Bacterial cytoplasm; Computer simulation; Energetic interactions; Hydrodynamic interactions; Macromolecular crowding

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84877079511     PISSN: 18672450     EISSN: 18672469     Source Type: Journal    
DOI: 10.1007/s12551-013-0110-6     Document Type: Review
Times cited : (38)

References (89)
  • 1
    • 78649876151 scopus 로고    scopus 로고
    • Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
    • doi:10.1073/pnas.1011354107
    • Ando T, Skolnick J (2010) Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci USA 107: 18457-18462. doi: 10. 1073/pnas. 1011354107.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 18457-18462
    • Ando, T.1    Skolnick, J.2
  • 2
    • 84865177208 scopus 로고    scopus 로고
    • Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations
    • doi:10.1063/1.4742347
    • Ando T, Chow E, Saad Y, Skolnick J (2012) Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations. J Chem Phys 137: 064106. doi: 10. 1063/1. 4742347.
    • (2012) J Chem Phys , vol.137 , pp. 064106
    • Ando, T.1    Chow, E.2    Saad, Y.3    Skolnick, J.4
  • 3
    • 33845204189 scopus 로고    scopus 로고
    • Stability and dynamics of virus capsids described by coarse-grained modeling
    • doi:10.1016/j.str.2006.10.003
    • Arkhipov A, Freddolino PL, Schulten K (2006) Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 14: 1767-1777. doi: 10. 1016/j. str. 2006. 10. 003.
    • (2006) Structure , vol.14 , pp. 1767-1777
    • Arkhipov, A.1    Freddolino, P.L.2    Schulten, K.3
  • 4
    • 53249125167 scopus 로고    scopus 로고
    • Four-scale description of membrane sculpting by BAR domains
    • doi:10.1529/biophysj.108.132563
    • Arkhipov A, Yin Y, Schulten K (2008) Four-scale description of membrane sculpting by BAR domains. Biophys J 95: 2806-2821. doi: 10. 1529/biophysj. 108. 132563.
    • (2008) Biophys J , vol.95 , pp. 2806-2821
    • Arkhipov, A.1    Yin, Y.2    Schulten, K.3
  • 5
    • 78650768713 scopus 로고    scopus 로고
    • In-cell NMR and protein leakage
    • doi:10.1002/prot.22906
    • Barnes CO, Pielak GJ (2011) In-cell NMR and protein leakage. Proteins 79: 347-351. doi: 10. 1002/prot. 22906.
    • (2011) Proteins , vol.79 , pp. 347-351
    • Barnes, C.O.1    Pielak, G.J.2
  • 6
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • doi:10.1038/nchembio.186
    • Bennett BD, Kimball EH, Gao M, Osterhout R, van Dien SJ, Rabinowitz JD (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 5: 593-599. doi: 10. 1038/nchembio. 186.
    • (2009) Nat Chem Biol , vol.5 , pp. 593-599
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    van Dien, S.J.5    Rabinowitz, J.D.6
  • 7
    • 5244275439 scopus 로고    scopus 로고
    • Stochastic dynamics simulations of macromolecular diffusion in a model of the cytoplasm of Escherichia coli
    • doi:10.1021/jp9525191
    • Bicout DJ, Field MJ (1996) Stochastic dynamics simulations of macromolecular diffusion in a model of the cytoplasm of Escherichia coli. J Phys Chem 100: 2489-2497. doi: 10. 1021/jp9525191.
    • (1996) J Phys Chem , vol.100 , pp. 2489-2497
    • Bicout, D.J.1    Field, M.J.2
  • 8
    • 0000233591 scopus 로고
    • Stokesian dynamics
    • doi:10.1146/annurev.fluid.20.1.111
    • Brady JF, Bossis G (1988) Stokesian dynamics. Annu Rev Fluid Mech 20: 111-157. doi: 10. 1146/annurev. fluid. 20. 1. 111.
    • (1988) Annu Rev Fluid Mech , vol.20 , pp. 111-157
    • Brady, J.F.1    Bossis, G.2
  • 9
    • 34547507851 scopus 로고    scopus 로고
    • Effects of crowding and confinement on the structures of the transition state ensemble in proteins
    • doi:10.1021/jp068201y
    • Cheung MS, Thirumalai D (2007) Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J Phys Chem B 111: 8250-8257. doi: 10. 1021/jp068201y.
    • (2007) J Phys Chem B , vol.111 , pp. 8250-8257
    • Cheung, M.S.1    Thirumalai, D.2
  • 10
    • 16344389134 scopus 로고    scopus 로고
    • Molecular crowding enhances native state stability and refolding rates of globular proteins
    • doi:10.1073/pnas.0409630102
    • Cheung MS, Klimov D, Thirumalai D (2005) Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci USA 102: 4753-4758. doi: 10. 1073/pnas. 0409630102.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4753-4758
    • Cheung, M.S.1    Klimov, D.2    Thirumalai, D.3
  • 11
    • 33646123091 scopus 로고    scopus 로고
    • Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
    • doi:10.1529/biophysj.105.073924
    • Chu JW, Voth GA (2006) Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys J 90: 1572-1582. doi: 10. 1529/biophysj. 105. 073924.
    • (2006) Biophys J , vol.90 , pp. 1572-1582
    • Chu, J.W.1    Voth, G.A.2
  • 12
    • 79959813206 scopus 로고    scopus 로고
    • A new view of the bacterial cytosol environment
    • doi:10.1371/J.pdbi.1002066
    • Cossins B, Jacobson MP, Guallar V (2011) A new view of the bacterial cytosol environment. PLoS Comput Biol 7: e1002066. doi: 10. 1371/J. pdbi. 1002066.
    • (2011) PLoS Comput Biol , vol.7
    • Cossins, B.1    Jacobson, M.P.2    Guallar, V.3
  • 13
    • 79955024130 scopus 로고    scopus 로고
    • Protein interactions in the Escherichia coli cytosol: an impediment to in-cell NMR spectroscopy
    • doi:10.1002/cbic.201100063
    • 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. doi: 10. 1002/cbic. 201100063.
    • (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 eukaryotic cells
    • doi:10.1016/j.bpj.2011.05.071
    • 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 eukaryotic cells. Biophys J 101: 421-430. doi: 10. 1016/j. bpj. 2011. 05. 071.
    • (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
    • 0036923039 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
    • doi:10.1016/S0022-2836(02)01112-9
    • Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (2002) Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol 324: 851-857. doi: 10. 1016/S0022-2836(02)01112-9.
    • (2002) J Mol Biol , vol.324 , pp. 851-857
    • Ding, F.1    Dokholyan, N.V.2    Buldyrev, S.V.3    Stanley, H.E.4    Shakhnovich, E.I.5
  • 16
    • 48249124302 scopus 로고    scopus 로고
    • Crowding effects on diffusion in solutions and cells
    • doi:10.1146/annurev.biophys.37.032807.125824
    • Dix JA, Verkman AS (2008) Crowding effects on diffusion in solutions and cells. Annu Rev Biophys 37: 247-263. doi: 10. 1146/annurev. biophys. 37. 032807. 125824.
    • (2008) Annu Rev Biophys , vol.37 , pp. 247-263
    • Dix, J.A.1    Verkman, A.S.2
  • 17
    • 0023525420 scopus 로고
    • Dynamic simulation of hydrodynamically interacting particles
    • doi:10.1017/S002211208700171X
    • Durlofsky L, Brady JF, Bossis G (1987) Dynamic simulation of hydrodynamically interacting particles. J Fluid Mech 180: 21-49. doi: 10. 1017/S002211208700171X.
    • (1987) J Fluid Mech , vol.180 , pp. 21-49
    • Durlofsky, L.1    Brady, J.F.2    Bossis, G.3
  • 18
    • 77951643591 scopus 로고    scopus 로고
    • Protein folding stability and dynamics imaged in a living cell
    • doi:10.1038/nmeth.1435
    • Ebbinghaus S, Dhar A, McDonald JD, Gruebele M (2010) Protein folding stability and dynamics imaged in a living cell. Nat Methods 7: 319-323. doi: 10. 1038/nmeth. 1435.
    • (2010) Nat Methods , vol.7 , pp. 319-323
    • Ebbinghaus, S.1    Dhar, A.2    McDonald, J.D.3    Gruebele, M.4
  • 19
    • 77951298407 scopus 로고    scopus 로고
    • Models of macromolecular crowding effects and the need for quantitative comparisons with experiment
    • doi:10.1016/j.sbi.2010.01.008
    • Elcock AH (2010) Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol 20: 196-206. doi: 10. 1016/j. sbi. 2010. 01. 008.
    • (2010) Curr Opin Struct Biol , vol.20 , pp. 196-206
    • Elcock, A.H.1
  • 20
    • 0344500752 scopus 로고    scopus 로고
    • Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin
    • doi:10.1006/jmbi.1999.2919
    • Elcock AH, Gabdoulline RR, Wade RC, McCammon JA (1999) Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. J Mol Biol 291: 149-162. doi: 10. 1006/jmbi. 1999. 2919.
    • (1999) J Mol Biol , vol.291 , pp. 149-162
    • Elcock, A.H.1    Gabdoulline, R.R.2    Wade, R.C.3    McCammon, J.A.4
  • 22
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • doi:10.1063/1.436761
    • Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69: 1352-1360. doi: 10. 1063/1. 436761.
    • (1978) J Chem Phys , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 23
    • 84855848788 scopus 로고    scopus 로고
    • Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding
    • doi:10.1021/jp209302e
    • 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. doi: 10. 1021/jp209302e.
    • (2012) J Phys Chem B , vol.116 , pp. 599-605
    • Feig, M.1    Sugita, Y.2
  • 24
    • 5844278702 scopus 로고
    • Construction of Langevin forces in the simulation of hydrodynamic interaction
    • doi:10.1021/ma00158a043
    • Fixman M (1986) Construction of Langevin forces in the simulation of hydrodynamic interaction. Macromolecules 19: 1204-1207. doi: 10. 1021/ma00158a043.
    • (1986) Macromolecules , vol.19 , pp. 1204-1207
    • Fixman, M.1
  • 25
    • 65249094240 scopus 로고    scopus 로고
    • Striking effects of hydrodynamic interactions on the simulated diffusion and folding of proteins
    • doi:10.1021/ct800499p
    • Frembgen-Kesner T, Elcock AH (2009) Striking effects of hydrodynamic interactions on the simulated diffusion and folding of proteins. J Chem Theory Comput 5: 242-256. doi: 10. 1021/ct800499p.
    • (2009) J Chem Theory Comput , vol.5 , pp. 242-256
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 26
    • 78349288528 scopus 로고    scopus 로고
    • Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association
    • doi:10.1016/j.bpj.2010.09.006
    • Frembgen-Kesner T, Elcock AH (2010) Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophys J 99: L75-L77. doi: 10. 1016/j. bpj. 2010. 09. 006.
    • (2010) Biophys J , vol.99
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 27
    • 33748501925 scopus 로고    scopus 로고
    • Effective charges for macromolecules in solvent
    • doi:10.1021/jp953109f
    • Gabdoulline RR, Wade RC (1996) Effective charges for macromolecules in solvent. J Phys Chem 100: 3868-3878. doi: 10. 1021/jp953109f.
    • (1996) J Phys Chem , vol.100 , pp. 3868-3878
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 28
    • 0030891436 scopus 로고    scopus 로고
    • Simulation of the diffusional association of barnase and barstar
    • doi:10.1016/S0006-3495(97)78838-6
    • Gabdoulline RR, Wade RC (1997) Simulation of the diffusional association of barnase and barstar. Biophys J 72: 1917-1929. doi: 10. 1016/S0006-3495(97)78838-6.
    • (1997) Biophys J , vol.72 , pp. 1917-1929
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 29
    • 67649983078 scopus 로고    scopus 로고
    • On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events
    • doi:10.1021/ja809567k
    • Gabdoulline RR, Wade RC (2009) On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events. J Am Chem Soc 131: 9230-9238. doi: 10. 1021/ja809567k.
    • (2009) J Am Chem Soc , vol.131 , pp. 9230-9238
    • Gabdoulline, R.R.1    Wade, R.C.2
  • 30
    • 8344247018 scopus 로고    scopus 로고
    • Dynamic instability in a DNA-segregating prokaryotic actin homolog
    • doi:10.1126/science.1101313
    • Garner EC, Campbell CS, Mullins RD (2004) Dynamic instability in a DNA-segregating prokaryotic actin homolog. Science 306: 1021-1025. doi: 10. 1126/science. 1101313.
    • (2004) Science , vol.306 , pp. 1021-1025
    • Garner, E.C.1    Campbell, C.S.2    Mullins, R.D.3
  • 31
    • 79551687316 scopus 로고    scopus 로고
    • Protein folding in the cell: challenges and progress
    • doi:10.1016/j.sbi.2010.11.001
    • Gershenson A, Gierasch LM (2011) Protein folding in the cell: challenges and progress. Curr Opin Struct Biol 21: 32-41. doi: 10. 1016/j. sbi. 2010. 11. 001.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 32-41
    • Gershenson, A.1    Gierasch, L.M.2
  • 32
    • 63149129721 scopus 로고    scopus 로고
    • An O(N-2) approximation for hydrodynamic interactions in Brownian dynamics simulations
    • doi:10.1063/1.3089668
    • Geyer T, Winter U (2009) An O(N-2) approximation for hydrodynamic interactions in Brownian dynamics simulations. J Chem Phys 130: 114905. doi: 10. 1063/1. 3089668.
    • (2009) J Chem Phys , vol.130 , pp. 114905
    • Geyer, T.1    Winter, U.2
  • 33
    • 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. doi: 10. 1038/nsb1001-879.
    • (2001) Nat Struct Biol , vol.8 , pp. 879-882
    • Ghaemmaghami, S.1    Oas, T.G.2
  • 34
    • 33644885029 scopus 로고    scopus 로고
    • Physical nature of bacterial cytoplasm
    • doi:10.1103/PhysRevLett.96.098102
    • Golding I, Cox EC (2006) Physical nature of bacterial cytoplasm. Phys Rev Lett 96: 098102. doi: 10. 1103/PhysRevLett. 96. 098102.
    • (2006) Phys Rev Lett , vol.96 , pp. 098102
    • Golding, I.1    Cox, E.C.2
  • 35
    • 0025869880 scopus 로고
    • Inside a living cell
    • doi:10.1016/0968-0004(91)90083-8
    • Goodsell DS (1991) Inside a living cell. Trends Biochem Sci 16: 203-206. doi: 10. 1016/0968-0004(91)90083-8.
    • (1991) Trends Biochem Sci , vol.16 , pp. 203-206
    • Goodsell, D.S.1
  • 36
    • 84858198890 scopus 로고    scopus 로고
    • Protein crowding affects hydration structure and dynamics
    • doi:10.1021/ja211115q
    • Harada R, Sugita Y, Feig M (2012) Protein crowding affects hydration structure and dynamics. J Am Chem Soc 134: 4842-4849. doi: 10. 1021/ja211115q.
    • (2012) J Am Chem Soc , vol.134 , pp. 4842-4849
    • Harada, R.1    Sugita, Y.2    Feig, M.3
  • 37
    • 42549173430 scopus 로고
    • Mean-field-hydrodynamics Brownian dynamics simulations of viscosity and self-diffusion of near-hard-sphere colloidal liquids
    • doi:10.1088/0953-8984/7/47/006
    • Heyes DM (1995) Mean-field-hydrodynamics Brownian dynamics simulations of viscosity and self-diffusion of near-hard-sphere colloidal liquids. J Phys Condens Matter 7: 8857-8865. doi: 10. 1088/0953-8984/7/47/006.
    • (1995) J Phys Condens Matter , vol.7 , pp. 8857-8865
    • Heyes, D.M.1
  • 39
    • 0347004717 scopus 로고    scopus 로고
    • Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling
    • doi:10.1073/pnas.0304533101
    • 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. doi: 10. 1073/pnas. 0304533101.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 523-528
    • Ignatova, Z.1    Gierasch, L.M.2
  • 40
    • 34247521095 scopus 로고    scopus 로고
    • From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein
    • doi:10.1002/bip.20665
    • Ignatova Z, Krishnan B, Bombardier JP, Marcelino AMC, Hong J, Gierasch LM (2007) From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein. Biopolymers 88: 157-163. doi: 10. 1002/bip. 20665.
    • (2007) Biopolymers , vol.88 , pp. 157-163
    • Ignatova, Z.1    Krishnan, B.2    Bombardier, J.P.3    Marcelino, A.M.C.4    Hong, J.5    Gierasch, L.M.6
  • 42
    • 24944542708 scopus 로고    scopus 로고
    • Statistical coil model of the unfolded state: resolving the reconciliation problem
    • doi:10.1073/pnas.0506078102
    • Jha AK, Colubri A, Freed KF, Sosnick TT (2005) Statistical coil model of the unfolded state: resolving the reconciliation problem. Proc Natl Acad Sci USA 102: 13099-13104. doi: 10. 1073/pnas. 0506078102.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13099-13104
    • Jha, A.K.1    Colubri, A.2    Freed, K.F.3    Sosnick, T.T.4
  • 43
    • 62649161932 scopus 로고    scopus 로고
    • Effect of macromolecular crowding on reaction rates: a computational and theoretical study
    • doi:10.1016/j.bpj.2008.11.030
    • Kim JS, Yethiraj A (2009) Effect of macromolecular crowding on reaction rates: a computational and theoretical study. Biophys J 96: 1333-1340. doi: 10. 1016/j. bpj. 2008. 11. 030.
    • (2009) Biophys J , vol.96 , pp. 1333-1340
    • Kim, J.S.1    Yethiraj, A.2
  • 44
    • 33749018832 scopus 로고    scopus 로고
    • Crowding and confinement effects on protein diffusion in vivo
    • doi:10.1128/JB.01982-05
    • Konopka MC, Shkel IA, Cayley S, Record MT, Weisshaar JC (2006) Crowding and confinement effects on protein diffusion in vivo. J Bacteriol 188: 6115-6123. doi: 10. 1128/JB. 01982-05.
    • (2006) J Bacteriol , vol.188 , pp. 6115-6123
    • Konopka, M.C.1    Shkel, I.A.2    Cayley, S.3    Record, M.T.4    Weisshaar, J.C.5
  • 46
    • 0030805979 scopus 로고    scopus 로고
    • Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12
    • doi:10.1002/elps.1150180807
    • Link AJ, Robison K, Church GM (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18: 1259-1313. doi: 10. 1002/elps. 1150180807.
    • (1997) Electrophoresis , vol.18 , pp. 1259-1313
    • Link, A.J.1    Robison, K.2    Church, G.M.3
  • 47
    • 11144264728 scopus 로고    scopus 로고
    • Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli
    • doi:10.1128/JB.187.1.45-53.2005
    • Lipkow K, Andrews SS, Bray D (2005) Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli. J Bacteriol 187: 45-53. doi: 10. 1128/JB. 187. 1. 45-53. 2005.
    • (2005) J Bacteriol , vol.187 , pp. 45-53
    • Lipkow, K.1    Andrews, S.S.2    Bray, D.3
  • 49
    • 77952294035 scopus 로고    scopus 로고
    • Elucidating anomalous protein diffusion in living cells with fluorescence correlation spectroscopy-facts and pitfalls
    • doi:10.1007/s10895-009-0517-4
    • Malchus N, Weiss M (2010) Elucidating anomalous protein diffusion in living cells with fluorescence correlation spectroscopy-facts and pitfalls. J Fluoresc 20: 19-26. doi: 10. 1007/s10895-009-0517-4.
    • (2010) J Fluoresc , vol.20 , pp. 19-26
    • Malchus, N.1    Weiss, M.2
  • 50
    • 0001418746 scopus 로고
    • Neighborship partition of the radial distribution function for simple liquids
    • doi:10.1063/1.463302
    • Mazur S (1992) Neighborship partition of the radial distribution function for simple liquids. J Chem Phys 97: 9276-9282. doi: 10. 1063/1. 463302.
    • (1992) J Chem Phys , vol.97 , pp. 9276-9282
    • Mazur, S.1
  • 51
    • 33748804712 scopus 로고    scopus 로고
    • Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems
    • doi:10.1021/ja0614058
    • McGuffee SR, Elcock AH (2006) Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. J Am Chem Soc 128: 12098-12110. doi: 10. 1021/ja0614058.
    • (2006) J Am Chem Soc , vol.128 , pp. 12098-12110
    • McGuffee, S.R.1    Elcock, A.H.2
  • 52
    • 77950792003 scopus 로고    scopus 로고
    • Diffusion, crowding and protein stability in a dynamic molecular model of the bacterial cytoplasm
    • doi:10.1371/J.pcbi.1000694
    • McGuffee SR, Elcock AH (2010) Diffusion, crowding and protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 6: e1000694. doi: 10. 1371/J. pcbi. 1000694.
    • (2010) PLoS Comput Biol , vol.6
    • McGuffee, S.R.1    Elcock, A.H.2
  • 53
    • 84864225957 scopus 로고    scopus 로고
    • Atomic detail Brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions
    • doi:10.1021/jp212532h
    • Mereghetti P, Wade RC (2012) Atomic detail Brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions. J Phys Chem B 116: 8523-8533. doi: 10. 1021/jp212532h.
    • (2012) J Phys Chem B , vol.116 , pp. 8523-8533
    • Mereghetti, P.1    Wade, R.C.2
  • 54
    • 78649859456 scopus 로고    scopus 로고
    • Brownian dynamics simulation of protein solutions: structural and dynamic properties
    • doi:10.1016/j.bpj.2010.10.035
    • Mereghetti P, Gabdoulline RR, Wade RC (2010) Brownian dynamics simulation of protein solutions: structural and dynamic properties. Biophys J 99: 3782-3791. doi: 10. 1016/j. bpj. 2010. 10. 035.
    • (2010) Biophys J , vol.99 , pp. 3782-3791
    • Mereghetti, P.1    Gabdoulline, R.R.2    Wade, R.C.3
  • 55
    • 79551523648 scopus 로고    scopus 로고
    • Macromolecular diffusion and confinement in prokaryotic cells
    • doi:10.1016/j.copbio.2010.09.009
    • Mika JT, Poolman B (2011) Macromolecular diffusion and confinement in prokaryotic cells. Curr Opin Biotechnol 22: 117-126. doi: 10. 1016/j. copbio. 2010. 09. 009.
    • (2011) Curr Opin Biotechnol , vol.22 , pp. 117-126
    • Mika, J.T.1    Poolman, B.2
  • 56
    • 79955698252 scopus 로고    scopus 로고
    • Protein crowding tunes protein stability
    • doi:10.1021/ja200067p
    • Miklos AC, Sarkar M, Wang Y, Pielak GJ (2011) Protein crowding tunes protein stability. J Am Chem Soc 133: 7116-7120. doi: 10. 1021/ja200067p.
    • (2011) J Am Chem Soc , vol.133 , pp. 7116-7120
    • Miklos, A.C.1    Sarkar, M.2    Wang, Y.3    Pielak, G.J.4
  • 57
    • 0035815743 scopus 로고    scopus 로고
    • The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
    • doi:10.1074/jbc.R100005200
    • Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276: 10577-10580. doi: 10. 1074/jbc. R100005200.
    • (2001) J Biol Chem , vol.276 , pp. 10577-10580
    • Minton, A.P.1
  • 58
    • 33646594697 scopus 로고    scopus 로고
    • Diffusion of green fluorescent protein in three cell environments in Escherichia coli
    • doi:10.1128/JB.188.10.3442-3448.2006
    • Mullineaux CW, Nenninger A, Ray N, Robinson C (2006) Diffusion of green fluorescent protein in three cell environments in Escherichia coli. J Bacteriol 188: 3442-3448. doi: 10. 1128/JB. 188. 10. 3442-3448. 2006.
    • (2006) J Bacteriol , vol.188 , pp. 3442-3448
    • Mullineaux, C.W.1    Nenninger, A.2    Ray, N.3    Robinson, C.4
  • 59
    • 84859848908 scopus 로고    scopus 로고
    • FRET microscopy in the living cell: different approaches, strengths and weaknesses
    • doi:10.1002/bies.201100086
    • Padilla-Parra S, Tramier M (2012) FRET microscopy in the living cell: different approaches, strengths and weaknesses. Bioessays 34: 369-376. doi: 10. 1002/bies. 201100086.
    • (2012) Bioessays , vol.34 , pp. 369-376
    • Padilla-Parra, S.1    Tramier, M.2
  • 60
    • 84857128232 scopus 로고    scopus 로고
    • Protein-binding dynamics imaged in a living cell
    • doi:10.1073/pnas.1112171109
    • Phillip Y, Kiss V, Schreiber G (2012) Protein-binding dynamics imaged in a living cell. Proc Natl Acad Sci USA 109: 1461-1466. doi: 10. 1073/pnas. 1112171109.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 1461-1466
    • Phillip, Y.1    Kiss, V.2    Schreiber, G.3
  • 61
    • 0001534927 scopus 로고
    • Hydrodynamic transport properties of hard-sphere dispersions. I. Suspensions of freely mobile particles
    • doi:10.1063/1.866914
    • Phillips RJ, Brady JF, Bossis G (1988) Hydrodynamic transport properties of hard-sphere dispersions. I. Suspensions of freely mobile particles. Phys Fluids 31: 3462-3472. doi: 10. 1063/1. 866914.
    • (1988) Phys Fluids , vol.31 , pp. 3462-3472
    • Phillips, R.J.1    Brady, J.F.2    Bossis, G.3
  • 63
    • 84861161529 scopus 로고    scopus 로고
    • FoldEco: a model for proteostasis in E. coli
    • doi:10.1016/j.celrep.2012.02.011
    • Powers ET, Powers DL, Gierasch LM (2012) FoldEco: a model for proteostasis in E. coli. Cell Rep 1: 265-276. doi: 10. 1016/j. celrep. 2012. 02. 011.
    • (2012) Cell Rep , vol.1 , pp. 265-276
    • Powers, E.T.1    Powers, D.L.2    Gierasch, L.M.3
  • 67
    • 84855896814 scopus 로고    scopus 로고
    • In-cell NMR spectroscopy in Escherichia coli
    • 3rd edn., 10.1007/978-1-61779-480-3_15, A. Shekhtman and D. S. Burz (Eds.), Totowa: Humana Press
    • Robinson KE, Reardon PN, Spicer LD (2012) In-cell NMR spectroscopy in Escherichia coli. In: Shekhtman A, Burz DS (eds) Protein NMR techniques, vol 831. Methods in Molecular Biology, 3rd edn. Humana Press, Totowa, pp 261-277. doi: 10. 1007/978-1-61779-480-3_15.
    • (2012) Protein NMR Techniques, Vol 831. Methods in Molecular Biology , pp. 261-277
    • Robinson, K.E.1    Reardon, P.N.2    Spicer, L.D.3
  • 69
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interaction in polymers
    • doi:10.1063/1.1670977
    • Rotne J, Prager S (1969) Variational treatment of hydrodynamic interaction in polymers. J Chem Phys 50: 4831-4837. doi: 10. 1063/1. 1670977.
    • (1969) J Chem Phys , vol.50 , pp. 4831-4837
    • Rotne, J.1    Prager, S.2
  • 70
    • 24644510813 scopus 로고    scopus 로고
    • Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure
    • doi:10.1038/nature03916
    • Sambashivan S, Liu Y, Sawaya MR, Gingery M, Eisenberg D (2005) Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Nature 438: 266-269. doi: 10. 1038/nature03916.
    • (2005) Nature , vol.438 , pp. 266-269
    • Sambashivan, S.1    Liu, Y.2    Sawaya, M.R.3    Gingery, M.4    Eisenberg, D.5
  • 71
    • 0029873697 scopus 로고    scopus 로고
    • Rapid, electrostatically assisted association of proteins
    • doi:10.1038/nsb0596-427
    • Schreiber G, Fersht AR (1996) Rapid, electrostatically assisted association of proteins. Nat Struct Biol 3: 427-431. doi: 10. 1038/nsb0596-427.
    • (1996) Nat Struct Biol , vol.3 , pp. 427-431
    • Schreiber, G.1    Fersht, A.R.2
  • 72
    • 0035913735 scopus 로고    scopus 로고
    • Evaluation of parameters critical to observing proteins inside living Escherichia coli by in-cell NMR spectroscopy
    • doi:10.1021/ja0112846
    • Serber Z, Ledwidge R, Miller SM, Doetsch V (2001) Evaluation of parameters critical to observing proteins inside living Escherichia coli by in-cell NMR spectroscopy. J Am Chem Soc 123: 8895-8901. doi: 10. 1021/ja0112846.
    • (2001) J Am Chem Soc , vol.123 , pp. 8895-8901
    • Serber, Z.1    Ledwidge, R.2    Miller, S.M.3    Doetsch, V.4
  • 73
    • 37649016316 scopus 로고    scopus 로고
    • Molecular crowding enhances the native structure and stability of α/β protein flavodoxin
    • doi:10.1073/pnas.0705127104
    • Stagg L, Zhang SQ, Cheung MS, Wittung-Stafshede P (2007) Molecular crowding enhances the native structure and stability of α/β protein flavodoxin. Proc Natl Acad Sci USA 104: 18976-18981. doi: 10. 1073/pnas. 0705127104.
    • (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
  • 74
    • 38449108386 scopus 로고    scopus 로고
    • Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects
    • doi:10.1063/1.2789434
    • Sun J, Weinstein H (2007) Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects. J Chem Phys 127: 155105. doi: 10. 1063/1. 2789434.
    • (2007) J Chem Phys , vol.127 , pp. 155105
    • Sun, J.1    Weinstein, H.2
  • 75
    • 84861163682 scopus 로고    scopus 로고
    • A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO)
    • doi:10.1016/j.bpj.2012.04.010
    • Wang Q, Cheung MS (2012) A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO). Biophys J 102: 2353-2361. doi: 10. 1016/j. bpj. 2012. 04. 010.
    • (2012) Biophys J , vol.102 , pp. 2353-2361
    • Wang, Q.1    Cheung, M.S.2
  • 76
    • 77955686807 scopus 로고    scopus 로고
    • Effects of proteins on protein diffusion
    • doi:10.1021/ja102296k
    • Wang YQ, Li CG, Pielak GJ (2010) Effects of proteins on protein diffusion. J Am Chem Soc 132: 9392-9397. doi: 10. 1021/ja102296k.
    • (2010) J Am Chem Soc , vol.132 , pp. 9392-9397
    • Wang, Y.Q.1    Li, C.G.2    Pielak, G.J.3
  • 77
    • 80055013471 scopus 로고    scopus 로고
    • Exploring weak, transient protein-protein interactions in crowed in vivo environments by in-cell nuclear magnetic resonance spectroscopy
    • doi:10.1021/bi201287e
    • Wang QH, Zhuravleva A, Gierasch LM (2011) Exploring weak, transient protein-protein interactions in crowed in vivo environments by in-cell nuclear magnetic resonance spectroscopy. Biochemistry 50: 9225-9236. doi: 10. 1021/bi201287e.
    • (2011) Biochemistry , vol.50 , pp. 9225-9236
    • Wang, Q.H.1    Zhuravleva, A.2    Gierasch, L.M.3
  • 78
    • 84866618652 scopus 로고    scopus 로고
    • Disordered protein diffusion under crowded conditions
    • doi:10.1021/jz3010915
    • Wang YQ, Benton LA, Singh V, Pielak GJ (2012a) Disordered protein diffusion under crowded conditions. J Phys Chem Lett 3: 2703-2706. doi: 10. 1021/jz3010915.
    • (2012) J Phys Chem Lett , vol.3 , pp. 2703-2706
    • Wang, Y.Q.1    Benton, L.A.2    Singh, V.3    Pielak, G.J.4
  • 79
    • 84867377395 scopus 로고    scopus 로고
    • Macromolecular crowding and protein stability
    • doi:10.1021/ja305300m
    • Wang YQ, Sarkar M, Smith AE, Krois AS, Pielak GJ (2012b) Macromolecular crowding and protein stability. J Am Chem Soc 134: 16614-16618. doi: 10. 1021/ja305300m.
    • (2012) J Am Chem Soc , vol.134 , pp. 16614-16618
    • Wang, Y.Q.1    Sarkar, M.2    Smith, A.E.3    Krois, A.S.4    Pielak, G.J.5
  • 80
    • 14844331313 scopus 로고    scopus 로고
    • Anomalous diffusion is a measure for cytoplasmic crowding in living cells
    • doi:10.1529/biophysj.104.044263
    • Weiss M, Elsner M, Kartberg F, Nilsson T (2004) Anomalous diffusion is a measure for cytoplasmic crowding in living cells. Biophys J 87: 3518-3524. doi: 10. 1529/biophysj. 104. 044263.
    • (2004) Biophys J , vol.87 , pp. 3518-3524
    • Weiss, M.1    Elsner, M.2    Kartberg, F.3    Nilsson, T.4
  • 81
    • 0042640726 scopus 로고
    • Some topics in the theory of fluids
    • doi:10.1063/1.1734110
    • Widom B (1963) Some topics in the theory of fluids. J Chem Phys 39: 2808-2812. doi: 10. 1063/1. 1734110.
    • (1963) J Chem Phys , vol.39 , pp. 2808-2812
    • Widom, B.1
  • 82
    • 58149360317 scopus 로고    scopus 로고
    • Influence of macromolecular crowding on protein-protein association rates-a Brownian dynamics study
    • doi:10.1529/biophysj.108.136291
    • Wieczorek G, Zielenkiewicz P (2008) Influence of macromolecular crowding on protein-protein association rates-a Brownian dynamics study. Biophys J 95: 5030-5036. doi: 10. 1529/biophysj. 108. 136291.
    • (2008) Biophys J , vol.95 , pp. 5030-5036
    • Wieczorek, G.1    Zielenkiewicz, P.2
  • 83
    • 0032780181 scopus 로고    scopus 로고
    • SITUS: a package for docking crystal structures into low-resolution maps from electron microscopy
    • doi:10.1006/jsbi.1998.4080
    • Wriggers W, Milligan RA, McCammon JA (1999) SITUS: a package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 125: 185-196. doi: 10. 1006/jsbi. 1998. 4080.
    • (1999) J Struct Biol , vol.125 , pp. 185-196
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 84
    • 48249095613 scopus 로고    scopus 로고
    • Single-molecule approach to molecular biology in living bacterial cells
    • doi:10.1146/annurev.biophys.37.092607.174640
    • Xie XS, Choi PJ, Li GW, Lee NK, Lia G (2008) Single-molecule approach to molecular biology in living bacterial cells. Annu Rev Biophys 37: 417-444. doi: 10. 1146/annurev. biophys. 37. 092607. 174640.
    • (2008) Annu Rev Biophys , vol.37 , pp. 417-444
    • Xie, X.S.1    Choi, P.J.2    Li, G.W.3    Lee, N.K.4    Lia, G.5
  • 85
    • 36849101815 scopus 로고
    • Transport properties of polymer chains in dilute solutions: hydrodynamic interaction
    • doi:10.1063/1.1673799
    • Yamakawa H (1970) Transport properties of polymer chains in dilute solutions: hydrodynamic interaction. J Chem Phys 53: 436-443. doi: 10. 1063/1. 1673799.
    • (1970) J Chem Phys , vol.53 , pp. 436-443
    • Yamakawa, H.1
  • 86
    • 41049090929 scopus 로고    scopus 로고
    • Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences
    • doi:10.1146/annurev.biophys.37.032807.125817
    • Zhou HX, Rivas G, Minton AP (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37: 375-397. doi: 10. 1146/annurev. biophys. 37. 032807. 125817.
    • (2008) Annu Rev Biophys , vol.37 , pp. 375-397
    • Zhou, H.X.1    Rivas, G.2    Minton, A.P.3
  • 87
    • 0027318513 scopus 로고
    • Macromolecular crowding-biochemical, biophysical, and physiological consequences
    • doi:10.1146/annurev.bb.22.060193.000331
    • Zimmerman SB, Minton AP (1993) Macromolecular crowding-biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct 22: 27-65. doi: 10. 1146/annurev. bb. 22. 060193. 000331.
    • (1993) Annu Rev Biophys Biomol Struct , vol.22 , pp. 27-65
    • Zimmerman, S.B.1    Minton, A.P.2
  • 88
    • 0026344818 scopus 로고
    • Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli
    • doi:10.1016/0022-2836(91)90499-V
    • 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. doi: 10. 1016/0022-2836(91)90499-V.
    • (1991) J Mol Biol , vol.222 , pp. 599-620
    • Zimmerman, S.B.1    Trach, S.O.2
  • 89
    • 33846291424 scopus 로고    scopus 로고
    • Translational and rotational motion of proteins in a crowded protein environment
    • doi:10.1016/j.bpc.2006.09.003
    • Zorrilla S, Hink MA, Visser AJWG, Lillo MP (2007) Translational and rotational motion of proteins in a crowded protein environment. Biophys Chem 125: 298-305. doi: 10. 1016/j. bpc. 2006. 09. 003.
    • (2007) Biophys Chem , vol.125 , pp. 298-305
    • Zorrilla, S.1    Hink, M.A.2    Visser, A.J.W.G.3    Lillo, M.P.4


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