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Volumn 10, Issue 5, 2014, Pages

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; IONIC STRENGTH; MOLECULAR DYNAMICS; MOLECULAR PHYSICS; POTENTIAL ENERGY; STABILITY;

EID: 84901675920     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003638     Document Type: Article
Times cited : (135)

References (70)
  • 1
    • 0035478585 scopus 로고    scopus 로고
    • Macromolecular crowding: Obvious but underappreciated
    • Ellis RJ, (2001) Macromolecular crowding: Obvious but underappreciated. Trends in Biochemical Sciences 26: 597-604.
    • (2001) Trends in Biochemical Sciences , vol.26 , pp. 597-604
    • Ellis, R.J.1
  • 2
    • 0041822089 scopus 로고    scopus 로고
    • Cell biology - Join the crowd
    • Ellis RJ, Minton AP, (2003) Cell biology- Join the crowd. Nature 425: 27-28.
    • (2003) Nature , vol.425 , pp. 27-28
    • Ellis, R.J.1    Minton, A.P.2
  • 3
    • 41049090929 scopus 로고    scopus 로고
    • Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
    • Zhou HX, Rivas GN, Minton AP, (2008) Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annual Review of Biophysics pp. 375-397.
    • (2008) Annual Review of Biophysics , pp. 375-397
    • Zhou, H.X.1    Rivas, G.N.2    Minton, A.P.3
  • 4
    • 77951298407 scopus 로고    scopus 로고
    • Models of macromolecular crowding effects and the need for quantitative comparisons with experiment
    • Elcock AH, (2010) Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Current Opinion in Structural Biology 20: 196-206.
    • (2010) Current Opinion in Structural Biology , vol.20 , pp. 196-206
    • Elcock, A.H.1
  • 5
    • 3142514201 scopus 로고    scopus 로고
    • Protein aggregation and neurodegenerative disease
    • Ross CA, Poirier MA, (2004) Protein aggregation and neurodegenerative disease. Nature Medicine 10: S10-S17.
    • (2004) Nature Medicine , vol.10
    • Ross, C.A.1    Poirier, M.A.2
  • 6
    • 57749098600 scopus 로고    scopus 로고
    • Amyloid formation by globular proteins under native conditions
    • Chiti F, Dobson CM, (2009) Amyloid formation by globular proteins under native conditions. Nature Chemical Biology 5: 15-22.
    • (2009) Nature Chemical Biology , vol.5 , pp. 15-22
    • Chiti, F.1    Dobson, C.M.2
  • 7
    • 16344364032 scopus 로고    scopus 로고
    • Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: Macromolecular crowding and protein stability revisited
    • Minton AP, (2005) Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: Macromolecular crowding and protein stability revisited. Biophysical Journal 88: 971-985.
    • (2005) Biophysical Journal , vol.88 , pp. 971-985
    • Minton, A.P.1
  • 9
    • 41449119304 scopus 로고    scopus 로고
    • Coarse-grained MD simulations of membrane protein-bilayer self-assembly
    • Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, et al. (2008) Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 16: 621-630.
    • (2008) Structure , vol.16 , pp. 621-630
    • Scott, K.A.1    Bond, P.J.2    Ivetac, A.3    Chetwynd, A.P.4    Khalid, S.5
  • 10
    • 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 Computational Biology 6: e1000694.
    • (2010) PLoS Computational Biology , vol.6
    • McGuffee, S.R.1    Elcock, A.H.2
  • 13
    • 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. The Journal of Physical Chemistry B 116: 599-605.
    • (2012) The Journal of Physical Chemistry B , vol.116 , pp. 599-605
    • Feig, M.1    Sugita, Y.2
  • 16
    • 84885405882 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other
    • Andrews CT, Elcock AH, (2013) Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other. Journal of Chemical Theory and Computation 9: 4585-4602.
    • (2013) Journal of Chemical Theory and Computation , vol.9 , pp. 4585-4602
    • Andrews, C.T.1    Elcock, A.H.2
  • 17
    • 0037627715 scopus 로고    scopus 로고
    • The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
    • Gsponer J, Haberthur U, Caflisch A, (2003) The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proceedings of the National Academy of Sciences of the United States of America 100: 5154-5159.
    • (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , pp. 5154-5159
    • Gsponer, J.1    Haberthur, U.2    Caflisch, A.3
  • 21
    • 33748689799 scopus 로고    scopus 로고
    • Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    • Ma B, Nussinov R, (2006) Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Current Opinion in Chemical Biology 10: 445-452.
    • (2006) Current Opinion in Chemical Biology , vol.10 , pp. 445-452
    • Ma, B.1    Nussinov, R.2
  • 22
    • 80054949314 scopus 로고    scopus 로고
    • Aggregation in protein-based biotherapeutics: Computational studies and tools to identify aggregation-prone regions
    • Agrawal NJ, Kumar S, Wang X, Helk B, Singh SK, et al. (2011) Aggregation in protein-based biotherapeutics: Computational studies and tools to identify aggregation-prone regions. Journal of Pharmaceutical Sciences 100: 5081-5095.
    • (2011) Journal of Pharmaceutical Sciences , vol.100 , pp. 5081-5095
    • Agrawal, N.J.1    Kumar, S.2    Wang, X.3    Helk, B.4    Singh, S.K.5
  • 27
    • 67650550291 scopus 로고    scopus 로고
    • Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis
    • Bunagan MR, Gao J, Kelly JW, Gai F, (2009) Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis. Journal of the American Chemical Society 131: 7470-7476.
    • (2009) Journal of the American Chemical Society , vol.131 , pp. 7470-7476
    • Bunagan, M.R.1    Gao, J.2    Kelly, J.W.3    Gai, F.4
  • 28
    • 84874843784 scopus 로고    scopus 로고
    • Reduced native state stability in crowded cellular environment due to protein-protein interactions
    • Harada R, Tochio N, Kigawa T, Sugita Y, Feig M, (2013) Reduced native state stability in crowded cellular environment due to protein-protein interactions. Journal of the American Chemical Society 135: 3696-3701.
    • (2013) Journal of the American Chemical Society , vol.135 , pp. 3696-3701
    • Harada, R.1    Tochio, N.2    Kigawa, T.3    Sugita, Y.4    Feig, M.5
  • 29
    • 0034891783 scopus 로고    scopus 로고
    • Oxidative modification of proteins during aging
    • Levine RL, Stadtman ER, (2001) Oxidative modification of proteins during aging. Experimental Gerontology 36: 1495-1502.
    • (2001) Experimental Gerontology , vol.36 , pp. 1495-1502
    • Levine, R.L.1    Stadtman, E.R.2
  • 31
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid, and human disease
    • Chiti F, Dobson CM, (2006) Protein misfolding, functional amyloid, and human disease. Annual review of biochemistry 75: 333-366.
    • (2006) Annual Review of Biochemistry , vol.75 , pp. 333-366
    • Chiti, F.1    Dobson, C.M.2
  • 32
    • 79955703833 scopus 로고    scopus 로고
    • Microscopic analysis of protein oxidative damage: Effect of carbonylation on structure, dynamics, and aggregability of villin headpiece
    • Petrov D, Zagrovic B, (2011) Microscopic analysis of protein oxidative damage: Effect of carbonylation on structure, dynamics, and aggregability of villin headpiece. Journal of the American Chemical Society 133: 7016-7024.
    • (2011) Journal of the American Chemical Society , vol.133 , pp. 7016-7024
    • Petrov, D.1    Zagrovic, B.2
  • 33
    • 0042467550 scopus 로고    scopus 로고
    • Rationalization of the effects of mutations on peptide and protein aggregation rates
    • Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM, (2003) Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 424: 805-808.
    • (2003) Nature , vol.424 , pp. 805-808
    • Chiti, F.1    Stefani, M.2    Taddei, N.3    Ramponi, G.4    Dobson, C.M.5
  • 34
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • Schuler L, Daura X, van Gunsteren W, (2001) An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. Journal of Computational Chemistry 22: 1205-1218.
    • (2001) Journal of Computational Chemistry , vol.22 , pp. 1205-1218
    • Schuler, L.1    Daura, X.2    van Gunsteren, W.3
  • 41
    • 33645408056 scopus 로고    scopus 로고
    • Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field
    • Chen JH, Im WP, Brooks CL, (2006) Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field. Journal of the American Chemical Society 128: 3728-3736.
    • (2006) Journal of the American Chemical Society , vol.128 , pp. 3728-3736
    • Chen, J.H.1    Im, W.P.2    Brooks, C.L.3
  • 42
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL, (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B 105: 6474-6487.
    • (2001) The Journal of Physical Chemistry B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 44
    • 0000267310 scopus 로고
    • Versuch einer mathematischen Theorie der Koagulationskinetik kolloidaler Lösungen
    • Von Smoluchowski M, (1917) Versuch einer mathematischen Theorie der Koagulationskinetik kolloidaler Lösungen. Zeitschrift fur Physikalische Chemie 92: 129-168.
    • (1917) Zeitschrift Fur Physikalische Chemie , vol.92 , pp. 129-168
    • Von Smoluchowski, M.1
  • 46
    • 72949113618 scopus 로고    scopus 로고
    • Conformational averaging in structural biology: issues, challenges and computational solutions
    • Kruschel D, Zagrovic B, (2009) Conformational averaging in structural biology: issues, challenges and computational solutions. Molecular Biosystems 5: 1606-1616.
    • (2009) Molecular Biosystems , vol.5 , pp. 1606-1616
    • Kruschel, D.1    Zagrovic, B.2
  • 47
    • 0034957763 scopus 로고    scopus 로고
    • Two-dimensional infrared correlation spectroscopy study of the aggregation of cytochrome c in the presence of dimyristoylphosphatidylglycerol
    • Paquet MJ, Laviolette M, Pezolet M, Auger M, (2001) Two-dimensional infrared correlation spectroscopy study of the aggregation of cytochrome c in the presence of dimyristoylphosphatidylglycerol. Biophysical Journal 81: 305-312.
    • (2001) Biophysical Journal , vol.81 , pp. 305-312
    • Paquet, M.J.1    Laviolette, M.2    Pezolet, M.3    Auger, M.4
  • 48
    • 0042823410 scopus 로고    scopus 로고
    • Two-dimensional infrared correlation spectroscopy study of sequential events in the heat-induced unfolding and aggregation process of myoglobin
    • Yan YB, Wang Q, He HW, Hu XY, Zhang RQ, et al. (2003) Two-dimensional infrared correlation spectroscopy study of sequential events in the heat-induced unfolding and aggregation process of myoglobin. Biophysical Journal 85: 1959-1967.
    • (2003) Biophysical Journal , vol.85 , pp. 1959-1967
    • Yan, Y.B.1    Wang, Q.2    He, H.W.3    Hu, X.Y.4    Zhang, R.Q.5
  • 49
    • 77950256062 scopus 로고    scopus 로고
    • Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy
    • Ganim Z, Jones KC, Tokmakoff A, (2010) Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy. Physical Chemistry Chemical Physics 12: 3579-3588.
    • (2010) Physical Chemistry Chemical Physics , vol.12 , pp. 3579-3588
    • Ganim, Z.1    Jones, K.C.2    Tokmakoff, A.3
  • 53
    • 20444403757 scopus 로고    scopus 로고
    • Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases
    • Pawar AP, DuBay KF, Zurdo J, Chiti F, Vendruscolo M, et al. (2005) Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. Journal of Molecular Biology 350: 379-392.
    • (2005) Journal of Molecular Biology , vol.350 , pp. 379-392
    • Pawar, A.P.1    DuBay, K.F.2    Zurdo, J.3    Chiti, F.4    Vendruscolo, M.5
  • 54
    • 20444440728 scopus 로고    scopus 로고
    • Structure of the cross-beta spine of amyloid-like fibrils
    • Nelson R, Sawaya MR, Balbirnie M, Madsen AO, Riekel C, et al. (2005) Structure of the cross-beta spine of amyloid-like fibrils. Nature 435: 773-778.
    • (2005) Nature , vol.435 , pp. 773-778
    • Nelson, R.1    Sawaya, M.R.2    Balbirnie, M.3    Madsen, A.O.4    Riekel, C.5
  • 56
    • 79959497750 scopus 로고    scopus 로고
    • Molecular and supramolecular studies on polyglycine and poly-L-proline
    • Lorusso M, Pepe A, Ibris N, Bochicchio B, (2011) Molecular and supramolecular studies on polyglycine and poly-L-proline. Soft Matter 7: 6327-6336.
    • (2011) Soft Matter , vol.7 , pp. 6327-6336
    • Lorusso, M.1    Pepe, A.2    Ibris, N.3    Bochicchio, B.4
  • 57
    • 0141990949 scopus 로고    scopus 로고
    • Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
    • Shirts MR, Pitera JW, Swope WC, Pande VS, (2003) Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins. Journal of Chemical Physics 119: 5740-5761.
    • (2003) Journal of Chemical Physics , vol.119 , pp. 5740-5761
    • Shirts, M.R.1    Pitera, J.W.2    Swope, W.C.3    Pande, V.S.4
  • 58
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink C, Villa A, Mark AE, van Gunsteren WF, (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry 25: 1656-1676.
    • (2004) Journal of Computational Chemistry , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 60
    • 79959720287 scopus 로고    scopus 로고
    • How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
    • Piana S, Lindorff-Larsen K, Shaw DE, (2011) How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization? Biophysical Journal 100: L47-L49.
    • (2011) Biophysical Journal , vol.100
    • Piana, S.1    Lindorff-Larsen, K.2    Shaw, D.E.3
  • 62
    • 61349154358 scopus 로고    scopus 로고
    • Are current molecular dynamics force fields too helical?
    • Best RB, Buchete N-V, Hummer G, (2008) Are current molecular dynamics force fields too helical? Biophysical Journal 95: 4494-4494.
    • (2008) Biophysical Journal , vol.95 , pp. 4494
    • Best, R.B.1    Buchete, N.-V.2    Hummer, G.3
  • 65
    • 84880813977 scopus 로고    scopus 로고
    • Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications
    • Margreitter C, Petrov D, Zagrovic B, (2013) Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Research 41: W422-426.
    • (2013) Nucleic Acids Research , vol.41
    • Margreitter, C.1    Petrov, D.2    Zagrovic, B.3
  • 68
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2


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