-
1
-
-
0026344818
-
Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli
-
Zimmerman SB, Trach SO, (1991) Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J Mol Biol 222: 599-620.
-
(1991)
J Mol Biol
, vol.222
, pp. 599-620
-
-
Zimmerman, S.B.1
Trach, S.O.2
-
2
-
-
0027318513
-
Macromolecular crowding: biochemical, biophysical, and physiological consequences
-
Zimmerman SB, Minton AP, (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct 22: 27-65.
-
(1993)
Annu Rev Biophys Biomol Struct
, vol.22
, pp. 27-65
-
-
Zimmerman, S.B.1
Minton, A.P.2
-
3
-
-
0033969150
-
Implications of macromolecular crowding for protein assembly
-
Minton AP, (2000) Implications of macromolecular crowding for protein assembly. Curr Opin Struct Biol 10: 34-39.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 34-39
-
-
Minton, A.P.1
-
4
-
-
0031022118
-
Influence of excluded volume upon macromolecular structure and associations in 'crowded' media
-
Minton AP, (1997) Influence of excluded volume upon macromolecular structure and associations in 'crowded' media. Curr Opin Biotechnol 8: 65-69.
-
(1997)
Curr Opin Biotechnol
, vol.8
, pp. 65-69
-
-
Minton, A.P.1
-
5
-
-
77951298407
-
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. Curr Opin Struct Biol 20: 196-206.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 196-206
-
-
Elcock, A.H.1
-
6
-
-
0035478585
-
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
-
7
-
-
41049090929
-
Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences
-
Zhou HX, Rivas G, Minton AP, (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37: 375-397.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 375-397
-
-
Zhou, H.X.1
Rivas, G.2
Minton, A.P.3
-
8
-
-
0037470574
-
Effect of dextran on protein stability and conformation attributed to macromolecular crowding
-
Sasahara K, McPhie P, Minton AP, (2003) Effect of dextran on protein stability and conformation attributed to macromolecular crowding. J Mol Biol 326: 1227-1237.
-
(2003)
J Mol Biol
, vol.326
, pp. 1227-1237
-
-
Sasahara, K.1
McPhie, P.2
Minton, A.P.3
-
9
-
-
78049291945
-
Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding
-
Dhar A, Samiotakis A, Ebbinghaus S, Nienhaus L, Homouz D, et al. (2010) Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding. Proc Natl Acad Sci U S A 107: 17586-17591.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 17586-17591
-
-
Dhar, A.1
Samiotakis, A.2
Ebbinghaus, S.3
Nienhaus, L.4
Homouz, D.5
-
10
-
-
37649016316
-
Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin
-
Stagg L, Zhang SQ, Cheung MS, Wittung-Stafshede P, (2007) Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin. Proc Natl Acad Sci U S A 104: 18976-18981.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 18976-18981
-
-
Stagg, L.1
Zhang, S.Q.2
Cheung, M.S.3
Wittung-Stafshede, P.4
-
11
-
-
77950792003
-
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
-
12
-
-
77955686807
-
Effects of proteins on protein diffusion
-
Wang Y, Li C, Pielak GJ, (2010) Effects of proteins on protein diffusion. J Am Chem Soc 132: 9392-9397.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 9392-9397
-
-
Wang, Y.1
Li, C.2
Pielak, G.J.3
-
13
-
-
84859933274
-
Molecular crowding creates traffic jams of kinesin motors on microtubules
-
Leduc C, Padberg-Gehle K, Varga V, Helbing D, Diez S, et al. (2012) Molecular crowding creates traffic jams of kinesin motors on microtubules. Proc Natl Acad Sci U S A 109: 6100-6105.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 6100-6105
-
-
Leduc, C.1
Padberg-Gehle, K.2
Varga, V.3
Helbing, D.4
Diez, S.5
-
14
-
-
79961243052
-
Processive phosphorylation of ERK MAP kinase in mammalian cells
-
Aoki K, Yamada M, Kunida K, Yasuda S, Matsuda M, (2011) Processive phosphorylation of ERK MAP kinase in mammalian cells. Proc Natl Acad Sci U S A 108: 12675-12680.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 12675-12680
-
-
Aoki, K.1
Yamada, M.2
Kunida, K.3
Yasuda, S.4
Matsuda, M.5
-
15
-
-
68949083274
-
Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences
-
Batra J, Xu K, Qin S, Zhou HX, (2009) Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences. Biophys J 97: 906-911.
-
(2009)
Biophys J
, vol.97
, pp. 906-911
-
-
Batra, J.1
Xu, K.2
Qin, S.3
Zhou, H.X.4
-
16
-
-
77956645458
-
Macromolecular crowding converts the human recombinant PrPC to the soluble neurotoxic beta-oligomers
-
Huang L, Jin R, Li J, Luo K, Huang T, et al. (2010) Macromolecular crowding converts the human recombinant PrPC to the soluble neurotoxic beta-oligomers. FASEB J 24: 3536-3543.
-
(2010)
FASEB J
, vol.24
, pp. 3536-3543
-
-
Huang, L.1
Jin, R.2
Li, J.3
Luo, K.4
Huang, T.5
-
17
-
-
80053106666
-
Fibril formation of the rabbit/human/bovine prion proteins
-
Zhou Z, Yan X, Pan K, Chen J, Xie ZS, et al. (2011) Fibril formation of the rabbit/human/bovine prion proteins. Biophys J 101: 1483-1492.
-
(2011)
Biophys J
, vol.101
, pp. 1483-1492
-
-
Zhou, Z.1
Yan, X.2
Pan, K.3
Chen, J.4
Xie, Z.S.5
-
18
-
-
84860446148
-
The contrasting effect of macromolecular crowding on amyloid fibril formation
-
Ma Q, Fan JB, Zhou Z, Zhou BR, Meng SR, et al. (2012) The contrasting effect of macromolecular crowding on amyloid fibril formation. PLoS One 7: e36288.
-
(2012)
PLoS One
, vol.7
-
-
Ma, Q.1
Fan, J.B.2
Zhou, Z.3
Zhou, B.R.4
Meng, S.R.5
-
20
-
-
0034255123
-
Speeding molecular recognition by using the folding funnel: the fly-casting mechanism
-
Shoemaker BA, Portman JJ, Wolynes PG, (2000) Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci U S A 97: 8868-8873.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 8868-8873
-
-
Shoemaker, B.A.1
Portman, J.J.2
Wolynes, P.G.3
-
21
-
-
0032749078
-
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
-
Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293: 321-331.
-
(1999)
J Mol Biol
, vol.293
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
22
-
-
0036468397
-
Coupling of folding and binding for unstructured proteins
-
Dyson HJ, Wright PE, (2002) Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12: 54-60.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 54-60
-
-
Dyson, H.J.1
Wright, P.E.2
-
23
-
-
60349087841
-
Biophysical characterization of intrinsically disordered proteins
-
Eliezer D, (2009) Biophysical characterization of intrinsically disordered proteins. Curr Opin Struct Biol 19: 23-30.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 23-30
-
-
Eliezer, D.1
-
24
-
-
33846913510
-
Atomic-level characterization of disordered protein ensembles
-
Mittag T, Forman-Kay JD, (2007) Atomic-level characterization of disordered protein ensembles. Curr Opin Struct Biol 17: 3-14.
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 3-14
-
-
Mittag, T.1
Forman-Kay, J.D.2
-
25
-
-
82655179700
-
Towards a robust description of intrinsic protein disorder using nuclear magnetic resonance spectroscopy
-
Schneider R, Huang JR, Yao M, Communie G, Ozenne V, et al. (2012) Towards a robust description of intrinsic protein disorder using nuclear magnetic resonance spectroscopy. Mol Biosyst 8: 58-68.
-
(2012)
Mol Biosyst
, vol.8
, pp. 58-68
-
-
Schneider, R.1
Huang, J.R.2
Yao, M.3
Communie, G.4
Ozenne, V.5
-
26
-
-
76649114676
-
Protein dynamics and conformational disorder in molecular recognition
-
Mittag T, Kay LE, Forman-Kay JD, (2010) Protein dynamics and conformational disorder in molecular recognition. J Mol Recognit 23: 105-116.
-
(2010)
J Mol Recognit
, vol.23
, pp. 105-116
-
-
Mittag, T.1
Kay, L.E.2
Forman-Kay, J.D.3
-
27
-
-
64849111005
-
Sending signals dynamically
-
Smock RG, Gierasch LM, (2009) Sending signals dynamically. Science 324: 198-203.
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
28
-
-
34547652267
-
CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices
-
Baker JM, Hudson RP, Kanelis V, Choy WY, Thibodeau PH, et al. (2007) CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices. Nat Struct Mol Biol 14: 738-745.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 738-745
-
-
Baker, J.M.1
Hudson, R.P.2
Kanelis, V.3
Choy, W.Y.4
Thibodeau, P.H.5
-
29
-
-
56649112976
-
Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor
-
Mittag T, Orlicky S, Choy WY, Tang X, Lin H, et al. (2008) Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. Proc Natl Acad Sci U S A 105: 17772-17777.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 17772-17777
-
-
Mittag, T.1
Orlicky, S.2
Choy, W.Y.3
Tang, X.4
Lin, H.5
-
30
-
-
84857698871
-
Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase
-
Tang X, Orlicky S, Mittag T, Csizmok V, Pawson T, et al. (2012) Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase. Proc Natl Acad Sci U S A 109: 3287-3292.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 3287-3292
-
-
Tang, X.1
Orlicky, S.2
Mittag, T.3
Csizmok, V.4
Pawson, T.5
-
31
-
-
0036792049
-
FlgM gains structure in living cells
-
Dedmon MM, Patel CN, Young GB, Pielak GJ, (2002) FlgM gains structure in living cells. Proc Natl Acad Sci U S A 99: 12681-12684.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 12681-12684
-
-
Dedmon, M.M.1
Patel, C.N.2
Young, G.B.3
Pielak, G.J.4
-
32
-
-
0034894258
-
Effects of macromolecular crowding on the intrinsically disordered proteins c-Fos and p27(Kip1)
-
Flaugh SL, Lumb KJ, (2001) Effects of macromolecular crowding on the intrinsically disordered proteins c-Fos and p27(Kip1). Biomacromolecules 2: 538-540.
-
(2001)
Biomacromolecules
, vol.2
, pp. 538-540
-
-
Flaugh, S.L.1
Lumb, K.J.2
-
33
-
-
79951841821
-
Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching
-
Johansen D, Jeffries CM, Hammouda B, Trewhella J, Goldenberg DP, (2011) Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching. Biophys J 100: 1120-1128.
-
(2011)
Biophys J
, vol.100
, pp. 1120-1128
-
-
Johansen, D.1
Jeffries, C.M.2
Hammouda, B.3
Trewhella, J.4
Goldenberg, D.P.5
-
34
-
-
79959807835
-
Protein disorder prevails under crowded conditions
-
Szasz CS, Alexa A, Toth K, Rakacs M, Langowski J, et al. (2011) Protein disorder prevails under crowded conditions. Biochemistry 50: 5834-5844.
-
(2011)
Biochemistry
, vol.50
, pp. 5834-5844
-
-
Szasz, C.S.1
Alexa, A.2
Toth, K.3
Rakacs, M.4
Langowski, J.5
-
35
-
-
72449139985
-
Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding
-
Uversky VN, (2009) Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein J 28: 305-325.
-
(2009)
Protein J
, vol.28
, pp. 305-325
-
-
Uversky, V.N.1
-
36
-
-
0000095902
-
Prothymosin alpha: isolation and properties of the major immunoreactive form of thymosin alpha 1 in rat thymus
-
Haritos AA, Goodall GJ, Horecker BL, (1984) Prothymosin alpha: isolation and properties of the major immunoreactive form of thymosin alpha 1 in rat thymus. Proc Natl Acad Sci U S A 81: 1008-1011.
-
(1984)
Proc Natl Acad Sci U S A
, vol.81
, pp. 1008-1011
-
-
Haritos, A.A.1
Goodall, G.J.2
Horecker, B.L.3
-
37
-
-
0028785802
-
Prothymosin alpha: a biologically active protein with random coil conformation
-
Gast K, Damaschun H, Eckert K, Schulze-Forster K, Maurer HR, et al. (1995) Prothymosin alpha: a biologically active protein with random coil conformation. Biochemistry 34: 13211-13218.
-
(1995)
Biochemistry
, vol.34
, pp. 13211-13218
-
-
Gast, K.1
Damaschun, H.2
Eckert, K.3
Schulze-Forster, K.4
Maurer, H.R.5
-
38
-
-
0033783289
-
Fifteen years of prothymosin alpha: contradictory past and new horizons
-
Piñeiro A, Cordero OJ, Nogueira M, (2000) Fifteen years of prothymosin alpha: contradictory past and new horizons. Peptides 21: 1433-1446.
-
(2000)
Peptides
, vol.21
, pp. 1433-1446
-
-
Piñeiro, A.1
Cordero, O.J.2
Nogueira, M.3
-
39
-
-
36249020870
-
A new protocol for high-yield purification of recombinant human prothymosin alpha expressed in Escherichia coli for NMR studies
-
Yi S, Brickenden A, Choy WY, (2008) A new protocol for high-yield purification of recombinant human prothymosin alpha expressed in Escherichia coli for NMR studies. Protein Expr Purif 57: 1-8.
-
(2008)
Protein Expr Purif
, vol.57
, pp. 1-8
-
-
Yi, S.1
Brickenden, A.2
Choy, W.Y.3
-
40
-
-
36048990877
-
Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch
-
Yi S, Boys BL, Brickenden A, Konermann L, Choy WY, (2007) Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch. Biochemistry 46: 13120-13130.
-
(2007)
Biochemistry
, vol.46
, pp. 13120-13130
-
-
Yi, S.1
Boys, B.L.2
Brickenden, A.3
Konermann, L.4
Choy, W.Y.5
-
41
-
-
0034329424
-
Cloning of TC-1 (C8orf4), a novel gene found to be overexpressed in thyroid cancer
-
Chua EL, Young L, Wu WM, Turtle JR, Dong Q, (2000) Cloning of TC-1 (C8orf4), a novel gene found to be overexpressed in thyroid cancer. Genomics 69: 342-347.
-
(2000)
Genomics
, vol.69
, pp. 342-347
-
-
Chua, E.L.1
Young, L.2
Wu, W.M.3
Turtle, J.R.4
Dong, Q.5
-
42
-
-
13844261745
-
TC-1 is a novel tumorigenic and natively disordered protein associated with thyroid cancer
-
Sunde M, McGrath KC, Young L, Matthews JM, Chua EL, et al. (2004) TC-1 is a novel tumorigenic and natively disordered protein associated with thyroid cancer. Cancer Res 64: 2766-2773.
-
(2004)
Cancer Res
, vol.64
, pp. 2766-2773
-
-
Sunde, M.1
McGrath, K.C.2
Young, L.3
Matthews, J.M.4
Chua, E.L.5
-
43
-
-
0033895709
-
Wnt signaling and cancer
-
Polakis P, (2000) Wnt signaling and cancer. Genes Dev 14: 1837-1851.
-
(2000)
Genes Dev
, vol.14
, pp. 1837-1851
-
-
Polakis, P.1
-
44
-
-
31544462050
-
TC1 (C8orf4) enhances the Wnt/beta-catenin pathway by relieving antagonistic activity of Chibby
-
Jung Y, Bang S, Choi K, Kim E, Kim Y, et al. (2006) TC1 (C8orf4) enhances the Wnt/beta-catenin pathway by relieving antagonistic activity of Chibby. Cancer Res 66: 723-728.
-
(2006)
Cancer Res
, vol.66
, pp. 723-728
-
-
Jung, Y.1
Bang, S.2
Choi, K.3
Kim, E.4
Kim, Y.5
-
45
-
-
0242515751
-
Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway
-
Takemaru K-I, Yamaguchi S, Lee YS, Zhang Y, Carthew RW, et al. (2003) Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway. Nature 422: 905-909.
-
(2003)
Nature
, vol.422
, pp. 905-909
-
-
Takemaru, K.-I.1
Yamaguchi, S.2
Lee, Y.S.3
Zhang, Y.4
Carthew, R.W.5
-
46
-
-
35648982507
-
The intrinsically disordered TC-1 interacts with Chibby via regions with high helical propensity
-
Gall C, Xu H, Brickenden A, Ai X, Choy WY, (2007) The intrinsically disordered TC-1 interacts with Chibby via regions with high helical propensity. Protein Sci 16: 2510-2518.
-
(2007)
Protein Sci
, vol.16
, pp. 2510-2518
-
-
Gall, C.1
Xu, H.2
Brickenden, A.3
Ai, X.4
Choy, W.Y.5
-
47
-
-
0036934774
-
NACP/alpha-synuclein, NAC, and beta-amyloid pathology of familial Alzheimer's disease with the E184D presenilin-1 mutation: a clinicopathological study of two autopsy cases
-
Yokota O, Terada S, Ishizu H, Ujike H, Ishihara T, et al. (2002) NACP/alpha-synuclein, NAC, and beta-amyloid pathology of familial Alzheimer's disease with the E184D presenilin-1 mutation: a clinicopathological study of two autopsy cases. Acta Neuropathol 104: 637-648.
-
(2002)
Acta Neuropathol
, vol.104
, pp. 637-648
-
-
Yokota, O.1
Terada, S.2
Ishizu, H.3
Ujike, H.4
Ishihara, T.5
-
48
-
-
29544433937
-
Macromolecular crowding in the Escherichia coli periplasm maintains alpha-synuclein disorder
-
McNulty BC, Young GB, Pielak GJ, (2006) Macromolecular crowding in the Escherichia coli periplasm maintains alpha-synuclein disorder. J Mol Biol 355: 893-897.
-
(2006)
J Mol Biol
, vol.355
, pp. 893-897
-
-
McNulty, B.C.1
Young, G.B.2
Pielak, G.J.3
-
49
-
-
0028215226
-
Characterization of DsbC, a periplasmic protein of Erwinia chrysanthemi and Escherichia coli with disulfide isomerase activity
-
Shevchik VE, Condemine G, Robert-Baudouy J, (1994) Characterization of DsbC, a periplasmic protein of Erwinia chrysanthemi and Escherichia coli with disulfide isomerase activity. EMBO J 13: 2007-2012.
-
(1994)
EMBO J
, vol.13
, pp. 2007-2012
-
-
Shevchik, V.E.1
Condemine, G.2
Robert-Baudouy, J.3
-
50
-
-
0029400480
-
NMRPipe: a multidimensional spectral processing system based on UNIX pipes
-
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277-293.
-
(1995)
J Biomol NMR
, vol.6
, pp. 277-293
-
-
Delaglio, F.1
Grzesiek, S.2
Vuister, G.W.3
Zhu, G.4
Pfeifer, J.5
-
51
-
-
4644259437
-
Using NMRView to visualize and analyze the NMR spectra of macromolecules
-
Johnson BA, (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278: 313-352.
-
(2004)
Methods Mol Biol
, vol.278
, pp. 313-352
-
-
Johnson, B.A.1
-
52
-
-
0033029875
-
Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation
-
Lee AL, Wand AJ, (1999) Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation. J Biomol NMR 13: 101-112.
-
(1999)
J Biomol NMR
, vol.13
, pp. 101-112
-
-
Lee, A.L.1
Wand, A.J.2
-
53
-
-
42649142233
-
Characterization of conformational and dynamic properties of natively unfolded human and mouse alpha-synuclein ensembles by NMR: implication for aggregation
-
Wu KP, Kim S, Fela DA, Baum J, (2008) Characterization of conformational and dynamic properties of natively unfolded human and mouse alpha-synuclein ensembles by NMR: implication for aggregation. J Mol Biol 378: 1104-1115.
-
(2008)
J Mol Biol
, vol.378
, pp. 1104-1115
-
-
Wu, K.P.1
Kim, S.2
Fela, D.A.3
Baum, J.4
-
54
-
-
38349077155
-
Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces
-
d'Auvergne EJ, Gooley PR, (2008) Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J Biomol NMR 40: 107-119.
-
(2008)
J Biomol NMR
, vol.40
, pp. 107-119
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
55
-
-
38349050193
-
Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor
-
d'Auvergne EJ, Gooley PR, (2008) Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J Biomol NMR 40: 121-133.
-
(2008)
J Biomol NMR
, vol.40
, pp. 121-133
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
56
-
-
37049014272
-
Version 1.2 of the Crystallography and NMR system
-
Brunger AT, (2007) Version 1.2 of the Crystallography and NMR system. Nat Protoc 2: 2728-2733.
-
(2007)
Nat Protoc
, vol.2
, pp. 2728-2733
-
-
Brunger, A.T.1
-
57
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput 4: 435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
58
-
-
4444282928
-
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. J Comput Chem 25: 1656-1676.
-
(2004)
J Comput Chem
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
van Gunsteren, W.F.4
-
59
-
-
21244467488
-
Validation of the 53A6 GROMOS force field
-
Oostenbrink C, Soares TA, van der Vegt NF, van Gunsteren WF, (2005) Validation of the 53A6 GROMOS force field. Eur Biophys J 34: 273-284.
-
(2005)
Eur Biophys J
, vol.34
, pp. 273-284
-
-
Oostenbrink, C.1
Soares, T.A.2
van der Vegt, N.F.3
van Gunsteren, W.F.4
-
60
-
-
84859224210
-
Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response
-
Cino EA, Wong-Ekkabut J, Karttunen M, Choy WY, (2011) Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response. PLoS One 6: e27371.
-
(2011)
PLoS One
, vol.6
-
-
Cino, E.A.1
Wong-Ekkabut, J.2
Karttunen, M.3
Choy, W.Y.4
-
61
-
-
84865088597
-
Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations
-
Cino EA, Choy WY, Karttunen M, (2012) Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations. J Chem Theory Comput 8: 2725-2740.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2725-2740
-
-
Cino, E.A.1
Choy, W.Y.2
Karttunen, M.3
-
62
-
-
84865084104
-
Assessment of common simulation protocols for simulations of nanopores, membrane proteins & channels
-
Wong-Ekkabut J, Karttunen M, (2012) Assessment of common simulation protocols for simulations of nanopores, membrane proteins & channels. J Chem Theory Comput 8: 2905-2911.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2905-2911
-
-
Wong-Ekkabut, J.1
Karttunen, M.2
-
63
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Dordrecht, Netherlands: Reidel
-
Berendsen HJC, Postma JPM, Gusteren WF (1981) Interaction models for water in relation to protein hydration. Intermolecular Forces Dordrecht, Netherlands: Reidel. 331-342.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Gusteren, W.F.3
-
64
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
Bussi G, Donadio D, Parrinello M, (2007) Canonical sampling through velocity rescaling. J Chem Phys 126: 014101.
-
(2007)
J Chem Phys
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
65
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
Parrinello Rahman, (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. J Appl Phys 52: 7182-7190.
-
(1981)
J Appl Phys
, vol.52
, pp. 7182-7190
-
-
Parrinello, R.1
-
66
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess B, Bekker H, Berendsen HJC, Johannes JGEM, (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18: 1463-1472.
-
(1997)
J Comput Chem
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Johannes, J.G.E.M.4
-
67
-
-
33846823909
-
Particle mesh Ewald: An N{dot operator} log (N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N{dot operator} log (N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
68
-
-
45849099466
-
Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading?
-
Karttunen M, Rottler J, Vattulainen I, Sagui C, (2008) Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading? Current Topics in Membranes 60: 49-89.
-
(2008)
Current Topics in Membranes
, vol.60
, pp. 49-89
-
-
Karttunen, M.1
Rottler, J.2
Vattulainen, I.3
Sagui, C.4
-
69
-
-
0343697622
-
A protocol for the interpretation of side-chain dynamics based on NMR relaxation: Application to phenylalanines in antamanide
-
Bremi T, Brüschweiler R, Ernst RR, (1997) A protocol for the interpretation of side-chain dynamics based on NMR relaxation: Application to phenylalanines in antamanide. J Am Chem Soc 119: 4272-4284.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 4272-4284
-
-
Bremi, T.1
Brüschweiler, R.2
Ernst, R.R.3
-
70
-
-
0001531472
-
Exponential analysis in physical phenomena
-
Istratov AA, Vyvenko OF, (1999) Exponential analysis in physical phenomena. Rev Sci Instrum 70: 1233.
-
(1999)
Rev Sci Instrum
, vol.70
, pp. 1233
-
-
Istratov, A.A.1
Vyvenko, O.F.2
-
71
-
-
80052820089
-
Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin?
-
Xue Y, Skrynnikov NR, (2011) Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? J Am Chem Soc 133: 14614-14628.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 14614-14628
-
-
Xue, Y.1
Skrynnikov, N.R.2
-
72
-
-
84864479275
-
Effects of macromolecular crowding on the structural stability of human α-lactalbumin
-
Zhang DL, Wu LJ, Chen J, Liang Y, (2012) Effects of macromolecular crowding on the structural stability of human α-lactalbumin. Acta Biochim Biophys Sin (Shanghai) 44: 703-711.
-
(2012)
Acta Biochim Biophys Sin (Shanghai)
, vol.44
, pp. 703-711
-
-
Zhang, D.L.1
Wu, L.J.2
Chen, J.3
Liang, Y.4
-
73
-
-
33751552347
-
Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation
-
Marsh JA, Singh VK, Jia Z, Forman-Kay JD, (2006) Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation. Protein Sci 15: 2795-2804.
-
(2006)
Protein Sci
, vol.15
, pp. 2795-2804
-
-
Marsh, J.A.1
Singh, V.K.2
Jia, Z.3
Forman-Kay, J.D.4
-
74
-
-
0024449503
-
Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease
-
Kay LE, Torchia DA, Bax A, (1989) Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28: 8972-8979.
-
(1989)
Biochemistry
, vol.28
, pp. 8972-8979
-
-
Kay, L.E.1
Torchia, D.A.2
Bax, A.3
-
75
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
-
Lipari G, Szabo A, (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104: 4546-4559.
-
(1982)
J Am Chem Soc
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
76
-
-
0025046144
-
Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
-
Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, et al. (1990) Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 112: 4989-4991.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 4989-4991
-
-
Clore, G.M.1
Szabo, A.2
Bax, A.3
Kay, L.E.4
Driscoll, P.C.5
-
77
-
-
0038069359
-
Model selection for the interpretation of protein side chain methyl dynamics
-
Choy WY, Kay LE, (2003) Model selection for the interpretation of protein side chain methyl dynamics. J Biomol NMR 25: 325-333.
-
(2003)
J Biomol NMR
, vol.25
, pp. 325-333
-
-
Choy, W.Y.1
Kay, L.E.2
-
78
-
-
28744436857
-
NMR Relaxation and Internal Dynamics of Ubiquitin from a 0.2 μs MD Simulation
-
Nederveen AJ, Bonvin AMJJ, (2005) NMR Relaxation and Internal Dynamics of Ubiquitin from a 0.2 μs MD Simulation. J Chem Theory Comput 1: 363-374.
-
(2005)
J Chem Theory Comput
, vol.1
, pp. 363-374
-
-
Nederveen, A.J.1
Bonvin, A.M.J.J.2
-
79
-
-
35948943745
-
Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field
-
Showalter SA, Brüschweiler R, (2007) Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field. J Chem Theory Comput 3: 961-975.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 961-975
-
-
Showalter, S.A.1
Brüschweiler, R.2
-
80
-
-
43949111008
-
Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy
-
Li C, Charlton LM, Lakkavaram A, Seagle C, Wang G, et al. (2008) Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy. J Am Chem Soc 130: 6310-6311.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 6310-6311
-
-
Li, C.1
Charlton, L.M.2
Lakkavaram, A.3
Seagle, C.4
Wang, G.5
-
81
-
-
33746591154
-
Fast local backbone dynamics of encapsulated ubiquitin
-
Simorellis AK, Flynn PF, (2006) Fast local backbone dynamics of encapsulated ubiquitin. J Am Chem Soc 128: 9580-9581.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 9580-9581
-
-
Simorellis, A.K.1
Flynn, P.F.2
-
83
-
-
0037376987
-
Apoptosis-related fragmentation, translocation, and properties of human prothymosin alpha
-
Evstafieva AG, Belov GA, Rubtsov YP, Kalkum M, Joseph B, et al. (2003) Apoptosis-related fragmentation, translocation, and properties of human prothymosin alpha. Exp Cell Res 284: 211-223.
-
(2003)
Exp Cell Res
, vol.284
, pp. 211-223
-
-
Evstafieva, A.G.1
Belov, G.A.2
Rubtsov, Y.P.3
Kalkum, M.4
Joseph, B.5
-
84
-
-
77955249021
-
Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c
-
Christiansen A, Wang Q, Samiotakis A, Cheung MS, Wittung-Stafshede P, (2010) Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c. Biochemistry 49: 6519-6530.
-
(2010)
Biochemistry
, vol.49
, pp. 6519-6530
-
-
Christiansen, A.1
Wang, Q.2
Samiotakis, A.3
Cheung, M.S.4
Wittung-Stafshede, P.5
-
85
-
-
0035815743
-
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
-
Minton AP, (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276: 10577-10580.
-
(2001)
J Biol Chem
, vol.276
, pp. 10577-10580
-
-
Minton, A.P.1
-
86
-
-
33747059858
-
Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes
-
Selenko P, Serber Z, Gadea B, Ruderman J, Wagner G, (2006) Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc Natl Acad Sci U S A 103: 11904-11909.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 11904-11909
-
-
Selenko, P.1
Serber, Z.2
Gadea, B.3
Ruderman, J.4
Wagner, G.5
-
88
-
-
59849113286
-
Protein nuclear magnetic resonance under physiological conditions
-
Pielak GJ, Li C, Miklos AC, Schlesinger AP, Slade KM, et al. (2009) Protein nuclear magnetic resonance under physiological conditions. Biochemistry 48: 226-234.
-
(2009)
Biochemistry
, vol.48
, pp. 226-234
-
-
Pielak, G.J.1
Li, C.2
Miklos, A.C.3
Schlesinger, A.P.4
Slade, K.M.5
-
89
-
-
61949315876
-
Protein structure determination in living cells by in-cell NMR spectroscopy
-
Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, et al. (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458: 102-105.
-
(2009)
Nature
, vol.458
, pp. 102-105
-
-
Sakakibara, D.1
Sasaki, A.2
Ikeya, T.3
Hamatsu, J.4
Hanashima, T.5
-
90
-
-
23744476746
-
Multidimensional NMR spectroscopy for protein characterization and assignment inside cells
-
Reardon PN, Spicer LD, (2005) Multidimensional NMR spectroscopy for protein characterization and assignment inside cells. J Am Chem Soc 127: 10848-10849.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 10848-10849
-
-
Reardon, P.N.1
Spicer, L.D.2
-
91
-
-
74849140345
-
Protein (19)F NMR in Escherichia coli
-
Li C, Wang GF, Wang Y, Creager-Allen R, Lutz EA, et al. (2010) Protein (19)F NMR in Escherichia coli. J Am Chem Soc 132: 321-327.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 321-327
-
-
Li, C.1
Wang, G.F.2
Wang, Y.3
Creager-Allen, R.4
Lutz, E.A.5
-
92
-
-
79957787217
-
Macromolecular crowding fails to fold a globular protein in cells
-
Schlesinger AP, Wang Y, Tadeo X, Millet O, Pielak GJ, (2011) Macromolecular crowding fails to fold a globular protein in cells. J Am Chem Soc 133: 8082-8085.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 8082-8085
-
-
Schlesinger, A.P.1
Wang, Y.2
Tadeo, X.3
Millet, O.4
Pielak, G.J.5
|