-
1
-
-
41049090929
-
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
-
H.-X. Zhou, G. Rivas, and A.P. Minton Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences Annu. Rev. Biophys. 37 2008 375-97
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 375-397
-
-
Zhou, H.-X.1
Rivas, G.2
Minton, A.P.3
-
6
-
-
0033515436
-
Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity
-
DOI 10.1006/jmbi.1999.2591
-
M.R. Betancourt, and D. Thirumalai Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity J. Mol. Biol. 287 1999 627 644 (Pubitemid 29168438)
-
(1999)
Journal of Molecular Biology
, vol.287
, Issue.3
, pp. 627-644
-
-
Betancourt, M.R.1
Thirumalai, D.2
-
7
-
-
0035949430
-
Stabilization of proteins in confined spaces
-
DOI 10.1021/bi0155504
-
H.X. Zhou, and K.A. Dill Stabilization of proteins in confined spaces Biochemistry 40 2001 11289 11293 (Pubitemid 32911271)
-
(2001)
Biochemistry
, vol.40
, Issue.38
, pp. 11289-11293
-
-
Zhou, H.-X.1
Dill, K.A.2
-
8
-
-
58149498257
-
Thermodynamics and kinetics of protein folding under confinement
-
J. Mittal, and R.B. Best Thermodynamics and kinetics of protein folding under confinement Proc. Natl. Acad. Sci. USA 105 2008 20233 20238
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 20233-20238
-
-
Mittal, J.1
Best, R.B.2
-
11
-
-
0037799371
-
Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist β-barrel protein
-
M. Friedel, D.J. Sheeler, and J.-E. Shea Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist β-barrel protein J. Chem. Phys. 118 2003 8106
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 8106
-
-
Friedel, M.1
Sheeler, D.J.2
Shea, J.-E.3
-
12
-
-
0043238073
-
Effects of confinement in chaperonin assisted protein folding: Rate enhancement by decreasing the roughness of the folding energy landscape
-
DOI 10.1016/S0022-2836(03)00929-X
-
A. Baumketner, A. Jewett, and J.E. Shea Effects of confinement in chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape J. Mol. Biol. 332 2003 701 713 (Pubitemid 37075991)
-
(2003)
Journal of Molecular Biology
, vol.332
, Issue.3
, pp. 701-713
-
-
Baumketner, A.1
Jewett, A.2
Shea, J.E.3
-
13
-
-
0035092041
-
Molecular confinement influences protein structure and enhances thermal protein stability
-
DOI 10.1110/ps.36201
-
D.K. Eggers, and J.S. Valentine Molecular confinement influences protein structure and enhances thermal protein stability Protein Sci. 10 2001 250 261 (Pubitemid 32229119)
-
(2001)
Protein Science
, vol.10
, Issue.2
, pp. 250-261
-
-
Eggers, D.K.1
Valentine, J.S.2
-
14
-
-
4644332696
-
Protein encapsulation in mesoporous silicate: The effects of confinement on protein stability, hydration, and volumetric properties
-
DOI 10.1021/ja046900n
-
R. Ravindra, and S. Zhao R. Winter Protein encapsulation in mesoporous silicate: the effects of confinement on protein stability, hydration, and volumetric properties J. Am. Chem. Soc. 126 2004 12224 12225 (Pubitemid 39304879)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.39
, pp. 12224-12225
-
-
Ravindra, R.1
Zhao, S.2
Gies, H.3
Winter, R.4
-
15
-
-
33745792576
-
Tuning the cooperativity of the helix-coil transition by aqueous reverse micelles
-
DOI 10.1021/jp062362k
-
S. Mukherjee, P. Chowdhury, and F. Gai Tuning the cooperativity of the helix-coil transition by aqueous reverse micelles J. Phys. Chem. B 110 2006 11615 11619 (Pubitemid 44024770)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.24
, pp. 11615-11619
-
-
Mukherjee, S.1
Chowdhury, P.2
Gai, F.3
-
16
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
DOI 10.1016/j.sbi.2004.03.009, PII S0959440X04000430
-
M. Feig, and C.L. Brooks 3rd Recent advances in the development and application of implicit solvent models in biomolecule simulations Curr. Opin. Struct. Biol. 14 2004 217 224 (Pubitemid 38495800)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.2
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
17
-
-
46749105987
-
A test on peptide stability of AMBER force fields with implicit solvation
-
M.S. Shell, R. Ritterson, and K.A. Dill A test on peptide stability of AMBER force fields with implicit solvation J. Phys. Chem. B 112 2008 6878 6886
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6878-6886
-
-
Shell, M.S.1
Ritterson, R.2
Dill, K.A.3
-
18
-
-
80053649541
-
Extended surfaces modulate hydrophobic interactions of neighboring solutes
-
A.J. Patel, and P. Varilly D. Chandler Extended surfaces modulate hydrophobic interactions of neighboring solutes Proc. Natl. Acad. Sci. USA 108 2011 17678 17683
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 17678-17683
-
-
Patel, A.J.1
Varilly, P.2
Chandler, D.3
-
20
-
-
33344476423
-
Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces
-
DOI 10.1016/j.jmb.2005.12.048, PII S0022283605016220
-
M.S. Cheung, and D. Thirumalai Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces J. Mol. Biol. 357 2006 632 643 (Pubitemid 43290761)
-
(2006)
Journal of Molecular Biology
, vol.357
, Issue.2
, pp. 632-643
-
-
Cheung, M.S.1
Thirumalai, D.2
-
21
-
-
79953898194
-
Assisted peptide folding by surface pattern recognition
-
Z. Zhuang, and A.I. Jewett J.E. Shea Assisted peptide folding by surface pattern recognition Biophys. J. 100 2011 1306 1315
-
(2011)
Biophys. J.
, vol.100
, pp. 1306-1315
-
-
Zhuang, Z.1
Jewett, A.I.2
Shea, J.E.3
-
22
-
-
79952745066
-
Modest protein-crowder attractive interactions can counteract enhancement of protein association by intermolecular excluded volume interactions
-
J. Rosen, Y.C. Kim, and J. Mittal Modest protein-crowder attractive interactions can counteract enhancement of protein association by intermolecular excluded volume interactions J. Phys. Chem. B 115 2011 2683 2689
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 2683-2689
-
-
Rosen, J.1
Kim, Y.C.2
Mittal, J.3
-
23
-
-
70349232202
-
Effect of macromolecular crowding on protein folding dynamics at the secondary structure level
-
S. Mukherjee, and M.M. Waegele F. Gai Effect of macromolecular crowding on protein folding dynamics at the secondary structure level J. Mol. Biol. 393 2009 227 236
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 227-236
-
-
Mukherjee, S.1
Waegele, M.M.2
Gai, F.3
-
24
-
-
77954320896
-
Balance between α and β structures in ab initio protein folding
-
R.B. Best, and J. Mittal Balance between α and β structures in ab initio protein folding J. Phys. Chem. B 114 2010 8790 8798
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8790-8798
-
-
Best, R.B.1
Mittal, J.2
-
25
-
-
79952476196
-
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
-
R.B. Best, and J. Mittal Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: similarities and differences Proteins 79 2011 1318 1328
-
(2011)
Proteins
, vol.79
, pp. 1318-1328
-
-
Best, R.B.1
Mittal, J.2
-
26
-
-
79960592580
-
Microscopic events in β-hairpin folding from alternative unfolded ensembles
-
R.B. Best, and J. Mittal Microscopic events in β-hairpin folding from alternative unfolded ensembles Proc. Natl. Acad. Sci. USA 108 2011 11087 11092
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 11087-11092
-
-
Best, R.B.1
Mittal, J.2
-
27
-
-
67649494492
-
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
-
R.B. Best, and G. Hummer Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides J. Phys. Chem. B 113 2009 9004 9015
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
28
-
-
77955606360
-
Tackling force-field bias in protein folding simulations: Folding of Villin HP35 and Pin WW domains in explicit water
-
J. Mittal, and R.B. Best Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water Biophys. J. 99 2010 L26 L28
-
(2010)
Biophys. J.
, vol.99
-
-
Mittal, J.1
Best, R.B.2
-
29
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Klein, M.L.3
-
30
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
PII S0009261499011239
-
Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 314 1999 141 151 (Pubitemid 129556751)
-
(1999)
Chemical Physics Letters
, vol.314
, Issue.1-2
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
32
-
-
77955225308
-
Interfacial thermodynamics of confined water near molecularly rough surfaces
-
discussion 367-393, 395-401
-
J. Mittal, and G. Hummer Interfacial thermodynamics of confined water near molecularly rough surfaces Faraday Discuss. 146 2010 341 352 discussion 367-393, 395-401
-
(2010)
Faraday Discuss.
, vol.146
, pp. 341-352
-
-
Mittal, J.1
Hummer, G.2
-
33
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
DOI 10.1002/jcc.20291
-
D. Van Der Spoel, and E. Lindahl H.J. Berendsen GROMACS: fast, flexible, and free J. Comput. Chem. 26 2005 1701 1718 (Pubitemid 43076182)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
34
-
-
75749153687
-
Coordinate-dependent diffusion in protein folding
-
R.B. Best, and G. Hummer Coordinate-dependent diffusion in protein folding Proc. Natl. Acad. Sci. USA 107 2010 1088 1093
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 1088-1093
-
-
Best, R.B.1
Hummer, G.2
-
35
-
-
56649097508
-
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability
-
S. Vaitheeswaran, and D. Thirumalai Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability Proc. Natl. Acad. Sci. USA 105 2008 17636 17641
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 17636-17641
-
-
Vaitheeswaran, S.1
Thirumalai, D.2
|