-
1
-
-
0041822089
-
Cell biology: Join the crowd
-
Ellis, R. J., and A. P. Minton. 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
-
2
-
-
34547496252
-
Protein folding under confinement: A role for solvent
-
Lucent, D., V. Vishal, and V. S. Pande. 2007. Protein folding under confinement: a role for solvent. Proc. Natl. Acad. Sci. USA. 104:10430-10434.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 10430-10434
-
-
Lucent, D.1
Vishal, V.2
Pande, V.S.3
-
3
-
-
0020668187
-
The effect of volume occupancy upon the thermodynamic activity of proteins: Some biochemical consequences
-
Minton, A. P. 1983. The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences. Mol. Cell. Biochem. 55:119-140.
-
(1983)
Mol. Cell. Biochem.
, vol.55
, pp. 119-140
-
-
Minton, A.P.1
-
4
-
-
16344389134
-
Molecular crowding enhances native state stability and refolding rates of globular proteins
-
Cheung, M. S., D. Klimov, and D. Thirumalai. 2005. Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc. Natl. Acad. Sci. USA. 102:4753-4758.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 4753-4758
-
-
Cheung, M.S.1
Klimov, D.2
Thirumalai, D.3
-
5
-
-
34547507851
-
Effects of crowding and confinement on the structures of the transition state ensemble in proteins
-
Cheung, M. S., and D. Thirumalai. 2007. Effects of crowding and confinement on the structures of the transition state ensemble in proteins. J. Phys. Chem. B. 111:8250-8257.
-
(2007)
J. Phys. Chem. B.
, vol.111
, pp. 8250-8257
-
-
Cheung, M.S.1
Thirumalai, D.2
-
6
-
-
33646536078
-
The influence of macromolecular crowding on HIV-1 protease internal dynamics
-
Minh, D. D., C. E. Chang,., J. A. McCammon. 2006. The influence of macromolecular crowding on HIV-1 protease internal dynamics. J. Am. Chem. Soc. 128:6006-6007.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 6006-6007
-
-
Minh, D.D.1
Chang, C.E.2
McCammon, J.A.3
-
7
-
-
37649016316
-
Molecular crowding enhances native structure and stability of α/β protein flavodoxin
-
Stagg, L., S. Q. Zhang, ., P. Wittung-Stafshede. 2007. Molecular crowding enhances native structure and stability of α/β protein flavodoxin. Proc. Natl. Acad. Sci. USA. 104:18976-18981.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 18976-18981
-
-
Stagg, L.1
Zhang, S.Q.2
Wittung-Stafshede, P.3
-
8
-
-
34548627238
-
Effects of macromolecular crowding on biochemical reaction equilibria: A molecular thermodynamic perspective
-
Hu, Z., J. Jiang, and R. Rajagopalan. 2007. Effects of macromolecular crowding on biochemical reaction equilibria: a molecular thermodynamic perspective. Biophys. J. 93:1464-1473.
-
(2007)
Biophys. J.
, vol.93
, pp. 1464-1473
-
-
Hu, Z.1
Jiang, J.2
Rajagopalan, R.3
-
9
-
-
41049090929
-
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
-
Zhou, H.-X., G. Rivas, and A. P. Minton. 2008. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Ann. Rev. Biophys. 37:375-397.
-
(2008)
Ann. Rev. Biophys.
, vol.37
, pp. 375-397
-
-
Zhou, H.-X.1
Rivas, G.2
Minton, A.P.3
-
10
-
-
63049088713
-
Crowding effects on the structural transitions in a flexible helical homopolymer
-
Kudlay, A., M. S. Cheung, and D. Thirumalai. 2009. Crowding effects on the structural transitions in a flexible helical homopolymer. Phys. Rev. Lett. 102:118101.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 118101
-
-
Kudlay, A.1
Cheung, M.S.2
Thirumalai, D.3
-
11
-
-
77049090450
-
Concentration and crowding effects on protein stability from a coarse-grained model
-
M. H. Zaman, editor. Cambridge University Press, Cambridge, UK
-
Cheung, J. K., V. K. Shen,., T. M. Truskett. 2009. Concentration and crowding effects on protein stability from a coarse-grained model. In Statistical Mechanics of Cellular Systems and Processes. M. H. Zaman, editor. Cambridge University Press, Cambridge, UK.
-
(2009)
Statistical Mechanics of Cellular Systems and Processes
-
-
Cheung, J.K.1
Shen, V.K.2
Truskett, T.M.3
-
12
-
-
70349921171
-
Insights into crowding effects on protein stability from a coarse-grained model
-
Shen, V. K., J. K. Cheung, J. R. Errington, and T. M. Truskett. 2009. Insights into crowding effects on protein stability from a coarse-grained model. J. Biomed. Eng. 131:071002-1-071002-7
-
(2009)
J. Biomed. Eng.
, vol.131
, pp. 0710021-0710027
-
-
Shen, V.K.1
Cheung, J.K.2
Errington, J.R.3
Truskett, T.M.4
-
13
-
-
16344364032
-
Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: Macromolecular crowding and protein stability revisited
-
Minton, A. P. 2005. Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited. Biophys. J. 88:971-985.
-
(2005)
Biophys. J.
, vol.88
, pp. 971-985
-
-
Minton, A.P.1
-
14
-
-
36849139794
-
Thermodynamic properties of mixtures of hard spheres
-
Lebowitz, J. L., and J. S. Rowlinson. 1964. Thermodynamic properties of mixtures of hard spheres. J. Chem. Phys. 41:133-138.
-
(1964)
J. Chem. Phys.
, vol.41
, pp. 133-138
-
-
Lebowitz, J.L.1
Rowlinson, J.S.2
-
15
-
-
34548759571
-
Solvation of proteins: Linking thermodynamics to geometry
-
Hansen-Goos, H., R. Roth,., S. Dietrich. 2007. Solvation of proteins: linking thermodynamics to geometry. Phys. Rev. Lett. 99:128101.
-
(2007)
Phys. Rev. Lett.
, vol.99
, pp. 128101
-
-
Hansen-Goos, H.1
Roth, R.2
Dietrich, S.3
-
16
-
-
36749103188
-
Protein folding in confined and crowded environments
-
Zhou, H.-X. 2008. Protein folding in confined and crowded environments. Arch. Biochem. Biophys. 469:76-82.
-
(2008)
Arch. Biochem. Biophys.
, vol.469
, pp. 76-82
-
-
Zhou, H.-X.1
-
17
-
-
0000345559
-
Diffusion-controlled reactions with mobile traps
-
Szabo, A., R. Zwanzig, and N. Agmon. 1988. Diffusion-controlled reactions with mobile traps. Phys. Rev. Lett. 61:2496-2499.
-
(1988)
Phys. Rev. Lett.
, vol.61
, pp. 2496-2499
-
-
Szabo, A.1
Zwanzig, R.2
Agmon, N.3
-
18
-
-
51349126098
-
Effect of mixed macromolecular crowding agents on protein folding
-
Zhou, H.-X. 2008. Effect of mixed macromolecular crowding agents on protein folding. Proteins. 72:1109-1113.
-
(2008)
Proteins
, vol.72
, pp. 1109-1113
-
-
Zhou, H.-X.1
-
19
-
-
1842637575
-
Folding of a three-helix bundle at the folding speed limit
-
Wang, T., Y. Zhu, and F. Gai. 2004. Folding of a three-helix bundle at the folding speed limit. J. Phys. Chem. B. 108:3694-3697.
-
(2004)
J. Phys. Chem. B.
, vol.108
, pp. 3694-3697
-
-
Wang, T.1
Zhu, Y.2
Gai, F.3
-
20
-
-
0034677663
-
The folding of an immunoglobulin- like Greek key protein is defined by a common-core nucleus and regions constrained by topology
-
Hamill, S. J., A. Steward, and J. Clarke. 2000. The folding of an immunoglobulin- like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J. Mol. Biol. 297:165-178.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 165-178
-
-
Hamill, S.J.1
Steward, A.2
Clarke, J.3
-
21
-
-
0033871567
-
Critical role of β-hairpin formation in protein G folding
-
McCallister, E. L., E. Alm, and D. Baker. 2000. Critical role of β-hairpin formation in protein G folding. Nat. Struct. Biol. 7:669-673.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 669-673
-
-
McCallister, E.L.1
Alm, E.2
Baker, D.3
-
22
-
-
0032568599
-
Folding funnels and frustration in off-lattice minimalist protein landscapes
-
Nymeyer, H., A. E. García, and J. N. Onuchic. 1998. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl. Acad. Sci. USA. 95:5921-5928.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 5921-5928
-
-
Nymeyer, H.1
García, A.E.2
Onuchic, J.N.3
-
23
-
-
38049119865
-
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations
-
Mickler, M., R. I. Dima,., M. Rief. 2007. Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations. Proc. Natl. Acad. Sci. USA. 104:20268-20273.
-
(2007)
Proc. Natl. Acad. Sci. USA.
, vol.104
, pp. 20268-20273
-
-
Mickler, M.1
Dima, R.I.2
Rief, M.3
-
24
-
-
0036785556
-
The origins of asymmetry in the folding transition states of protein L and protein G
-
Karanicolas, J., and C. L. Brooks, 3rd. 2002. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 11:2351-2361.
-
(2002)
Protein Sci.
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks Iii, C.L.2
-
25
-
-
33748557507
-
Recent successes of the energy landscape theory of protein folding and function
-
Wolynes, P. G. 2005. Recent successes of the energy landscape theory of protein folding and function. Q. Rev. Biophys. 38:405-410.
-
(2005)
Q. Rev. Biophys.
, vol.38
, pp. 405-410
-
-
Wolynes, P.G.1
-
26
-
-
0034321011
-
Energetic frustration and the nature of the transition state in protein folding
-
Shea, J.-E., J. N. Onuchic, and C. L. Brooks, III. 2000. Energetic frustration and the nature of the transition state in protein folding. J. Chem. Phys. 113:7663-7671.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 7663-7671
-
-
Shea, J.-E.1
Onuchic, J.N.2
Brooks Iii, C.L.3
-
28
-
-
3142782241
-
Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
-
Chavez, L. L., J. N. Onuchic, and C. Clementi. 2004. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. J. Am. Chem. Soc. 126:8426-8432.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 8426-8432
-
-
Chavez, L.L.1
Onuchic, J.N.2
Clementi, C.3
-
29
-
-
18744387720
-
Reaction coordinates and rates from transition paths
-
Best, R. B., and G. Hummer. 2005. Reaction coordinates and rates from transition paths. Proc. Natl. Acad. Sci. USA. 102:6732-6737.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 6732-6737
-
-
Best, R.B.1
Hummer, G.2
-
30
-
-
48749137581
-
Stochastic boundary conditions for molecular dynamics simulations of ST2 water
-
Brooks, III, C. L., A. Brünger, and M. Karplus. 1984. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105:495-500.
-
(1984)
Chem. Phys. Lett.
, vol.105
, pp. 495-500
-
-
Brooks Iii, C.L.1
Brünger, A.2
Karplus, M.3
-
31
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, ., M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Karplus, M.3
-
32
-
-
33646987405
-
Optimized Monte Carlo data analysis
-
Ferrenberg, A. M., and R. H. Swendsen. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63:1195-1198.
-
(1989)
Phys. Rev. Lett.
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
33
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method
-
Kumar, S., D. Bouzida,., J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13:1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Rosenberg, J.M.3
-
34
-
-
33744952224
-
Diffusive model of protein folding dynamics with Kramer's turnover in rate
-
Best, R. B., and G. Hummer. 2006. Diffusive model of protein folding dynamics with Kramer's turnover in rate. Phys. Rev. Lett. 96:228104.
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 228104
-
-
Best, R.B.1
Hummer, G.2
-
35
-
-
58149498257
-
Thermodynamics and kinetics of protein folding under confinement
-
Mittal, J., and R. B. Best. 2008. Thermodynamics and kinetics of protein folding under confinement. Proc. Natl. Acad. Sci. USA. 105:20233-20238.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 20233-20238
-
-
Mittal, J.1
Best, R.B.2
-
37
-
-
0141482088
-
How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations
-
Takagi, F., N. Koga, and S. Takada. 2003. How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations. Proc. Natl. Acad. Sci. USA. 100:11367-11372.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11367-11372
-
-
Takagi, F.1
Koga, N.2
Takada, S.3
-
38
-
-
33645999511
-
On interaction between two bodies immersed in a solution of macromolecules
-
Asakura, S., and F. Oosawa. 1954. On interaction between two bodies immersed in a solution of macromolecules. J. Chem. Phys. 22: 1255-1256.
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1255-1256
-
-
Asakura, S.1
Oosawa, F.2
-
39
-
-
0000749561
-
Free polymer in a colloidal solution
-
Shaw, M. R., and D. Thirumalai. 1991. Free polymer in a colloidal solution. Phys. Rev. A. 44:R4797-R4800.
-
(1991)
Phys. Rev. A
, vol.44
-
-
Shaw, M.R.1
Thirumalai, D.2
-
40
-
-
0034683316
-
Can polymer coils be modeled as "soft colloids"?
-
Louis, A. A., P. G. Bolhuis,., E. J. Meijer. 2000. Can polymer coils be modeled as "soft colloids"? Phys. Rev. Lett. 85:2522-2525.
-
(2000)
Phys. Rev. Lett.
, vol.85
, pp. 2522-2525
-
-
Louis, A.A.1
Bolhuis, P.G.2
Meijer, E.J.3
-
41
-
-
0037162257
-
Density profiles and surface tension of polymers near colloidal surfaces
-
Louis, A. A., P. G. Bolhuis, and E. J. Meijer. 2002. Density profiles and surface tension of polymers near colloidal surfaces. J. Chem. Phys. 116:10547-10555.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 10547-10555
-
-
Louis, A.A.1
Bolhuis, P.G.2
Meijer, E.J.3
-
42
-
-
0001193912
-
Computer simulation of polymerinduced clustering of colloids
-
Meijer, E. J., and D. Frenkel. 1991. Computer simulation of polymerinduced clustering of colloids. Phys. Rev. Lett. 67:1110-1113.
-
(1991)
Phys. Rev. Lett.
, vol.67
, pp. 1110-1113
-
-
Meijer, E.J.1
Frenkel, D.2
-
43
-
-
68949110044
-
Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability
-
Qin, S. B., and H.-X. Zhou. 2009. Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability. Biophys. J. 97:12-19.
-
(2009)
Biophys. J.
, vol.97
, pp. 12-19
-
-
Qin, S.B.1
Zhou, H.-X.2
-
44
-
-
34547275473
-
Brownian motion in a field of force and the diffusion model of chemical reactions
-
Kramers, H. A. 1940. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica. 7:284-303.
-
(1940)
Physica.
, vol.7
, pp. 284-303
-
-
Kramers, H.A.1
-
45
-
-
33750806263
-
Mixed macromolecular crowding accelerates the refolding of rabbit muscle creatine kinase: Implications for protein folding in physiological environments
-
Du, F., Z. Zhou, ., Y. Liang. 2006. Mixed macromolecular crowding accelerates the refolding of rabbit muscle creatine kinase: implications for protein folding in physiological environments. J. Mol. Biol. 364:469-482.
-
(2006)
J. Mol. Biol.
, vol.364
, pp. 469-482
-
-
Du, F.1
Zhou, Z.2
Liang, Y.3
|