-
1
-
-
0035868526
-
Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics
-
Portman, J. J., Takada, S., and Wolynes, P. G. (2003) Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics, J. Chem. Phys. 114, 5082.
-
(2003)
J. Chem. Phys
, vol.114
, pp. 5082
-
-
Portman, J.J.1
Takada, S.2
Wolynes, P.G.3
-
3
-
-
0000710672
-
Diffusive dynamics of the reaction coordinate for protein folding funnels
-
Socci, N. D., Onuchic, J. N., and Wolynes, P. G. (1996) Diffusive dynamics of the reaction coordinate for protein folding funnels, J. Chem. Phys. 104, 5860.
-
(1996)
J. Chem. Phys
, vol.104
, pp. 5860
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
4
-
-
0033060613
-
Searching for "downhill scenarios" in protein folding
-
Eaton, W. A. (1999) Searching for "downhill scenarios" in protein folding, Proc. Natl. Acad. Sci. U.S.A. 96, 5897.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 5897
-
-
Eaton, W.A.1
-
5
-
-
0035965724
-
Dihedral Ψ angle dependence of the Amide III vibration: A uniquely sensitive UV Resonance Raman secondary structural probe
-
Asher, S. A., Ianoul, A., Mix, G., Boyden, M. N., and Karnoup, A. (2001) Dihedral Ψ angle dependence of the Amide III vibration: A uniquely sensitive UV Resonance Raman secondary structural probe, J. Am. Chem. Soc. 123, 11775.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 11775
-
-
Asher, S.A.1
Ianoul, A.2
Mix, G.3
Boyden, M.N.4
Karnoup, A.5
-
6
-
-
32544446167
-
Peptide secondary structure folding reaction coordinate: Correlation between UV Raman Amide III frequency, Ψ Ramachandran angle, and hydrogen bonding
-
Mikhonin, A. V., Bykov, S. V., Myshakina, N. S., and Asher, S. A. (2006) Peptide secondary structure folding reaction coordinate: Correlation between UV Raman Amide III frequency, Ψ Ramachandran angle, and hydrogen bonding, J. Phys. Chem. B 110, 1928.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 1928
-
-
Mikhonin, A.V.1
Bykov, S.V.2
Myshakina, N.S.3
Asher, S.A.4
-
7
-
-
3142754280
-
UV Raman demonstrates that α-helical polyalanine peptides melt to polyproline II conformations
-
Asher, S. A., Mikhonin, A. V., and Bykov, S. (2004) UV Raman demonstrates that α-helical polyalanine peptides melt to polyproline II conformations, J. Am. Chem. Soc. 126, 8433.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 8433
-
-
Asher, S.A.1
Mikhonin, A.V.2
Bykov, S.3
-
8
-
-
33746615772
-
10-helix and π-bulge premelting during α-helix unfolding
-
10-helix and π-bulge premelting during α-helix unfolding, J. Am. Chem. Soc. 128, 13789.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 13789
-
-
Mikhonin, A.V.1
Asher, S.A.2
-
9
-
-
0027119143
-
Internal Stark effect measurement of the electric field at the amino terminus of an alpha helix
-
Lockhart, D. J., and Kim, P. S. (1992) Internal Stark effect measurement of the electric field at the amino terminus of an alpha helix, Science 257, 947.
-
(1992)
Science
, vol.257
, pp. 947
-
-
Lockhart, D.J.1
Kim, P.S.2
-
10
-
-
0027912723
-
Electrostatic screening of charge and dipole interactions with the helix backbone
-
Lockhart, D. J., and Kim, P. S. (1993) Electrostatic screening of charge and dipole interactions with the helix backbone, Science 260, 198.
-
(1993)
Science
, vol.260
, pp. 198
-
-
Lockhart, D.J.1
Kim, P.S.2
-
11
-
-
0030046906
-
Fast events in protein folding: Helix melting and formation in a small peptide
-
Williams, S. et al. (1996) Fast events in protein folding: Helix melting and formation in a small peptide, Biochemistry 35, 691.
-
(1996)
Biochemistry
, vol.35
, pp. 691
-
-
Williams, S.1
-
12
-
-
0030789351
-
Laser temperature jump study of the helix reversible arrow coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model
-
Thompson, P. A., Eaton, W. A., and Hofrichter, J. (1997) Laser temperature jump study of the helix reversible arrow coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model, Biochemistry 36, 9200.
-
(1997)
Biochemistry
, vol.36
, pp. 9200
-
-
Thompson, P.A.1
Eaton, W.A.2
Hofrichter, J.3
-
13
-
-
0034812787
-
Transient UV Raman Spectroscopy finds no crossing barrier between the peptide α-helix and fully random coil conformation
-
Lednev, I. K., Karnoup, A. S., Sparrow, M. C., and Asher, S. A. (2001) Transient UV Raman Spectroscopy finds no crossing barrier between the peptide α-helix and fully random coil conformation, J. Am. Chem. Soc. 123, 2388.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 2388
-
-
Lednev, I.K.1
Karnoup, A.S.2
Sparrow, M.C.3
Asher, S.A.4
-
14
-
-
0037022662
-
α-helical stabilization by side chain shielding of backbone hydrogen bonds
-
Garcia, A. E., and Sanbonmatsu, K. Y. (2002) α-helical stabilization by side chain shielding of backbone hydrogen bonds, Proc. Natl. Acad. Sci. U.S.A. 99, 2782.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A
, vol.99
, pp. 2782
-
-
Garcia, A.E.1
Sanbonmatsu, K.Y.2
-
15
-
-
2942754061
-
Fs-21 peptides can form both single helix and helix-turn-helix
-
Zhang, W., Lei, H., Chowdhury, S., and Duan, Y. (2004) Fs-21 peptides can form both single helix and helix-turn-helix, J. Phys. Chem. B 108, 7479.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 7479
-
-
Zhang, W.1
Lei, H.2
Chowdhury, S.3
Duan, Y.4
-
16
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
Sorin, E. J., and Pande, V. S. (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations, Biophys. J 88, 2472.
-
(2005)
Biophys. J
, vol.88
, pp. 2472
-
-
Sorin, E.J.1
Pande, V.S.2
-
17
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
Chodera, J. D., Singhal, N., Pande, V. S., Dill, K. A., and Swope, W. C. (2007) Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics, J. Chem. Phys. 126, 155101.
-
(2007)
J. Chem. Phys
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
18
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D. et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc. 117, 5179.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
-
19
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of protein based on condensed-phase quantum mechanical calculations
-
Duan, Y. et al. (2003) A point-charge force field for molecular mechanics simulations of protein based on condensed-phase quantum mechanical calculations, J. Comput. Chem 24, 1999.
-
(1999)
J. Comput. Chem
, vol.24
-
-
Duan, Y.1
-
20
-
-
0344702698
-
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
Nymeyer, H., and Garcia, A. E. (2003) Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent, Proc. Natl. Acad. Sci. U.S.A. 100, 13934.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A
, vol.100
, pp. 13934
-
-
Nymeyer, H.1
Garcia, A.E.2
-
21
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak, V. et al. (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters, Protein: Struct. Funct. Bioinf. 65, 712.
-
(2006)
Protein: Struct. Funct. Bioinf
, vol.65
, pp. 712
-
-
Hornak, V.1
-
22
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79, 926.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
23
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D. A. et al. (2005) The Amber biomolecular simulation programs, J. Comput. Chem. 26, 1668.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1668
-
-
Case, D.A.1
-
24
-
-
0345862082
-
Characterization of non-alpha helical conformations in ala peptides
-
Garcia, A. E. (2004) Characterization of non-alpha helical conformations in ala peptides, Polymer 45, 669.
-
(2004)
Polymer
, vol.45
, pp. 669
-
-
Garcia, A.E.1
-
25
-
-
0029887269
-
A microscopic view of helix propagation: N- and C-terminal helix growth in alanine helices
-
Young, W. S., and Brooks, C. L., III (1996) A microscopic view of helix propagation: N- and C-terminal helix growth in alanine helices, J. Mol. Biol. 259, 560-572.
-
(1996)
J. Mol. Biol
, vol.259
, pp. 560-572
-
-
Young, W.S.1
Brooks III, C.L.2
-
26
-
-
0025767212
-
Thermodynamics and mechanism of α-helix initiation in alanine and valine peptides
-
Tobias, D. J., and Brooks, III, C. L. (1991) Thermodynamics and mechanism of α-helix initiation in alanine and valine peptides, Biochemistry 30, 6059-6070.
-
(1991)
Biochemistry
, vol.30
, pp. 6059-6070
-
-
Tobias, D.J.1
Brooks III, C.L.2
-
27
-
-
0033536452
-
Alpha-Helix Peptide Folding and Unfolding Activation Barriers: A Nanosecond UV Resonance Raman Study
-
Lednev, I. K., Karnoup, M. C., Sparrow, M. C., and Asher, S. A. (1999) Alpha-Helix Peptide Folding and Unfolding Activation Barriers: A Nanosecond UV Resonance Raman Study, J. Am. Chem. Soc. 121, 8074-8086.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 8074-8086
-
-
Lednev, I.K.1
Karnoup, M.C.2
Sparrow, M.C.3
Asher, S.A.4
-
28
-
-
34147143434
-
UV Raman Spatially Resolved Melting Dynamics of Isotopically Labeled Polyalanyl Peptide: Slow α-Helix Melting Follows 310-Helices and π-Bulges Premelting
-
Mikhonin, A., Asher, S. A., Bykov, S., and Murza, A. (2007) UV Raman Spatially Resolved Melting Dynamics of Isotopically Labeled Polyalanyl Peptide: Slow α-Helix Melting Follows 310-Helices and π-Bulges Premelting, J. Phys. Chem. B. 111, 3280-3292.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 3280-3292
-
-
Mikhonin, A.1
Asher, S.A.2
Bykov, S.3
Murza, A.4
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