-
1
-
-
0023675175
-
Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations
-
Anderson, A. G., and Hermans, J. 1988. Microfolding: conformational probability map for the alanine dipeptide in water from molecular dynamics simulations. Proteins 3, 262-265.
-
(1988)
Proteins
, vol.3
, pp. 262-265
-
-
Anderson, A.G.1
Hermans, J.2
-
2
-
-
0022114079
-
Protein states and proteinquakes
-
Ansari, A., Berendzen, J., Bowne, S. F., Frauenfelder, H., Iben, I. E., Sauke, T. B., Shyamsunder, E., and Young, R. D. 1985. Protein states and proteinquakes. Proc. Natl Acad. Sci. USA 82, 5000-5004.
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 5000-5004
-
-
Ansari, A.1
Berendzen, J.2
Bowne, S.F.3
Frauenfelder, H.4
Iben, I.E.5
Sauke, T.B.6
Shyamsunder, E.7
Young, R.D.8
-
3
-
-
0014199111
-
J. Biol. Chem.
-
Aune, K. C., Salahuddin, A., Zarlengo, M. H., and Tanford, C. 1967. J. Biol. Chem. 242, 4486-4489.
-
(1967)
, vol.242
, pp. 4486-4489
-
-
Aune, K.C.1
Salahuddin, A.2
Zarlengo, M.H.3
Tanford, C.4
-
4
-
-
0037022289
-
Role of backbone solvation in determining thermodynamic beta propensities of the amino acids
-
Avbelj, F. and Baldwin, R. L. 2002. Role of backbone solvation in determining thermodynamic beta propensities of the amino acids. Proc. Natl Acad. Sci. USA 99, 1309-1313.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 1309-1313
-
-
Avbelj, F.1
Baldwin, R.L.2
-
5
-
-
0037610743
-
Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi
-
Avbelj, F. and Baldwin, R. L. 2003. Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi. Proc. Natl Acad. Sci. USA 100, 5742-5747.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5742-5747
-
-
Avbelj, F.1
Baldwin, R.L.2
-
6
-
-
0034718590
-
Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities
-
Avbelj, F., Luo, P., and Baldwin, R. L. 2000. Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities. Proc. Natl Acad. Sci. USA 97, 10786-10791.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 10786-10791
-
-
Avbelj, F.1
Luo, P.2
Baldwin, R.L.3
-
7
-
-
0037093649
-
Geometry and physics of proteins
-
Banavar, J., Maritan, A., Micheletti, C., and Trovato, A. 2002. Geometry and physics of proteins. Proteins 47, 315-322.
-
(2002)
Proteins
, vol.47
, pp. 315-322
-
-
Banavar, J.1
Maritan, A.2
Micheletti, C.3
Trovato, A.4
-
8
-
-
0037705435
-
In search of the energetic role of peptide hydrogen bonds
-
Baldwin, R. L. 2003. In search of the energetic role of peptide hydrogen bonds. J. Biol. Chem. 278, 17581-17588.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 17581-17588
-
-
Baldwin, R.L.1
-
9
-
-
0032972986
-
Is protein folding hierarchic? I. Local structure and peptide folding
-
Baldwin, R. L. and Rose, G. D. 1999a. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24, 26-33.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 26-33
-
-
Baldwin, R.L.1
Rose, G.D.2
-
10
-
-
0033080081
-
Is protein folding hierarchic? II. Folding intermediates and transition states
-
Baldwin, R. L. and Rose, G. D. 1999b. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24, 77-83.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 77-83
-
-
Baldwin, R.L.1
Rose, G.D.2
-
11
-
-
0033731782
-
Are denatured proteins ever random coils? Proc
-
Baldwin, R. L. and Zimm, B. H. 2000. Are denatured proteins ever random coils? Proc. Natl Acad. Sci. USA 97, 12391-12392.
-
(2000)
Natl Acad. Sci. USA
, vol.97
, pp. 12391-12392
-
-
Baldwin, R.L.1
Zimm, B.H.2
-
12
-
-
0020119906
-
A salt-bridge stabilizes the helix formed by isolated C-peptide of RNase A
-
Bierzynski, A., Kim, P. S., and Baldwin, R. L. 1982. A salt-bridge stabilizes the helix formed by isolated C-peptide of RNase A. Proc. Natl Acad. Sci. USA 79, 2470-2474.
-
(1982)
Proc. Natl Acad. Sci. USA
, vol.79
, pp. 2470-2474
-
-
Bierzynski, A.1
Kim, P.S.2
Baldwin, R.L.3
-
13
-
-
33947481462
-
The thermodynamics of protein denaturation. I. The denaturation of chymotrypsinogen
-
Brandts, J. F. 1964a. The thermodynamics of protein denaturation. I. The denaturation of chymotrypsinogen. J. Am. Chem. Soc. 86, 4291-4301.
-
(1964)
J. Am. Chem. Soc.
, vol.86
, pp. 4291-4301
-
-
Brandts, J.F.1
-
14
-
-
0001059847
-
The thermodynamics of protein denaturation. II. A model of reversible denaturation and interpretations regarding the stability of chymotrypsinogen
-
Brandts, J. F. 1964b. The thermodynamics of protein denaturation. II. A model of reversible denaturation and interpretations regarding the stability of chymotrypsinogen. J. Am. Chem. Soc. 86, 4302-4314.
-
(1964)
J. Am. Chem. Soc.
, vol.86
, pp. 4302-4314
-
-
Brandts, J.F.1
-
15
-
-
0015207557
-
Helix-coil transition of the isolated amino terminus of ribonuclease
-
Brown, J. E. and Klee, W. A. 1971. Helix-coil transition of the isolated amino terminus of ribonuclease. Biochemistry 10, 470-476.
-
(1971)
Biochemistry
, vol.10
, pp. 470-476
-
-
Brown, J.E.1
Klee, W.A.2
-
16
-
-
0028947257
-
Funnels, pathways and the energy landscape of protein folding-a synthesis
-
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., and Wolynes, P. G. 1995. Funnels, pathways and the energy landscape of protein folding-a synthesis. Proteins Struct. Funct. Genet. 21, 167-195.
-
(1995)
Proteins Struct. Funct. Genet.
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
18
-
-
0025906282
-
Polymer principles in protein structure and stability
-
Chan, H. S. and Dill, K. A. 1991. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Chem. 20, 447-490.
-
(1991)
Annu. Rev. Biophys. Chem.
, vol.20
, pp. 447-490
-
-
Chan, H.S.1
Dill, K.A.2
-
19
-
-
0020621373
-
The van der Waals picture of liquids, solids and phase transformations
-
Chandler, D., Weeks, J. D., and Andersen, H. C. 1983. The van der Waals picture of liquids, solids and phase transformations. Science 220, 787-794.
-
(1983)
Science
, vol.220
, pp. 787-794
-
-
Chandler, D.1
Weeks, J.D.2
Andersen, H.C.3
-
20
-
-
0037216990
-
Universality classes in folding times of proteins
-
Cieplak, M. and Hoang, T. X. 2003. Universality classes in folding times of proteins. Biophys. J. 84, 475-488.
-
(2003)
Biophys. J.
, vol.84
, pp. 475-488
-
-
Cieplak, M.1
Hoang, T.X.2
-
21
-
-
0031692650
-
Left-handed polyproline II helix formation is (very) locally driven
-
Creamer, T. P. 1998. Left-handed polyproline II helix formation is (very) locally driven. Proteins 33, 218-226.
-
(1998)
Proteins
, vol.33
, pp. 218-226
-
-
Creamer, T.P.1
-
22
-
-
0029981188
-
Structure of the transition state for folding of a protein derived from experiment and simulation
-
Daggett, V., Li, A., Itzhaki, L. S., Otzen, D. E., and Fersht, A. R. 1996. Structure of the transition state for folding of a protein derived from experiment and simulation. J. Mol. Biol. 257, 430-440.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 430-440
-
-
Daggett, V.1
Li, A.2
Itzhaki, L.S.3
Otzen, D.E.4
Fersht, A.R.5
-
23
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill, K. A. and Chan, H. S. 1997. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4, 10-19.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
24
-
-
0025856806
-
Denatured states of proteins
-
Dill, K. A. and Shortle, D. 1991. Denatured states of proteins. Annu. Rev. Biochem. 60, 795-825.
-
(1991)
Annu. Rev. Biochem.
, vol.60
, pp. 795-825
-
-
Dill, K.A.1
Shortle, D.2
-
25
-
-
0030733858
-
Proteins Struct. Funct. Genet.
-
Doyle, R., Simons, K., Qian, H., and Baker, D. 1997. Proteins Struct. Funct. Genet. 29, 282-291.
-
(1997)
, vol.29
, pp. 282-291
-
-
Doyle, R.1
Simons, K.2
Qian, H.3
Baker, D.4
-
26
-
-
1542366657
-
The role of solvent in determining conformational preferences of alanine dipeptide in water
-
Drozdov, A. N., Grossfield, A., and Pappu, R. V. 2004. The role of solvent in determining conformational preferences of alanine dipeptide in water. J. Am. Chem. Soc. 126, 2574-2581.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 2574-2581
-
-
Drozdov, A.N.1
Grossfield, A.2
Pappu, R.V.3
-
27
-
-
0024278597
-
Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn
-
Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A., and Wright, P. E. 1988. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 201, 161-200.
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 161-200
-
-
Dyson, H.J.1
Rance, M.2
Houghten, R.A.3
Lerner, R.A.4
Wright, P.E.5
-
28
-
-
0026743136
-
Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding II. Plastocyanin
-
Dyson, H. J., Sayre, J. R., Merutka, G., Shin, H. C., Lerner, R. A., and Wright, P. E. 1992. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding II. Plastocyanin. J. Mol. Biol. 226, 819-835.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 819-835
-
-
Dyson, H.J.1
Sayre, J.R.2
Merutka, G.3
Shin, H.C.4
Lerner, R.A.5
Wright, P.E.6
-
29
-
-
0028948518
-
Hsien Wu and the first theory of protein denaturation (1931)
-
(eds D. S. Eisenberg, and F. M. Richards), Academic Press, San Diego
-
Edsall, J. T. 1995. Hsien Wu and the first theory of protein denaturation (1931). In Advances in Protein Chemistry (eds D. S. Eisenberg, and F. M. Richards), pp. 1-26. Academic Press, San Diego.
-
(1995)
Advances in Protein Chemistry
, pp. 1-26
-
-
Edsall, J.T.1
-
30
-
-
0003870776
-
Investigations on the Theory of Brownian Movement
-
Dover Publications, New York
-
Einstein, A. 1956. Investigations on the Theory of Brownian Movement. Dover Publications, New York.
-
(1956)
-
-
Einstein, A.1
-
31
-
-
1342268081
-
Steric restrictions in protein folding: an α-helix cannot be followed by a contiguous β-strand
-
Fitzkee, N. C. and Rose, G. D. 2004. Steric restrictions in protein folding: an α-helix cannot be followed by a contiguous β-strand. Protein Sci. 13, 633-639.
-
(2004)
Protein Sci
, vol.13
, pp. 633-639
-
-
Fitzkee, N.C.1
Rose, G.D.2
-
32
-
-
0003411482
-
Principles of Polymer Chemistry
-
Cornell University Press, New York
-
Flory, P. J. 1953. Principles of Polymer Chemistry. Cornell University Press, New York.
-
(1953)
-
-
Flory, P.J.1
-
33
-
-
0003478685
-
Statistical Mechanics of Chain Molecules
-
Wiley, New York
-
Flory, P. J. 1969. Statistical Mechanics of Chain Molecules. Wiley, New York.
-
(1969)
-
-
Flory, P.J.1
-
34
-
-
0035017534
-
NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation
-
Garcia, P., Serrano, L., Durand, D., Rico, M., and Bruix, M. 2001. NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation. Protein Science 10, 1100-1112.
-
(2001)
Protein Science
, vol.10
, pp. 1100-1112
-
-
Garcia, P.1
Serrano, L.2
Durand, D.3
Rico, M.4
Bruix, M.5
-
35
-
-
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, 669-676.
-
(2004)
Polymer
, vol.45
, pp. 669-676
-
-
Garcia, A.E.1
-
36
-
-
0024784280
-
A hydrophobic cluster forms early in the folding of dihydrofolate reductase
-
Garvey, E. P., Swank, J., and Matthews, C. R. 1989. A hydrophobic cluster forms early in the folding of dihydrofolate reductase. Proteins Struct. Funct. Genet. 6, 259-266.
-
(1989)
Proteins Struct. Funct. Genet.
, vol.6
, pp. 259-266
-
-
Garvey, E.P.1
Swank, J.2
Matthews, C.R.3
-
37
-
-
0000368236
-
Some specific ion effects on the conformation and thermal stability of ribonuclease
-
Ginsburg, A. and Carroll, W. R. 1965. Some specific ion effects on the conformation and thermal stability of ribonuclease. Biochemistry 4, 2159-2174.
-
(1965)
Biochemistry
, vol.4
, pp. 2159-2174
-
-
Ginsburg, A.1
Carroll, W.R.2
-
38
-
-
0021543572
-
The consistency principle in protein structure and pathways of folding
-
Go, N. 1984. The consistency principle in protein structure and pathways of folding. Adv. Biophys. 18, 149-164.
-
(1984)
Adv. Biophys.
, vol.18
, pp. 149-164
-
-
Go, N.1
-
39
-
-
0037424614
-
Computational simulation of the statistidal properties of unfolded proteins
-
Goldenberg, D. P. 2003. Computational simulation of the statistidal properties of unfolded proteins. J. Mol. Biol. 326, 1615-1633.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1615-1633
-
-
Goldenberg, D.P.1
-
40
-
-
0025612447
-
Ab initio selfconsistent field and potentialdependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N0-methyl-alanineamide
-
Grant, J. A., Williams, R. L., and Scheraga, H. A. 1990. Ab initio selfconsistent field and potentialdependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N0-methyl-alanineamide. Biopolymers 30, 929-949.
-
(1990)
Biopolymers
, vol.30
, pp. 929-949
-
-
Grant, J.A.1
Williams, R.L.2
Scheraga, H.A.3
-
41
-
-
11644317783
-
Theoretical study of aqueous N-acetyl-L-alanine N0-methylamide: structures and raman, VCD and ROA spectra
-
Han, W.-G., Jalkanen, K. J., Elstner, M., and Suhai, S. 1998. Theoretical study of aqueous N-acetyl-L-alanine N0-methylamide: structures and raman, VCD and ROA spectra. J. Phys. Chem. B 102, 2587-2602.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 2587-2602
-
-
Han, W.-G.1
Jalkanen, K.J.2
Elstner, M.3
Suhai, S.4
-
42
-
-
24144452444
-
What determines the native state folds of proteins?
-
Hoang, T. X., Trovato, A., Seno, F., Banavar, J., and Maritan, A. 2004. What determines the native state folds of proteins?. submitted.
-
(2004)
submitted
-
-
Hoang, T.X.1
Trovato, A.2
Seno, F.3
Banavar, J.4
Maritan, A.5
-
43
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki, L. S., Otzen, D. E., and Fersht, A. R. 1995. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
44
-
-
0030556776
-
N-Acetyl-L-Alanine N0-methylamide: a density functional analysis of the vibrational absorption and birational circular dichroism spectra
-
Jalkanen, K. J. and Suhai, S. 1996. N-Acetyl-L-Alanine N0-methylamide: a density functional analysis of the vibrational absorption and birational circular dichroism spectra. Chem. Phys. 208, 81-116.
-
(1996)
Chem. Phys.
, vol.208
, pp. 81-116
-
-
Jalkanen, K.J.1
Suhai, S.2
-
45
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1-63.
-
(1959)
Adv. Protein Chem.
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
46
-
-
0035836687
-
Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution
-
Kazmirski, S. L., Wong, K. B., Freund, S. M. V., Tan, Y. J., Fersht, A. R., and Daggett, V. 2001. Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proc. Natl Acad. Sci. USA 98, 4349-4354.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4349-4354
-
-
Kazmirski, S.L.1
Wong, K.B.2
Freund, S.M.V.3
Tan, Y.J.4
Fersht, A.R.5
Daggett, V.6
-
47
-
-
1842500993
-
Unfolded state of polyalanine is a segmented polyproline II helix
-
Kentsis, A., Gindin, T., Mezei, M., and Osman, R. 2004. Unfolded state of polyalanine is a segmented polyproline II helix. Proteins 55, 493-501.
-
(2004)
Proteins
, vol.55
, pp. 493-501
-
-
Kentsis, A.1
Gindin, T.2
Mezei, M.3
Osman, R.4
-
48
-
-
0013825955
-
Precision spacefilling atomic models
-
Koltun, W. L. 1965. Precision spacefilling atomic models. Biopolymers 3, 665-679.
-
(1965)
Biopolymers
, vol.3
, pp. 665-679
-
-
Koltun, W.L.1
-
49
-
-
0000243829
-
PROCHECK: a program to check the stereochemical quality of protein structures
-
Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
-
(1993)
J. Appl. Cryst.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
50
-
-
0031465967
-
Science
-
Lazaridis, T. and Karplus, M. 1997. Science 278, 1928-1931.
-
(1997)
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
51
-
-
0001861319
-
How to fold graciously. Mossbauer spectroscopy in Biological Systems
-
University of Illinois Bull
-
Levinthal, C. 1969. How to fold graciously. Mossbauer spectroscopy in Biological Systems. Proceedings. University of Illinois Bull. 41, 22-24.
-
(1969)
Proceedings
, vol.41
, pp. 22-24
-
-
Levinthal, C.1
-
52
-
-
0346219438
-
On the origin of residual dipolar couplings from denatured proteins
-
Louhivuori, M., Paakkonen, K., Fredriksson, K., Permi, P., Lounila, J., and Annila, A. 2003. On the origin of residual dipolar couplings from denatured proteins. J. Am. Chem. Soc. 125, 15647-15650.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 15647-15650
-
-
Louhivuori, M.1
Paakkonen, K.2
Fredriksson, K.3
Permi, P.4
Lounila, J.5
Annila, A.6
-
53
-
-
0025260032
-
Side chain contributions to the stability of alpha-helical structure in peptides
-
Lyu, P. C., Liff, M. I., Marky, L. A., and Kallenbach, N. R. 1990. Side chain contributions to the stability of alpha-helical structure in peptides. Science 250, 669-673.
-
(1990)
Science
, vol.250
, pp. 669-673
-
-
Lyu, P.C.1
Liff, M.I.2
Marky, L.A.3
Kallenbach, N.R.4
-
54
-
-
84982067211
-
Diamide model for the optical activity of collagen and polyproline I and II
-
Madison, V. and Schellman, J. A. 1970. Diamide model for the optical activity of collagen and polyproline I and II. Biopolymers 9, 65-94.
-
(1970)
Biopolymers
, vol.9
, pp. 65-94
-
-
Madison, V.1
Schellman, J.A.2
-
55
-
-
0034691565
-
Optimal shapes of compact strings
-
Maritan, A., Micheletti, C., Trovato, A., and Banavar, J. 2000. Optimal shapes of compact strings. Nature 406, 287-290.
-
(2000)
Nature
, vol.406
, pp. 287-290
-
-
Maritan, A.1
Micheletti, C.2
Trovato, A.3
Banavar, J.4
-
56
-
-
0024997237
-
Effect of central-residue replacements on the helical stability of a monomeric peptide
-
Merutka, G., Lipton, W., Shalongo, W., Park, S. H., and Stellwagen, E. 1990. Effect of central-residue replacements on the helical stability of a monomeric peptide. Biochemistry 29, 7511-7515.
-
(1990)
Biochemistry
, vol.29
, pp. 7511-7515
-
-
Merutka, G.1
Lipton, W.2
Shalongo, W.3
Park, S.H.4
Stellwagen, E.5
-
57
-
-
1842500992
-
Polyproline II helix is the preferred conformation for unfolded polyalaine in water
-
Mezei, M., Fleming, P. J., Srinivasan, R., and Rose, G. D. 2004. Polyproline II helix is the preferred conformation for unfolded polyalaine in water. Proteins 55, 502-507.
-
(2004)
Proteins
, vol.55
, pp. 502-507
-
-
Mezei, M.1
Fleming, P.J.2
Srinivasan, R.3
Rose, G.D.4
-
58
-
-
0036401140
-
Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins
-
Millett, I. S., Doniach, S., and Plaxco, K. W. 2002. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv. Protein Chem. 62, 241-262.
-
(2002)
Adv. Protein Chem.
, vol.62
, pp. 241-262
-
-
Millett, I.S.1
Doniach, S.2
Plaxco, K.W.3
-
59
-
-
0000648204
-
On the structure of native, denatured, and coagulated proteins
-
Mirsky, A. E. and Pauling, L. 1936. On the structure of native, denatured, and coagulated proteins. Proc. Natl Acad. Sci. USA 22, 439-447.
-
(1936)
Proc. Natl Acad. Sci. USA
, vol.22
, pp. 439-447
-
-
Mirsky, A.E.1
Pauling, L.2
-
60
-
-
0038502170
-
Nature
-
Munoz, V., Thompson, P. A., Hofrichter, J., and Eaton, W. A. 1997. Nature 390, 196-199.
-
(1997)
, vol.390
, pp. 196-199
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
61
-
-
0026672305
-
NMR determination of residual structure in a urea-denatured protein, the 434-repressor
-
Neri, D., Billeter, M., Wider, G., and Wuthricht, K. 1992. NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science 257, 1559-1563.
-
(1992)
Science
, vol.257
, pp. 1559-1563
-
-
Neri, D.1
Billeter, M.2
Wider, G.3
Wuthricht, K.4
-
62
-
-
0025222978
-
A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
-
O'Neil, K. T. and DeGrado, W. F. 1990. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250, 646-651.
-
(1990)
Science
, vol.250
, pp. 646-651
-
-
O'Neil, K.T.1
DeGrado, W.F.2
-
63
-
-
0345564821
-
Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and C-peptide from RNase A
-
Ohkubo, Y. Z. and Brooks, C. L. 2003. Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and C-peptide from RNase A. Proc. Natl Acad. Sci. USA 100, 13916-13921.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13916-13921
-
-
Ohkubo, Y.Z.1
Brooks, C.L.2
-
64
-
-
0025253106
-
Relative helixforming tendencies of nonpolar amino acids
-
Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., and Baldwin, R. L. 1990. Relative helixforming tendencies of nonpolar amino acids. Nature 344, 268-270.
-
(1990)
Nature
, vol.344
, pp. 268-270
-
-
Padmanabhan, S.1
Marqusee, S.2
Ridgeway, T.3
Laue, T.M.4
Baldwin, R.L.5
-
65
-
-
0036784642
-
A simple model for polyproline II structure in unfolded states of alaninebased peptides
-
Pappu, R. V. and Rose, G. D. 2002. A simple model for polyproline II structure in unfolded states of alaninebased peptides. Protein Sci. 11, 2437-2455.
-
(2002)
Protein Sci.
, vol.11
, pp. 2437-2455
-
-
Pappu, R.V.1
Rose, G.D.2
-
66
-
-
0033730431
-
The flory isolatedpair hypothesis is not valid for polypeptide chains: implications for protein folding
-
Pappu, R. V., Srinivasan, R., and Rose, G. D. 2000. The flory isolatedpair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc. Natl Acad. Sci. USA 97, 12565-12570.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 12565-12570
-
-
Pappu, R.V.1
Srinivasan, R.2
Rose, G.D.3
-
67
-
-
76549252207
-
The structures of proteins: two hydrogen-bonded helical configurations of the polypeptide chain
-
Pauling, L., Corey, R. B., and Branson, H. R. 1951. The structures of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl Acad. Sci. USA 37, 205-210.
-
(1951)
Proc. Natl Acad. Sci. USA
, vol.37
, pp. 205-210
-
-
Pauling, L.1
Corey, R.B.2
Branson, H.R.3
-
68
-
-
0034886552
-
Unfolded, yes, but random? Never! Nat
-
Plaxco, K. W. and Gross, M. 2001. Unfolded, yes, but random? Never! Nat. Struct. Biol. 8, 659-660.
-
(2001)
Struct. Biol.
, vol.8
, pp. 659-660
-
-
Plaxco, K.W.1
Gross, M.2
-
69
-
-
0034647237
-
Do bridging water molecules dictate the structure of a model dipeptide in aqueous solution?
-
Poon, C.-D. and Samulski, E. T. 2000. Do bridging water molecules dictate the structure of a model dipeptide in aqueous solution?. J. Am. Chem. Soc. 122, 5642-5643.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 5642-5643
-
-
Poon, C.-D.1
Samulski, E.T.2
-
71
-
-
73649194755
-
Stereochemistry of polypeptide chain configurations
-
Ramachandran, G. N., Ramakrishnan, C., and Sasisekharan, V. 1963. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95-99.
-
(1963)
J. Mol. Biol.
, vol.7
, pp. 95-99
-
-
Ramachandran, G.N.1
Ramakrishnan, C.2
Sasisekharan, V.3
-
72
-
-
0017429069
-
Areas, volumes, packing, and protein structure
-
Richards, F. M. 1977. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6, 151-176.
-
(1977)
Annu. Rev. Biophys. Bioeng.
, vol.6
, pp. 151-176
-
-
Richards, F.M.1
-
73
-
-
0041319047
-
Host-guest scale of left-handed polyproline II helix formation
-
Rucker, A. L., Pager, C. T., Campbell, M. N., Qualls, J. E., and Creamer, T. P. 2003. Host-guest scale of left-handed polyproline II helix formation. Proteins 53, 68-75.
-
(2003)
Proteins
, vol.53
, pp. 68-75
-
-
Rucker, A.L.1
Pager, C.T.2
Campbell, M.N.3
Qualls, J.E.4
Creamer, T.P.5
-
74
-
-
0028270634
-
Kinetics of protein folding-a lattice model study of the requirements for folding to the native state
-
Sali, A., Shakhnovich, E., and Karplus, M. 1994a. Kinetics of protein folding-a lattice model study of the requirements for folding to the native state. J. Mol. Biol. 5, 1614-1636.
-
(1994)
J. Mol. Biol.
, vol.5
, pp. 1614-1636
-
-
Sali, A.1
Shakhnovich, E.2
Karplus, M.3
-
75
-
-
0028174310
-
How does a protein fold?
-
Sali, A., Shakhnovich, E. I., and Karplus, M. 1994b. How does a protein fold? Nature 477, 248-251.
-
(1994)
Nature
, vol.477
, pp. 248-251
-
-
Sali, A.1
Shakhnovich, E.I.2
Karplus, M.3
-
76
-
-
0345304461
-
Origin of Unusual f-values in protein folding: evidence against specific nucleation sites
-
Sanchez, I. E., and Kiefhaber, T. 2003. Origin of Unusual f-values in protein folding: evidence against specific nucleation sites. J. Mol. Biol. 334, 1077-1085.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 1077-1085
-
-
Sanchez, I.E.1
Kiefhaber, T.2
-
77
-
-
0345304461
-
Origin of unusual f-values in protein folding: evidence against specific nucleation sites
-
Sanchez, I. E. and Kiefhaber, T. 2003. Origin of unusual f-values in protein folding: evidence against specific nucleation sites. J. Mol. Biol. 334, 1077-1085.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 1077-1085
-
-
Sanchez, I.E.1
Kiefhaber, T.2
-
78
-
-
0037007485
-
Fifty years of solvent denaturation
-
Schellman, J. A. 2002. Fifty years of solvent denaturation. Biophys. Chem. 96, 91-101.
-
(2002)
Biophys. Chem.
, vol.96
, pp. 91-101
-
-
Schellman, J.A.1
-
79
-
-
4244080951
-
In The Proteins: Composition, Structure and Function
-
2nd edn, Academic Press, New York
-
Schellman, J. A. and Schellman, C. G. 1964. In The Proteins: Composition, Structure and Function, 2nd edn, Vol 2, pp. 1-37. Academic Press, New York.
-
(1964)
, vol.2
, pp. 1-37
-
-
Schellman, J.A.1
Schellman, C.G.2
-
81
-
-
0025849701
-
Calorimetric determination of the enthalpy change for the alphahelix to coil transition of an alanine peptide in water
-
Scholtz, J. M., Marqusee, S., Baldwin, R. L., York, E. J., Stewart, J. M., Santoro, M., and Bolen, D. W. 1991. Calorimetric determination of the enthalpy change for the alphahelix to coil transition of an alanine peptide in water. Proc. Natl Acad. Sci. USA 88, 2854-2858.
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 2854-2858
-
-
Scholtz, J.M.1
Marqusee, S.2
Baldwin, R.L.3
York, E.J.4
Stewart, J.M.5
Santoro, M.6
Bolen, D.W.7
-
82
-
-
0028901085
-
The folding mechanism of barstar: evidence for multiple pathways and multiple intermediates
-
Shastry, M. C. and Udgaonkar, J. B. 1995. The folding mechanism of barstar: evidence for multiple pathways and multiple intermediates. J. Mol. Biol. 247, 1013-1027.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 1013-1027
-
-
Shastry, M.C.1
Udgaonkar, J.B.2
-
83
-
-
0037047134
-
Polyproline II structure in a sequence of seven alanine residues
-
Shi, Z., Olson, C. A., Rose, G. D., Baldwin, R. L., and Kallenbach, N. R. 2002a. Polyproline II structure in a sequence of seven alanine residues. Proc. Natl Acad. Sci. USA 2002, 9190-9195.
-
(2002)
Proc. Natl Acad. Sci. USA
, pp. 9190-9195
-
-
Shi, Z.1
Olson, C.A.2
Rose, G.D.3
Baldwin, R.L.4
Kallenbach, N.R.5
-
84
-
-
0036400325
-
Is polyproline II a major backbone conformation in unfolded proteins?
-
Shi, Z., Woody, R. W., and Kallenbach, N. R. 2002b. Is polyproline II a major backbone conformation in unfolded proteins? Adv. Protein Chem. 62, 163-240.
-
(2002)
Adv. Protein Chem.
, vol.62
, pp. 163-240
-
-
Shi, Z.1
Woody, R.W.2
Kallenbach, N.R.3
-
85
-
-
0035919635
-
Persistence of native-like topology in a denatured protein in 8 M urea
-
Shortle, D. and Ackerman, M. 2001. Persistence of native-like topology in a denatured protein in 8 M urea. Science 293, 487-489.
-
(2001)
Science
, vol.293
, pp. 487-489
-
-
Shortle, D.1
Ackerman, M.2
-
86
-
-
0000114334
-
The kinetics of protein denaturation
-
Simpson, R. B. and Kauzmann, W. 1953. The kinetics of protein denaturation. J. Am. Chem. Soc. 75, 5139-5192.
-
(1953)
J. Am. Chem. Soc.
, vol.75
, pp. 5139-5192
-
-
Simpson, R.B.1
Kauzmann, W.2
-
87
-
-
0029978353
-
Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations
-
Smith, L. J., Bolin, K. A., Schwalbe, H., MacArthur, M. W., Thornton, J. M., and Dobson, C. M. 1996. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J. Mol. Biol. 255, 494-506.
-
(1996)
J. Mol. Biol.
, vol.255
, pp. 494-506
-
-
Smith, L.J.1
Bolin, K.A.2
Schwalbe, H.3
MacArthur, M.W.4
Thornton, J.M.5
Dobson, C.M.6
-
88
-
-
1542358783
-
Increasing stability reduces conformational heterogeneity in a protein folding intermediate ensemble
-
Sridevi, K., Lakshmikanth, G. S., Krishnamoorthy, G., and Udgaonkar, J. B. 2004. Increasing stability reduces conformational heterogeneity in a protein folding intermediate ensemble. J. Mol. Biol. 337, 669-711.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 669-711
-
-
Sridevi, K.1
Lakshmikanth, G.S.2
Krishnamoorthy, G.3
Udgaonkar, J.B.4
-
89
-
-
0033405203
-
A physical basis for protein secondary structure
-
Srinivasan, R. and Rose, G. D. 1999. A physical basis for protein secondary structure. Proc. Natl Acad. Sci. USA 96, 14258-14263.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 14258-14263
-
-
Srinivasan, R.1
Rose, G.D.2
-
90
-
-
0032980562
-
A survery of left-handed polyproline II helices
-
Stapley, B. J. and Creamer, T. P. 1999. A survery of left-handed polyproline II helices. Protein Sci. 8, 587-595.
-
(1999)
Protein Sci.
, vol.8
, pp. 587-595
-
-
Stapley, B.J.1
Creamer, T.P.2
-
91
-
-
0014364651
-
Protein denaturation
-
Tanford, C. 1968. Protein denaturation. Adv. Protein Chem. 23, 121-282.
-
(1968)
Adv. Protein Chem.
, vol.23
, pp. 121-282
-
-
Tanford, C.1
-
92
-
-
0014718113
-
Protein denaturation. Part C. Theoretical models for the mechanism of denaturation
-
Tanford, C. 1970. Protein denaturation. Part C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 24, 1-95.
-
(1970)
Adv. Protein Chem.
, vol.24
, pp. 1-95
-
-
Tanford, C.1
-
93
-
-
0013880080
-
Equilibrium and kinetics of the unfolding of lysozyme (muramidase) by guanidine hydrochloride
-
Tanford, C., Pain, R. H., and Otchin, N. S. 1966. Equilibrium and kinetics of the unfolding of lysozyme (muramidase) by guanidine hydrochloride. J. Mol. Biol. 15, 489-504.
-
(1966)
J. Mol. Biol.
, vol.15
, pp. 489-504
-
-
Tanford, C.1
Pain, R.H.2
Otchin, N.S.3
-
94
-
-
0034656952
-
Hiking in the energy landscape in sequence space: a bumpy road to good folders
-
Tiana, G., Broglia, R. A., and Shakhnovich, E. I. 2000. Hiking in the energy landscape in sequence space: a bumpy road to good folders. Proteins 39, 244-251.
-
(2000)
Proteins
, vol.39
, pp. 244-251
-
-
Tiana, G.1
Broglia, R.A.2
Shakhnovich, E.I.3
-
95
-
-
0014378447
-
Biopolymers
-
Tiffany, M. L. and Krimm, S. 1968a. Biopolymers 6, 1767-1770.
-
(1968)
, vol.6
, pp. 1767-1770
-
-
Tiffany, M.L.1
Krimm, S.2
-
96
-
-
0014227144
-
New chain conformations of poly(glutamic acid) and polylysine
-
Tiffany, M. L. and Krimm, S. 1968b. New chain conformations of poly(glutamic acid) and polylysine. Biopolymers 6, 1379-1382
-
(1968)
Biopolymers
, vol.6
, pp. 1379-1382
-
-
Tiffany, M.L.1
Krimm, S.2
-
97
-
-
0035910479
-
The key to solving the protein-folding problem lies in an accurate description of the denatured state
-
Van Gunsteren, W. F., Bürgi, R., Peter, C., and Daura, X. 2001. The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew. Chem. Int. Ed. 40, 351-355
-
(2001)
Angew. Chem. Int. Ed.
, vol.40
, pp. 351-355
-
-
Van Gunsteren, W.F.1
Bürgi, R.2
Peter, C.3
Daura, X.4
-
98
-
-
0003605587
-
Physical Biochemistry
-
Prentice-Hall, Englewood Cliffs, NJ
-
Van Holde, K. E. 1971. Physical Biochemistry. Prentice-Hall, Englewood Cliffs, NJ
-
(1971)
-
-
Van Holde, K.E.1
-
99
-
-
0003605587
-
Physical Biochemistry
-
Prentice-Hall, Upper Saddle River, NJ
-
Van Holde, K. E., Johnson, W. C., and Ho, P. S. 1998. Physical Biochemistry. Prentice-Hall, Upper Saddle River, NJ.
-
(1998)
-
-
Van Holde, K.E.1
Johnson, W.C.2
Ho, P.S.3
-
100
-
-
0029760326
-
Different folding transition states may result in the same native structure
-
Viguera, A. R., Serrano, L., and Wilmanns, M. 1996. Different folding transition states may result in the same native structure. Nat. Struct. Biol. 3, 874-880.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 874-880
-
-
Viguera, A.R.1
Serrano, L.2
Wilmanns, M.3
-
101
-
-
0001189175
-
Studies on denaturation of proteins. XIII. A theory of denaturation
-
Wu, H. 1931. Studies on denaturation of proteins. XIII. A theory of denaturation. Chin. J. Physiol. V, 321-344.
-
(1931)
Chin. J. Physiol.
, vol.V
, pp. 321-344
-
-
Wu, H.1
-
102
-
-
0034705338
-
NMR characterization of residual structure in the denatured state of protein L
-
Yi, Q., Scalley-Kim, M. L., Alm, E. J., and Baker, D. 2000. NMR characterization of residual structure in the denatured state of protein L. J. Mol. Biol. 299, 1341-1351.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 1341-1351
-
-
Yi, Q.1
Scalley-Kim, M.L.2
Alm, E.J.3
Baker, D.4
-
103
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
Zagrovic, B., Snow, C. Khaliq, S., Shirts, M., and Pande, V. 2002. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323, 153-164.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 153-164
-
-
Zagrovic, B.1
Snow, C.2
Khaliq, S.3
Shirts, M.4
Pande, V.5
-
104
-
-
0042701995
-
Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides
-
Zaman, M. H., Shen, M. Y., Berry, R. S., Freed, K. F., and Sosnick, T. R. 2003. Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. J. Mol. Biol. 331, 693-711.
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 693-711
-
-
Zaman, M.H.1
Shen, M.Y.2
Berry, R.S.3
Freed, K.F.4
Sosnick, T.R.5
-
105
-
-
0000668407
-
Theory of the phase transition between helix and random coil in polypeptide chains
-
Zimm, B. H. and Bragg, J. K. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31, 526-535.
-
(1959)
J. Chem. Phys.
, vol.31
, pp. 526-535
-
-
Zimm, B.H.1
Bragg, J.K.2
|