-
1
-
-
0014958182
-
Stereochemistry of cooperative effects in haemoglobin
-
Perutz MF. Stereochemistry of cooperative effects in haemoglobin. Nature 1970; 228: 726-739.
-
(1970)
Nature
, vol.228
, pp. 726-739
-
-
Perutz, M.F.1
-
2
-
-
20344370764
-
Allosteric mechanisms of signal transduction
-
Changeux JP, Edelstein SJ. Allosteric mechanisms of signal transduction. Science 2005; 308: 1424-1428.
-
(2005)
Science
, vol.308
, pp. 1424-1428
-
-
Changeux, J.P.1
Edelstein, S.J.2
-
3
-
-
18744371588
-
Molecular dynamics and protein function
-
Karplus M, Kuriyan J. Molecular dynamics and protein function. Proc Natl Acad Sci USA 2005; 102: 6679-6685.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
4
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005; 438: 117-121.
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
5
-
-
1842473098
-
Direct access to the cooperative substructure of proteins and the protein ensemble via cold denaturation
-
Babu CR, Hilser VJ, Wand AJ. Direct access to the cooperative substructure of proteins and the protein ensemble via cold denaturation. Nat Struct Mol Biol 2004; 11: 352-357.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 352-357
-
-
Babu, C.R.1
Hilser, V.J.2
Wand, A.J.3
-
6
-
-
33748663531
-
Revealing the nature of the native state ensemble through cold denaturation
-
Whitten ST, Kurtz AJ, Pometun MS, Wand AJ, Hilser VJ. Revealing the nature of the native state ensemble through cold denaturation. Biochemistry 2006; 45: 10163-10174.
-
(2006)
Biochemistry
, vol.45
, pp. 10163-10174
-
-
Whitten, S.T.1
Kurtz, A.J.2
Pometun, M.S.3
Wand, A.J.4
Hilser, V.J.5
-
7
-
-
0026567099
-
The molecular basis of cooperativity in protein folding: thermodynamic dissection of interdomain interactions in phosphoglycerate kinase
-
Freire E, Murphy KP, Sanchez-Ruiz JM, Galisteo ML, Privalov PL. The molecular basis of cooperativity in protein folding: thermodynamic dissection of interdomain interactions in phosphoglycerate kinase. Biochemistry 1992; 31: 250-256.
-
(1992)
Biochemistry
, vol.31
, pp. 250-256
-
-
Freire, E.1
Murphy, K.P.2
Sanchez-Ruiz, J.M.3
Galisteo, M.L.4
Privalov, P.L.5
-
8
-
-
0024578735
-
Heat and cold denaturation of phosphoglycerate kinase (interaction of domains)
-
Griko YV, Venyaminov SY, Privalov PL. Heat and cold denaturation of phosphoglycerate kinase (interaction of domains). FEBS Lett 1989; 244: 276-278.
-
(1989)
FEBS Lett
, vol.244
, pp. 276-278
-
-
Griko, Y.V.1
Venyaminov, S.Y.2
Privalov, P.L.3
-
9
-
-
0000180763
-
Temperature dependence of the hydrophobic interaction in protein folding
-
Baldwin RL. Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci USA 1986; 83: 8069-8072.
-
(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 8069-8072
-
-
Baldwin, R.L.1
-
10
-
-
44949259971
-
Mechanistic elements of protein cold denaturation
-
Lopez CF, Darst RK, Rossky PJ. Mechanistic elements of protein cold denaturation. J Phys Chem B 2008; 112: 5961-5967.
-
(2008)
J Phys Chem B
, vol.112
, pp. 5961-5967
-
-
Lopez, C.F.1
Darst, R.K.2
Rossky, P.J.3
-
11
-
-
0025125438
-
Cold denaturation of proteins
-
Privalov PL. Cold denaturation of proteins. Crit Rev Biochem Mol Biol 1990; 25; 281-305.
-
(1990)
Crit Rev Biochem Mol Biol
, vol.25
, pp. 281-305
-
-
Privalov, P.L.1
-
15
-
-
0030580089
-
Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
-
Hilser VJ, Freire E. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J Mol Biol 1996; 262: 756-772.
-
(1996)
J Mol Biol
, vol.262
, pp. 756-772
-
-
Hilser, V.J.1
Freire, E.2
-
16
-
-
0026649261
-
Molecular basis of co-operativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates
-
Murphy KP, Bhakuni V, Xie D, Freire E. Molecular basis of co-operativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates. J Mol Biol 1992; 227: 293-306.
-
(1992)
J Mol Biol
, vol.227
, pp. 293-306
-
-
Murphy, K.P.1
Bhakuni, V.2
Xie, D.3
Freire, E.4
-
17
-
-
0028146012
-
Structure-based prediction of protein-folding intermediates
-
Xie D, Freire E. Structure-based prediction of protein-folding intermediates. J Mol Biol 1994; 242: 62-80.
-
(1994)
J Mol Biol
, vol.242
, pp. 62-80
-
-
Xie, D.1
Freire, E.2
-
18
-
-
0026756702
-
Thermodynamics of structural stability and cooperative folding behavior in proteins
-
Murphy KP, Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem 1992; 43: 313-361.
-
(1992)
Adv Protein Chem
, vol.43
, pp. 313-361
-
-
Murphy, K.P.1
Freire, E.2
-
20
-
-
0029941271
-
Energetics of hydrogen bonding in proteins: a model compound study
-
Habermann SM, Murphy KP. Energetics of hydrogen bonding in proteins: a model compound study. Protein Sci 1996; 5: 1229-1239.
-
(1996)
Protein Sci
, vol.5
, pp. 1229-1239
-
-
Habermann, S.M.1
Murphy, K.P.2
-
21
-
-
0029900846
-
The magnitude of the backbone conformational entropy change in protein folding
-
D'Aquino JA, Gomez J, Hilser VJ, Lee KH, Amzel LM, Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins 1996; 25: 143-156.
-
(1996)
Proteins
, vol.25
, pp. 143-156
-
-
D'Aquino, J.A.1
Gomez, J.2
Hilser, V.J.3
Lee, K.H.4
Amzel, L.M.5
Freire, E.6
-
22
-
-
0027991081
-
Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation
-
Lee KH, Xie D, Freire E, Amzel LM. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 1994; 20: 68-84.
-
(1994)
Proteins
, vol.20
, pp. 68-84
-
-
Lee, K.H.1
Xie, D.2
Freire, E.3
Amzel, L.M.4
-
23
-
-
0029958659
-
Structure-based thermodynamic scale of R-helix propensities in amino acids
-
Luque I, Mayorga OL, Freire E. Structure-based thermodynamic scale of R-helix propensities in amino acids. Biochemistry 1996; 35: 13681-13688.
-
(1996)
Biochemistry
, vol.35
, pp. 13681-13688
-
-
Luque, I.1
Mayorga, O.L.2
Freire, E.3
-
24
-
-
0028936999
-
Staphylococcal nuclease: a showcase of m-value effects
-
Shortle D. Staphylococcal nuclease: a showcase of m-value effects. Adv Protein Chem 1995; 46: 217-247.
-
(1995)
Adv Protein Chem
, vol.46
, pp. 217-247
-
-
Shortle, D.1
-
25
-
-
0025005525
-
Contributions of the large hydrophobic amino acids to the stability of Staphylococcal nuclease
-
Shortle D, Stites WE, Meeker AK. Contributions of the large hydrophobic amino acids to the stability of Staphylococcal nuclease. Biochemistry 1990; 29: 8033-8041.
-
(1990)
Biochemistry
, vol.29
, pp. 8033-8041
-
-
Shortle, D.1
Stites, W.E.2
Meeker, A.K.3
-
26
-
-
0028577248
-
Thermodynamic characterization of an equilibrium folding intermediate of Staphylococcal nuclease
-
Xie D, Fox RO, Freire E. Thermodynamic characterization of an equilibrium folding intermediate of Staphylococcal nuclease. Protein Sci 1994; 3: 2175-2184.
-
(1994)
Protein Sci
, vol.3
, pp. 2175-2184
-
-
Xie, D.1
Fox, R.O.2
Freire, E.3
-
27
-
-
0027953952
-
Three-state thermodynamic analysis of the denaturation of Staphylococcal nuclease mutants
-
Carra JH, Anderson EA, Privalov PL. Three-state thermodynamic analysis of the denaturation of Staphylococcal nuclease mutants. Biochemistry 1994; 33: 10842-10850.
-
(1994)
Biochemistry
, vol.33
, pp. 10842-10850
-
-
Carra, J.H.1
Anderson, E.A.2
Privalov, P.L.3
-
28
-
-
0028968250
-
Energetics of denaturation and m values of Staphylococcal nuclease mutants
-
Carra JH, Privalov PL. Energetics of denaturation and m values of Staphylococcal nuclease mutants. Biochemistry 1995; 34: 2034-2041.
-
(1995)
Biochemistry
, vol.34
, pp. 2034-2041
-
-
Carra, J.H.1
Privalov, P.L.2
-
29
-
-
0027384577
-
Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2
-
Jackson SE, Moracci M, elMasry N, Johnson CM, Fersht AR. Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. Biochemistry 1993; 32: 11259-11269.
-
(1993)
Biochemistry
, vol.32
, pp. 11259-11269
-
-
Jackson, S.E.1
Moracci, M.2
elMasry, N.3
Johnson, C.M.4
Fersht, A.R.5
-
30
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki LS, Otzen DE, Fersht AR. The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 1995; 254: 260-288.
-
(1995)
J Mol Biol
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
31
-
-
10644261303
-
Differences in the folding transition state of ubiquitin indicated by phi and psi analyses
-
Sosnick TR, Dothager RS, Krantz BA. Differences in the folding transition state of ubiquitin indicated by phi and psi analyses. Proc Natl Acad Sci USA 2004; 101: 17377-17382.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 17377-17382
-
-
Sosnick, T.R.1
Dothager, R.S.2
Krantz, B.A.3
-
32
-
-
0030993784
-
Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: structural mapping of cooperative interactions
-
Hilser VJ, Townsend BD, Freire E. Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: structural mapping of cooperative interactions. Biophys Chem 1997; 64: 69-79.
-
(1997)
Biophys Chem
, vol.64
, pp. 69-79
-
-
Hilser, V.J.1
Townsend, B.D.2
Freire, E.3
-
33
-
-
0031042186
-
Predicting the equilibrium protein folding pathway: structure-based analysis of Staphylococcal nuclease
-
Hilser VJ, Freire E. Predicting the equilibrium protein folding pathway: structure-based analysis of Staphylococcal nuclease. Proteins 1997; 27: 171-183.
-
(1997)
Proteins
, vol.27
, pp. 171-183
-
-
Hilser, V.J.1
Freire, E.2
-
34
-
-
0034636991
-
Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins
-
Wooll JO, Wrabl JO, Hilser VJ. Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins. J Mol Biol 2000; 301: 247-256.
-
(2000)
J Mol Biol
, vol.301
, pp. 247-256
-
-
Wooll, J.O.1
Wrabl, J.O.2
Hilser, V.J.3
-
35
-
-
15444362906
-
Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins
-
Whitten ST, García-Moreno EB, Hilser VJ. Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins. Proc Natl Acad Sci USA 2005; 102: 4282-4287.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 4282-4287
-
-
Whitten, S.T.1
García-Moreno, E.B.2
Hilser, V.J.3
-
36
-
-
0034710950
-
Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
-
Pan H, Lee JC, Hilser VJ. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc Natl Acad Sci USA 2000; 97: 12020-12025.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12020-12025
-
-
Pan, H.1
Lee, J.C.2
Hilser, V.J.3
-
37
-
-
34248332629
-
Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble
-
Liu T, Whitten ST, Hilser VJ. Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble. Proc Natl Acad Sci USA 2007; 104: 4347-4352.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 4347-4352
-
-
Liu, T.1
Whitten, S.T.2
Hilser, V.J.3
-
38
-
-
0025877987
-
The crystal structure of Staphylococcal nuclease refined at 1.7-A resolution
-
Hynes TR, Fox RO. The crystal structure of Staphylococcal nuclease refined at 1.7-A resolution. Proteins 1991; 10: 92-105.
-
(1991)
Proteins
, vol.10
, pp. 92-105
-
-
Hynes, T.R.1
Fox, R.O.2
-
39
-
-
0023652256
-
Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds
-
McPhalen CA, James MN. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry 1987; 26: 261-269.
-
(1987)
Biochemistry
, vol.26
, pp. 261-269
-
-
McPhalen, C.A.1
James, M.N.2
-
40
-
-
0023644679
-
Structure of ubiquitin refined at 1.8 A resolution
-
Vijay-Kumar S, Bugg CE, Cook WJ. Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 1987; 194: 531-544.
-
(1987)
J Mol Biol
, vol.194
, pp. 531-544
-
-
Vijay-Kumar, S.1
Bugg, C.E.2
Cook, W.J.3
-
41
-
-
0024298839
-
Stability mutants of Staphylococcal nuclease: large compensating enthalpy-entropy changes for the reversible denaturation reaction
-
Shortle D, Meeker AK, Freire E. Stability mutants of Staphylococcal nuclease: large compensating enthalpy-entropy changes for the reversible denaturation reaction. Biochemistry 1988; 27: 4761-4768.
-
(1988)
Biochemistry
, vol.27
, pp. 4761-4768
-
-
Shortle, D.1
Meeker, A.K.2
Freire, E.3
-
43
-
-
0025877673
-
Prediction of the thermodynamics of protein unfolding: the helix-coil transition of poly(L-alanine)
-
Ooi T, Oobatake M. Prediction of the thermodynamics of protein unfolding: the helix-coil transition of poly(L-alanine). Proc Natl Acad Sci USA 1991; 88: 2859-2863.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 2859-2863
-
-
Ooi, T.1
Oobatake, M.2
-
44
-
-
0030022713
-
Thermodynamics of denaturation of Staphylococcal nuclease mutants: an intermediate state in protein folding
-
Carra JH, Privalov PL. Thermodynamics of denaturation of Staphylococcal nuclease mutants: an intermediate state in protein folding. FASEB J 1996; 10: 67-74.
-
(1996)
FASEB J
, vol.10
, pp. 67-74
-
-
Carra, J.H.1
Privalov, P.L.2
-
45
-
-
0027245421
-
Three-state analysis of sperm whale apomyglobin folding
-
Barrick D, Baldwin RL. Three-state analysis of sperm whale apomyglobin folding. Biochemistry 1993; 32: 3790-3796.
-
(1993)
Biochemistry
, vol.32
, pp. 3790-3796
-
-
Barrick, D.1
Baldwin, R.L.2
-
46
-
-
0017178548
-
Three-state denaturation of a-lactalbumin by guanidine hydrochloride
-
Kuwajima K, Nitta K, Yoneyama M, Sugai S. Three-state denaturation of a-lactalbumin by guanidine hydrochloride. J Mol Biol 1976; 106: 359-373.
-
(1976)
J Mol Biol
, vol.106
, pp. 359-373
-
-
Kuwajima, K.1
Nitta, K.2
Yoneyama, M.3
Sugai, S.4
-
47
-
-
0031808804
-
Chemical denaturation: potential impact of undetected intermediates in the free energy of unfolding and m-values obtained from a two-state assumption
-
Soulages JL. Chemical denaturation: potential impact of undetected intermediates in the free energy of unfolding and m-values obtained from a two-state assumption. Biophys J 1998; 75: 484-492.
-
(1998)
Biophys J
, vol.75
, pp. 484-492
-
-
Soulages, J.L.1
-
48
-
-
0028820703
-
Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding
-
Myers JK, Pace CN, Scholtz JM. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci 1995; 4: 2138-2148.
-
(1995)
Protein Sci
, vol.4
, pp. 2138-2148
-
-
Myers, J.K.1
Pace, C.N.2
Scholtz, J.M.3
-
49
-
-
0022555885
-
Determination and analysis of urea and guanidine hydrochloride denaturation curves
-
Pace CN. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 1986; 131: 266-280.
-
(1986)
Methods Enzymol
, vol.131
, pp. 266-280
-
-
Pace, C.N.1
-
50
-
-
0023697408
-
Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl a-chymotrypsin using different denaturants
-
Santoro MM, Bolen DW. Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl a-chymotrypsin using different denaturants. Biochemistry 1988; 27: 8063-8068.
-
(1988)
Biochemistry
, vol.27
, pp. 8063-8068
-
-
Santoro, M.M.1
Bolen, D.W.2
-
51
-
-
0033600572
-
The peculiar nature of the guanidine hydrochloride-induced two-state denaturation of Staphylococcal nuclease: a calorimetric study
-
Yang M, Liu D, Bolen DW. The peculiar nature of the guanidine hydrochloride-induced two-state denaturation of Staphylococcal nuclease: a calorimetric study. Biochemistry 1999; 38: 11216-11222.
-
(1999)
Biochemistry
, vol.38
, pp. 11216-11222
-
-
Yang, M.1
Liu, D.2
Bolen, D.W.3
-
52
-
-
0032558991
-
Monitoring the sizes of denatured ensembles of Staphylococcal nuclease proteins: implications regarding m values, intermediates, and thermodynamics
-
Baskakov IV, Bolen DW. Monitoring the sizes of denatured ensembles of Staphylococcal nuclease proteins: implications regarding m values, intermediates, and thermodynamics. Biochemistry 1998; 37: 18010-18017.
-
(1998)
Biochemistry
, vol.37
, pp. 18010-18017
-
-
Baskakov, I.V.1
Bolen, D.W.2
-
53
-
-
0035061715
-
Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition
-
Wrabl JO, Larson SA, Hilser VJ. Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition. Protein Sci 2001; 10: 1032-1045.
-
(2001)
Protein Sci
, vol.10
, pp. 1032-1045
-
-
Wrabl, J.O.1
Larson, S.A.2
Hilser, V.J.3
-
54
-
-
3042572569
-
Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization
-
Larson SA, Hilser VJ. Analysis of the "thermodynamic information content" of a Homo sapiens structural database reveals hierarchical thermodynamic organization. Protein Sci 2004; 13: 1787-17801.
-
(2004)
Protein Sci
, vol.13
, pp. 1787-17801
-
-
Larson, S.A.1
Hilser, V.J.2
-
55
-
-
48749084868
-
Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding
-
Wang S, Gu J, Larson SA, Whitten ST, Hilser VJ. Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding. J Mol Biol 2008; 381: 1184-1201.
-
(2008)
J Mol Biol
, vol.381
, pp. 1184-1201
-
-
Wang, S.1
Gu, J.2
Larson, S.A.3
Whitten, S.T.4
Hilser, V.J.5
-
56
-
-
0023783477
-
Conformational stability and activity of ribonuclease T1 with zero, one, and two intact disulfide bonds
-
Pace CN, Grimsley GR, Thomson JA, Barnett BJ. Conformational stability and activity of ribonuclease T1 with zero, one, and two intact disulfide bonds. J Biol Chem 1988; 263: 11820-11825.
-
(1988)
J Biol Chem
, vol.263
, pp. 11820-11825
-
-
Pace, C.N.1
Grimsley, G.R.2
Thomson, J.A.3
Barnett, B.J.4
-
57
-
-
0023661639
-
An engineered disulfide bond in dihydrofolate reductase
-
Villafranca JE, Howell EE, Oatley SJ, Xuong NH, Kraut J. An engineered disulfide bond in dihydrofolate reductase. Biochemistry 1987; 26: 2182-2189.
-
(1987)
Biochemistry
, vol.26
, pp. 2182-2189
-
-
Villafranca, J.E.1
Howell, E.E.2
Oatley, S.J.3
Xuong, N.H.4
Kraut, J.5
-
58
-
-
0032879755
-
A model of the changes in denatured state structure underlying m value effects in Staphylococcal nuclease
-
Wrabl J, Shortle D. A model of the changes in denatured state structure underlying m value effects in Staphylococcal nuclease. Nat Struct Biol 1999; 6: 876-883.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 876-883
-
-
Wrabl, J.1
Shortle, D.2
|