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1
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0026756702
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Thermodynamics of structural stability and cooperative folding behavior in proteins
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Murphy K.P., Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem. 43:1992;313-361.
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(1992)
Adv Protein Chem
, vol.43
, pp. 313-361
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Murphy, K.P.1
Freire, E.2
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2
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0032311808
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Prediction of binding energetics from structure using empirical parameterization
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Baker B.M., Murphy K.P. Prediction of binding energetics from structure using empirical parameterization. Methods Enzymol. 295:1998;294-315.
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(1998)
Methods Enzymol
, vol.295
, pp. 294-315
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Baker, B.M.1
Murphy, K.P.2
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3
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0033025809
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Predicting binding energetics from structure: Looking beyond Δg
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Murphy K.P. Predicting binding energetics from structure: looking beyond ΔG. Med Res Rev. 19:1999;333-339.
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(1999)
Med Res Rev
, vol.19
, pp. 333-339
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Murphy, K.P.1
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4
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0027980359
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Molecular basis of cooperativity in protein folding. v. Thermodynamic and structural conditions for the stabilization of compact denatured states
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Xie D., Freire E. Molecular basis of cooperativity in protein folding. v. Thermodynamic and structural conditions for the stabilization of compact denatured states. Proteins. 19:1994;291-301.
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(1994)
Proteins
, vol.19
, pp. 291-301
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Xie, D.1
Freire, E.2
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5
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0026665778
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Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities
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Creamer T.P., Rose G.D. Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc Natl Acad Sci USA. 89:1992;5937-5941.
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(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 5937-5941
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Creamer, T.P.1
Rose, G.D.2
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6
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0027991081
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Entropy changes in biological processes: Loss of side chain configurational entropy in binding and folding
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Lee K.H., Xie D., Freire E., Amzel L.M. Entropy changes in biological processes: loss of side chain configurational entropy in binding and folding. Proteins. 20:1994;68-84.
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(1994)
Proteins
, vol.20
, pp. 68-84
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Lee, K.H.1
Xie, D.2
Freire, E.3
Amzel, L.M.4
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7
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0029900846
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The magnitude of the backbone conformational entropy change in protein folding
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D'Aquino J.A., Gómez J., Hilser V.J., Lee K.H., Amzel L.M., Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins. 25:1996;143-156.
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(1996)
Proteins
, vol.25
, pp. 143-156
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D'Aquino, J.A.1
Gómez, J.2
Hilser, V.J.3
Lee, K.H.4
Amzel, L.M.5
Freire, E.6
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8
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0027166270
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Empirical scale of side-chain conformational entropy in protein folding
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Pickett S.D., Sternberg M.J.E. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol. 231:1993;825-839.
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J Mol Biol
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, pp. 825-839
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Pickett, S.D.1
Sternberg, M.J.E.2
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9
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0000180763
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Temperature dependence of the hydrophobic interaction in protein folding
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Baldwin R.L. Temperature dependence of the hydrophobic interaction in protein folding. Proc Natl Acad Sci USA. 83:1986;8069-8072.
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(1986)
Proc Natl Acad Sci USA
, vol.83
, pp. 8069-8072
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Baldwin, R.L.1
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10
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0025098571
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Common features of protein unfolding and dissolution of hydrophobic compounds
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Murphy K.P., Privalov P.L., Gill S.J. Common features of protein unfolding and dissolution of hydrophobic compounds. Science. 247:1990;559-561.
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(1990)
Science
, vol.247
, pp. 559-561
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Murphy, K.P.1
Privalov, P.L.2
Gill, S.J.3
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11
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0024745871
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The price of lost freedom: Entropy of bimolecular complex formation
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Finkelstein A.V., Janin J. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng. 3:1989;1-3.
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(1989)
Protein Eng
, vol.3
, pp. 1-3
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Finkelstein, A.V.1
Janin, J.2
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13
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0028127923
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Entropy in biological binding processes: Estimation of translational entropy loss
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Murphy K.P., Xie D., Thompson K.S., Amzel L.M., Freire E. Entropy in biological binding processes: estimation of translational entropy loss. Proteins. 18:1994;63-67.
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(1994)
Proteins
, vol.18
, pp. 63-67
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Murphy, K.P.1
Xie, D.2
Thompson, K.S.3
Amzel, L.M.4
Freire, E.5
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14
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0030917908
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Loss of translational entropy in binding, folding, and catalysis
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Amzel L.M. Loss of translational entropy in binding, folding, and catalysis. Proteins. 28:1997;144-149.
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(1997)
Proteins
, vol.28
, pp. 144-149
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Amzel, L.M.1
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15
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0029941271
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Energetics of hydrogen bonding in proteins: A model compound study
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Habermann S.M., Murphy K.P. Energetics of hydrogen bonding in proteins: a model compound study. Protein Sci. 5:1996;1229-1239.
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(1996)
Protein Sci
, vol.5
, pp. 1229-1239
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Habermann, S.M.1
Murphy, K.P.2
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17
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0000159569
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Protein structure and the energetics of protein stability
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Robertson A.D., Murphy K.P. Protein structure and the energetics of protein stability. Chem Rev. 97:1997;1251-1267.
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(1997)
Chem Rev
, vol.97
, pp. 1251-1267
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Robertson, A.D.1
Murphy, K.P.2
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18
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0027537127
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Structural energetics of peptide recognition: Angiotensin ii / antibody binding
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Murphy K.P., Xie D., Garcia K.C., Amzel L.M., Freire E. Structural energetics of peptide recognition: angiotensin ii / antibody binding. Proteins. 15:1993;113-120.
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(1993)
Proteins
, vol.15
, pp. 113-120
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Murphy, K.P.1
Xie, D.2
Garcia, K.C.3
Amzel, L.M.4
Freire, E.5
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19
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0029080864
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Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin
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Gómez J., Freire E. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J Mol Biol. 252:1995;337-350.
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(1995)
J Mol Biol
, vol.252
, pp. 337-350
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Gómez, J.1
Freire, E.2
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20
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0031547981
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Dissecting the energetics of a protein-protein interaction: The binding of ovomucoid third domain to elastase
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Baker B.M., Murphy K.P. Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase. J Mol Biol. 268:1997;557-569.
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(1997)
J Mol Biol
, vol.268
, pp. 557-569
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Baker, B.M.1
Murphy, K.P.2
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21
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0030905238
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Structure-based thermodynamic analysis of HIV-1 protease inhibitors
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Bardi J.S., Luque I., Freire E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors. Biochemistry. 36:1997;6588-6596.
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(1997)
Biochemistry
, vol.36
, pp. 6588-6596
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Bardi, J.S.1
Luque, I.2
Freire, E.3
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22
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0033550047
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Analysis of the binding of hydroxamic acid and carboxylic acid inhibitors to the stromelysin-1 (matrix metalloproteinase-3) catalytic domain by isothermal titration calorimetry
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This study provides an excellent example of how detailed energetics and structure can be used together to provide a clearer understanding of protein-ligand interactions.
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Parker M.H., Lunney E.A., Ortwine D.F., Pavlovsky A.G., Humblet C., Brouillette C.G. Analysis of the binding of hydroxamic acid and carboxylic acid inhibitors to the stromelysin-1 (matrix metalloproteinase-3) catalytic domain by isothermal titration calorimetry. Biochemistry. 38:1999;13592-13601. This study provides an excellent example of how detailed energetics and structure can be used together to provide a clearer understanding of protein-ligand interactions.
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(1999)
Biochemistry
, vol.38
, pp. 13592-13601
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Parker, M.H.1
Lunney, E.A.2
Ortwine, D.F.3
Pavlovsky, A.G.4
Humblet, C.5
Brouillette, C.G.6
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23
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0000035228
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Contribution of translational and rotational entropy to the unfolding of a dimeric coiled-coil
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This is an experimental investigation of the contribution of translational and rotational entropy to binding. The results clearly show that this contribution is much smaller than some theoretical estimates.
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Yu Y.B., Lavigne P., Kay C.M., Hodges R.S., Privalov P.L. Contribution of translational and rotational entropy to the unfolding of a dimeric coiled-coil. J Phys Chem B. 103:1999;2270-2278. This is an experimental investigation of the contribution of translational and rotational entropy to binding. The results clearly show that this contribution is much smaller than some theoretical estimates.
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(1999)
J Phys Chem B
, vol.103
, pp. 2270-2278
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Yu, Y.B.1
Lavigne, P.2
Kay, C.M.3
Hodges, R.S.4
Privalov, P.L.5
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25
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0029957505
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The enthalpy change in protein folding and binding: Refinement of parameters for structure-based calculations
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Hilser V.J., Gómez J., Freire E. The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations. Proteins. 26:1996;123-133.
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(1996)
Proteins
, vol.26
, pp. 123-133
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Hilser, V.J.1
Gómez, J.2
Freire, E.3
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26
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0002050426
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Conformational transitions of proteins in water and in aqueous mixtures
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S.N. Timasheff, & G.D. Fasman. New York: Marcel Dekker
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Brandts J.F. Conformational transitions of proteins in water and in aqueous mixtures. Timasheff S.N., Fasman G.D. Structure and Stability of Biological Macromolecules. 1969;213-290 Marcel Dekker, New York.
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(1969)
Structure and Stability of Biological Macromolecules
, pp. 213-290
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Brandts, J.F.1
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27
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0030580089
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Structure based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
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Hilser V.J., Freire E. Structure based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J Mol Biol. 262:1996;756-772.
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(1996)
J Mol Biol
, vol.262
, pp. 756-772
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Hilser, V.J.1
Freire, E.2
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28
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0013994339
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Hydrogen exchange in proteins
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Hvidt A., Nielsen S.O. Hydrogen exchange in proteins. Adv Protein Chem. 21:1966;287-386.
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(1966)
Adv Protein Chem
, vol.21
, pp. 287-386
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Hvidt, A.1
Nielsen, S.O.2
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29
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0027489832
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Thermodynamics of unfolding for turkey ovomucoid third domain: Thermal and chemical denaturation
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Swint L., Robertson A.D. Thermodynamics of unfolding for turkey ovomucoid third domain: thermal and chemical denaturation. Protein Sci. 2:1993;2037-2049.
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(1993)
Protein Sci
, vol.2
, pp. 2037-2049
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Swint, L.1
Robertson, A.D.2
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30
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0029643523
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Protein folding intermediates: Native-state hydrogen exchange
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Bai Y., Sosnick T.R., Mayne L., Englander S.W. Protein folding intermediates: native-state hydrogen exchange. Science. 269:1995;192-197.
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(1995)
Science
, vol.269
, pp. 192-197
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Bai, Y.1
Sosnick, T.R.2
Mayne, L.3
Englander, S.W.4
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31
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0032544060
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The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble
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Cooperativity in protein folding is fundamental to protein function. In this paper, the authors examine the origin and behavior of folding cooperativity. They show that cooperativity is not uniformly distributed throughout the structure and that it varies with conditions.
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Hilser V.J., Dowdy D., Oas T.G., Freire E. The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. Proc Natl Acad Sci USA. 95:1998;9903-9908. Cooperativity in protein folding is fundamental to protein function. In this paper, the authors examine the origin and behavior of folding cooperativity. They show that cooperativity is not uniformly distributed throughout the structure and that it varies with conditions.
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(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 9903-9908
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Hilser, V.J.1
Dowdy, D.2
Oas, T.G.3
Freire, E.4
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32
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0030993784
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Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: Structural mapping of cooperative interactions
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Hilser V.J., Townsend B.D., Freire E. Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: structural mapping of cooperative interactions. Biophys Chem. 64:1997;69-79.
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(1997)
Biophys Chem
, vol.64
, pp. 69-79
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Hilser, V.J.1
Townsend, B.D.2
Freire, E.3
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33
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0033621118
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The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme
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An understanding of protein stabilization and cooperativity in terms of a native-state ensemble provides new insights into protein function. Here the author shows how binding to one region of a protein can have significant effects on the stability and cooperativity of the rest of the protein. The ability to predict these effects can provide a route to designing non-competitive inhibitors.
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Freire E. The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc Natl Acad Sci USA. 96:1999;10118-10122. An understanding of protein stabilization and cooperativity in terms of a native-state ensemble provides new insights into protein function. Here the author shows how binding to one region of a protein can have significant effects on the stability and cooperativity of the rest of the protein. The ability to predict these effects can provide a route to designing non-competitive inhibitors.
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(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 10118-10122
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Freire, E.1
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34
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0029968247
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Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies
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Williams D.C., Benjamin D.C., Poljak R.J., Rule G.S. Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies. J Mol Biol. 257:1996;866-876.
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J Mol Biol
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Williams, D.C.1
Benjamin, D.C.2
Poljak, R.J.3
Rule, G.S.4
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35
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0032561137
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The structural stability of the HIV-1 protease
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Todd M., Semo N., Freire E. The structural stability of the HIV-1 protease. J Mol Biol. 283:1998;475-488.
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(1998)
J Mol Biol
, vol.283
, pp. 475-488
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Todd, M.1
Semo, N.2
Freire, E.3
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36
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0033181015
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The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease
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Todd M.J., Freire E. The effect of inhibitor binding on the structural stability and cooperativity of the HIV-1 protease. Proteins. 36:1999;147-156.
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(1999)
Proteins
, vol.36
, pp. 147-156
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Todd, M.J.1
Freire, E.2
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37
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0032318864
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Structure-based prediction of binding affinities and molecular design of peptide ligands
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Luque I., Freire E. Structure-based prediction of binding affinities and molecular design of peptide ligands. Methods Enzymol. 295:1998;100-127.
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(1998)
Methods Enzymol
, vol.295
, pp. 100-127
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Luque, I.1
Freire, E.2
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38
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0040321024
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Experimental measurement of the effective dielectric in the hydrophobic core of a protein
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Garcia-Moreno B., Dwyer J.J., Gittis A.G., Lattman E.E., Spencer D.S., Stites W.E. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys J. 64:1997;211-224.
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, pp. 211-224
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Garcia-Moreno, B.1
Dwyer, J.J.2
Gittis, A.G.3
Lattman, E.E.4
Spencer, D.S.5
Stites, W.E.6
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39
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23444450909
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Coupling of local folding to site-specific binding of proteins to DNA
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Spolar R.S., Record M.T. Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784.
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, vol.263
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Spolar, R.S.1
Record M.T., Jr.2
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40
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0033153360
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Adenine base unstacking dominates the observed enthalpy and heat capacity changes for the Escherichia coli SSB tetramer binding to single-stranded oligoadenylates
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Kozlov A.G., Lohman T.M. Adenine base unstacking dominates the observed enthalpy and heat capacity changes for the Escherichia coli SSB tetramer binding to single-stranded oligoadenylates. Biochemistry. 38:1999;7388-7397.
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Biochemistry
, vol.38
, pp. 7388-7397
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Kozlov, A.G.1
Lohman, T.M.2
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41
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0032577337
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The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic Archaeon
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O'Brien R., DeDecker B., Fleming K.G., Sigler P.B. The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic Archaeon. J Mol Biol. 279:1998;117-125.
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(1998)
J Mol Biol
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, pp. 117-125
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O'Brien, R.1
Dedecker, B.2
Fleming, K.G.3
Sigler, P.B.4
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42
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0040040750
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Structural bases of lectin-carbohydrate affinities: Comparison with protein-folding energetics
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The application of structural energetics to systems containing functional groups that are either unrepresented or under-represented in proteins can require the development of new parameters. Here the authors look at the differences between protein folding and protein-carbohydrate interactions.
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Garcia-Hernandez E., Hernandez-Arana A. Structural bases of lectin-carbohydrate affinities: comparison with protein-folding energetics. Protein Sci. 8:1999;1075-1086. The application of structural energetics to systems containing functional groups that are either unrepresented or under-represented in proteins can require the development of new parameters. Here the authors look at the differences between protein folding and protein-carbohydrate interactions.
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(1999)
Protein Sci
, vol.8
, pp. 1075-1086
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Garcia-Hernandez, E.1
Hernandez-Arana, A.2
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43
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0026344361
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Solid model compounds and the thermodynamics of protein unfolding
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Murphy K.P., Gill S.J. Solid model compounds and the thermodynamics of protein unfolding. J Mol Biol. 222:1991;699-709.
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(1991)
J Mol Biol
, vol.222
, pp. 699-709
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Murphy, K.P.1
Gill, S.J.2
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44
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0026327183
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The molecular basis of cooperativity in protein folding
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Freire E., Murphy K.P. The molecular basis of cooperativity in protein folding. J Mol Biol. 222:1991;687-698.
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(1991)
J Mol Biol
, vol.222
, pp. 687-698
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Freire, E.1
Murphy, K.P.2
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