-
1
-
-
0025370815
-
Dominant forces in protein folding
-
Dill K.A. Dominant forces in protein folding. Biochemistry. 29:1990;7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
2
-
-
0024507791
-
Alternative packing arrangements in the hydrophobic core of lambda repressor
-
Lim W.A., Sauer R.T. Alternative packing arrangements in the hydrophobic core of lambda repressor. Nature. 339:1989;31-36.
-
(1989)
Nature
, vol.339
, pp. 31-36
-
-
Lim, W.A.1
Sauer, R.T.2
-
3
-
-
0029980972
-
Active barnase variants with completely random hydrophobic cores
-
Axe D.D., Foster N.W., Fersht A.R. Active barnase variants with completely random hydrophobic cores. Proc. Natl Acad. Sci. USA. 93:1996;5590-5594.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 5590-5594
-
-
Axe, D.D.1
Foster, N.W.2
Fersht, A.R.3
-
4
-
-
0027716138
-
The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme
-
Baldwin E.P., Hajiseyedjavadi O., Baase W.A., Matthews B.W. The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Science. 262:1993;1715-1718.
-
(1993)
Science
, vol.262
, pp. 1715-1718
-
-
Baldwin, E.P.1
Hajiseyedjavadi, O.2
Baase, W.A.3
Matthews, B.W.4
-
5
-
-
0029958604
-
A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme
-
Gassner N.C., Baase W.A., Matthews B.W. A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc. Natl Acad. Sci. USA. 93:1996;12155-12158.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 12155-12158
-
-
Gassner, N.C.1
Baase, W.A.2
Matthews, B.W.3
-
6
-
-
0033533387
-
Core-directed protein design. II. Rescue of a multiply mutated and destabilized variant of ubiquitin
-
Finucane M.D., Woolfson D.N. Core-directed protein design. II. Rescue of a multiply mutated and destabilized variant of ubiquitin. Biochemistry. 38:1999;11613-11623.
-
(1999)
Biochemistry
, vol.38
, pp. 11613-11623
-
-
Finucane, M.D.1
Woolfson, D.N.2
-
8
-
-
0032254437
-
Hydrophobic core packing and protein design
-
Lazar G.A., Handel T.M. Hydrophobic core packing and protein design. Curr. Opin. Chem. Biol. 2:1998;675-679.
-
(1998)
Curr. Opin. Chem. Biol.
, vol.2
, pp. 675-679
-
-
Lazar, G.A.1
Handel, T.M.2
-
9
-
-
0030987610
-
Probing the role of packing specificity in protein design
-
Dahiyat B.I., Mayo S.L. Probing the role of packing specificity in protein design. Proc. Natl Acad. Sci. USA. 94:1997;10172-10177.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 10172-10177
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
10
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA. 97:2000;10383-10388.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
11
-
-
0031893269
-
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
-
Xu J., Baase W.A., Baldwin E., Matthews B.W. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci. 7:1998;158-177.
-
(1998)
Protein Sci.
, vol.7
, pp. 158-177
-
-
Xu, J.1
Baase, W.A.2
Baldwin, E.3
Matthews, B.W.4
-
12
-
-
0033555677
-
A correlation between the loss of hydrophobic core packing interactions and protein stability
-
Vlassi M., Cesareni G., Kokkinidis M. A correlation between the loss of hydrophobic core packing interactions and protein stability. J. Mol. Biol. 285:1999;817-827.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 817-827
-
-
Vlassi, M.1
Cesareni, G.2
Kokkinidis, M.3
-
13
-
-
0034633945
-
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics
-
Ratnaparkhi G.S., Varadarajan R. Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics. Biochemistry. 39:2000;12365-12374.
-
(2000)
Biochemistry
, vol.39
, pp. 12365-12374
-
-
Ratnaparkhi, G.S.1
Varadarajan, R.2
-
14
-
-
0034142174
-
Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations
-
Kono H., Saito M., Sarai A. Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations. Proteins: Struct. Funct. Genet. 38:2000;197-209.
-
(2000)
Proteins: Struct. Funct. Genet.
, vol.38
, pp. 197-209
-
-
Kono, H.1
Saito, M.2
Sarai, A.3
-
15
-
-
0037200114
-
A procedure for detection and quantitation of cavity volumes in proteins. Application to measure the strength of the hydrophobic driving force in protein folding
-
Chakravarty S., Bhinge A., Varadarajan R. A procedure for detection and quantitation of cavity volumes in proteins. Application to measure the strength of the hydrophobic driving force in protein folding. J. Biol. Chem. 277:2002;31345-31353.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 31345-31353
-
-
Chakravarty, S.1
Bhinge, A.2
Varadarajan, R.3
-
16
-
-
0034614649
-
The introduction of strain and its effects on the structure and stability of T4 lysozyme
-
Liu R., Baase W.A., Matthews B.W. The introduction of strain and its effects on the structure and stability of T4 lysozyme. J. Mol. Biol. 295:2000;127-145.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 127-145
-
-
Liu, R.1
Baase, W.A.2
Matthews, B.W.3
-
17
-
-
0026567907
-
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
-
Eriksson A.E., Baase W.A., Zhang X.J., Heinz D.W., Blaber M., Baldwin E.P., Matthews B.W. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 255:1992;178-183.
-
(1992)
Science
, vol.255
, pp. 178-183
-
-
Eriksson, A.E.1
Baase, W.A.2
Zhang, X.J.3
Heinz, D.W.4
Blaber, M.5
Baldwin, E.P.6
Matthews, B.W.7
-
18
-
-
0032574698
-
Context-dependent nature of destabilizing mutations on the stability of FKBP12
-
Main E.R., Fulton K.F., Jackson S.E. Context-dependent nature of destabilizing mutations on the stability of FKBP12. Biochemistry. 37:1998;6145-6153.
-
(1998)
Biochemistry
, vol.37
, pp. 6145-6153
-
-
Main, E.R.1
Fulton, K.F.2
Jackson, S.E.3
-
19
-
-
0034703474
-
Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability
-
Cota E., Hamill S.J., Fowler S.B., Clarke J. Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability. J. Mol. Biol. 302:2000;713-725.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 713-725
-
-
Cota, E.1
Hamill, S.J.2
Fowler, S.B.3
Clarke, J.4
-
20
-
-
0035909809
-
Packing is a key selection factor in the evolution of protein hydrophobic cores
-
Chen J., Stites W.E. Packing is a key selection factor in the evolution of protein hydrophobic cores. Biochemistry. 40:2001;15280-15289.
-
(2001)
Biochemistry
, vol.40
, pp. 15280-15289
-
-
Chen, J.1
Stites, W.E.2
-
21
-
-
0032692339
-
Conserved structural features and sequence patterns in the GroES fold family
-
Taneja B., Mande S.C. Conserved structural features and sequence patterns in the GroES fold family. Protein Eng. 12:1999;815-818.
-
(1999)
Protein Eng.
, vol.12
, pp. 815-818
-
-
Taneja, B.1
Mande, S.C.2
-
22
-
-
0032773506
-
The immunoglobulin fold family: Sequence analysis and 3D structure comparisons
-
Halaby D.M., Poupon A., Mornon J. The immunoglobulin fold family: sequence analysis and 3D structure comparisons. Protein Eng. 12:1999;563-571.
-
(1999)
Protein Eng.
, vol.12
, pp. 563-571
-
-
Halaby, D.M.1
Poupon, A.2
Mornon, J.3
-
23
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey J.G., Di Nardo A.A., Davidson A.R. Hydrophobic core packing in the SH3 domain folding transition state. Nature Struct. Biol. 9:2002;126-130.
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 126-130
-
-
Northey, J.G.1
Di Nardo, A.A.2
Davidson, A.R.3
-
24
-
-
0034486070
-
The identification of conserved interactions within the SH3 domain by alignment of sequences and structures
-
Larson S.M., Davidson A.R. The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci. 9:2000;2170-2180.
-
(2000)
Protein Sci.
, vol.9
, pp. 2170-2180
-
-
Larson, S.M.1
Davidson, A.R.2
-
25
-
-
0032542018
-
Mutagenesis of a buried polar interaction in an SH3 domain: Sequence conservation provides the best prediction of stability effects
-
Maxwell K.L., Davidson A.R. Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects. Biochemistry. 37:1998;16172-16182.
-
(1998)
Biochemistry
, vol.37
, pp. 16172-16182
-
-
Maxwell, K.L.1
Davidson, A.R.2
-
26
-
-
0028331876
-
Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition
-
Viguera A.R., Martinez J.C., Filimonov V.V., Mateo P.L., Serrano L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry. 33:1994;2142-2150.
-
(1994)
Biochemistry
, vol.33
, pp. 2142-2150
-
-
Viguera, A.R.1
Martinez, J.C.2
Filimonov, V.V.3
Mateo, P.L.4
Serrano, L.5
-
27
-
-
0032562182
-
The folding kinetics and thermodynamics of the Fyn-SH3 domain
-
Plaxco K.W., Guijarro J.I., Morton C.J., Pitkeathly M., Campbell I.D., Dobson C.M. The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry. 37:1998;2529-2537.
-
(1998)
Biochemistry
, vol.37
, pp. 2529-2537
-
-
Plaxco, K.W.1
Guijarro, J.I.2
Morton, C.J.3
Pitkeathly, M.4
Campbell, I.D.5
Dobson, C.M.6
-
28
-
-
0031444104
-
Folding dynamics of the src SH3 domain
-
Grantcharova V.P., Baker D. Folding dynamics of the src SH3 domain. Biochemistry. 36:1997;15685-15692.
-
(1997)
Biochemistry
, vol.36
, pp. 15685-15692
-
-
Grantcharova, V.P.1
Baker, D.2
-
29
-
-
0031418201
-
SH3 domains and drug design: Ligands, structure, and biological function
-
Dalgarno D.C., Botfield M.C., Rickles R.J. SH3 domains and drug design: ligands, structure, and biological function. Biopolymers. 43:1997;383-400.
-
(1997)
Biopolymers
, vol.43
, pp. 383-400
-
-
Dalgarno, D.C.1
Botfield, M.C.2
Rickles, R.J.3
-
30
-
-
0032560623
-
Hydrophobic core substitutions in calbindin D9k: Effects on stability and structure
-
Julenius K., Thulin E., Linse S., Finn B.E. Hydrophobic core substitutions in calbindin D9k: effects on stability and structure. Biochemistry. 37:1998;8915-8925.
-
(1998)
Biochemistry
, vol.37
, pp. 8915-8925
-
-
Julenius, K.1
Thulin, E.2
Linse, S.3
Finn, B.E.4
-
31
-
-
0036266942
-
Conformational strain in the hydrophobic core and its implications for protein folding and design
-
Ventura S., Vega M.C., Lacroix E., Angrand I., Spagnolo L., Serrano L. Conformational strain in the hydrophobic core and its implications for protein folding and design. Nature Struct. Biol. 9:2002;485-493.
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 485-493
-
-
Ventura, S.1
Vega, M.C.2
Lacroix, E.3
Angrand, I.4
Spagnolo, L.5
Serrano, L.6
-
32
-
-
0002940127
-
The molten globule state
-
T.E. Creighton. New York: W. H. Freeman and Co
-
Ptitsyn O.B. The molten globule state. Creighton T.E. Protein Folding. 1992;243-300 W. H. Freeman and Co, New York.
-
(1992)
Protein Folding
, pp. 243-300
-
-
Ptitsyn, O.B.1
-
33
-
-
0033546123
-
NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions
-
Mok Y.K., Kay C.M., Kay L.E., Forman-Kay J. NOE data demonstrating a compact unfolded state for an SH3 domain under non-denaturing conditions. J. Mol. Biol. 289:1999;619-638.
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 619-638
-
-
Mok, Y.K.1
Kay, C.M.2
Kay, L.E.3
Forman-Kay, J.4
-
34
-
-
0034646562
-
Similarities between the spectrin SH3 domain denatured state and its folding transition state
-
Kortemme T., Kelly M.J., Kay L.E., Forman-Kay J., Serrano L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J. Mol. Biol. 297:2000;1217-1229.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 1217-1229
-
-
Kortemme, T.1
Kelly, M.J.2
Kay, L.E.3
Forman-Kay, J.4
Serrano, L.5
-
35
-
-
0028811162
-
Phage display selection of ligand residues important for Src homology 3 domain binding specificity
-
Rickles R.J., Botfield M.C., Zhou X.M., Henry P.A., Brugge J.S., Zoller M.J. Phage display selection of ligand residues important for Src homology 3 domain binding specificity. Proc. Natl Acad. Sci. USA. 92:1995;10909-10913.
-
(1995)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 10909-10913
-
-
Rickles, R.J.1
Botfield, M.C.2
Zhou, X.M.3
Henry, P.A.4
Brugge, J.S.5
Zoller, M.J.6
-
36
-
-
0034721944
-
Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
-
Larson S.M., Di Nardo A.A., Davidson A.R. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303:2000;433-446.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 433-446
-
-
Larson, S.M.1
Di Nardo, A.A.2
Davidson, A.R.3
-
37
-
-
0028147533
-
The crystal structure of a mutant protein with altered but improved hydrophobic core packing
-
Lim W.A., Hodel A., Sauer R.T., Richards F.M. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc. Natl Acad. Sci. USA. 91:1994;423-427.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 423-427
-
-
Lim, W.A.1
Hodel, A.2
Sauer, R.T.3
Richards, F.M.4
-
38
-
-
0345062357
-
Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
-
Mirny L.A., Shakhnovich E.I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291:1999;177-196.
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 177-196
-
-
Mirny, L.A.1
Shakhnovich, E.I.2
-
39
-
-
0035957514
-
Evolutionary conservation of the folding nucleus
-
Mirny L., Shakhnovich E. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308:2001;123-129.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 123-129
-
-
Mirny, L.1
Shakhnovich, E.2
-
40
-
-
0034724558
-
Evolutionary conservation in protein folding kinetics
-
Plaxco K.W., Larson S., Ruczinski I., Riddle D.S., Thayer E.C., Buchwitz B., et al. Evolutionary conservation in protein folding kinetics. J. Mol. Biol. 298:2000;303-312.
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 303-312
-
-
Plaxco, K.W.1
Larson, S.2
Ruczinski, I.3
Riddle, D.S.4
Thayer, E.C.5
Buchwitz, B.6
-
41
-
-
0036295887
-
Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation
-
Larson S.M., Ruczinski I., Davidson A.R., Baker D., Plaxco K.W. Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. J. Mol. Biol. 316:2002;225-233.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 225-233
-
-
Larson, S.M.1
Ruczinski, I.2
Davidson, A.R.3
Baker, D.4
Plaxco, K.W.5
-
42
-
-
0034595515
-
Protein packing: Dependence on protein size, secondary structure and amino acid composition
-
Fleming P.J., Richards F.M. Protein packing: dependence on protein size, secondary structure and amino acid composition. J. Mol. Biol. 299:2000;487-498.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 487-498
-
-
Fleming, P.J.1
Richards, F.M.2
-
43
-
-
0032525298
-
Thermal unfolding of small proteins with SH3 domain folding pattern
-
Knapp S., Mattson P.T., Christova P., Berndt K.D., Karshikoff A., Vihinen M., et al. Thermal unfolding of small proteins with SH3 domain folding pattern. Proteins: Struct. Funct. Genet. 31:1998;309-319.
-
(1998)
Proteins: Struct. Funct. Genet.
, vol.31
, pp. 309-319
-
-
Knapp, S.1
Mattson, P.T.2
Christova, P.3
Berndt, K.D.4
Karshikoff, A.5
Vihinen, M.6
-
44
-
-
0033045105
-
A thermodynamic analysis of a family of small globular proteins: SH3 domains
-
Filimonov V.V., Azuaga A.I., Viguera A.R., Serrano L., Mateo P.L. A thermodynamic analysis of a family of small globular proteins: SH3 domains. Biophys. Chem. 77:1999;195-208.
-
(1999)
Biophys. Chem.
, vol.77
, pp. 195-208
-
-
Filimonov, V.V.1
Azuaga, A.I.2
Viguera, A.R.3
Serrano, L.4
Mateo, P.L.5
-
45
-
-
0029760326
-
Different folding transition states may result in the same native structure
-
Viguera A.R., Serrano L., Wilmanns M. Different folding transition states may result in the same native structure. Nature Struct. Biol. 3:1996;874-880.
-
(1996)
Nature Struct. Biol.
, vol.3
, pp. 874-880
-
-
Viguera, A.R.1
Serrano, L.2
Wilmanns, M.3
-
46
-
-
0031853167
-
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
-
Grantcharova V.P., Riddle D.S., Santiago J.V., Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature Struct. Biol. 5:1998;714-720.
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 714-720
-
-
Grantcharova, V.P.1
Riddle, D.S.2
Santiago, J.V.3
Baker, D.4
-
47
-
-
0025005525
-
Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease
-
Shortle D., Stites W.E., Meeker A.K. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry. 29:1990;8033-8041.
-
(1990)
Biochemistry
, vol.29
, pp. 8033-8041
-
-
Shortle, D.1
Stites, W.E.2
Meeker, A.K.3
-
48
-
-
0026553768
-
The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
-
Serrano L., Kellis J.T. Jr, Cann P., Matouschek A., Fersht A.R. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224:1992;783-804.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 783-804
-
-
Serrano, L.1
Kellis J.T., Jr.2
Cann, P.3
Matouschek, A.4
Fersht, A.R.5
-
49
-
-
0024498471
-
A new method for determining the heat capacity change for protein folding
-
Pace C.N., Laurents D.V. A new method for determining the heat capacity change for protein folding. Biochemistry. 28:1989;2520-2525.
-
(1989)
Biochemistry
, vol.28
, pp. 2520-2525
-
-
Pace, C.N.1
Laurents, D.V.2
-
50
-
-
0000484499
-
Hydrophobic parameters of amino acid side chains from the partitioning of N-acetyl-amino acid amides
-
Fauchere J.L., Pliska V. Hydrophobic parameters of amino acid side chains from the partitioning of N-acetyl-amino acid amides. Eur. J. Med. Chem. 18:1983;369-375.
-
(1983)
Eur. J. Med. Chem.
, vol.18
, pp. 369-375
-
-
Fauchere, J.L.1
Pliska, V.2
|