-
1
-
-
0030059689
-
Forces contributing to the conformational stability of proteins
-
Pace CN, Shirley BA, McNutt M, Gajiwala K. Forces contributing to the conformational stability of proteins. FASEB J 1996;10:75-83.
-
(1996)
FASEB J
, vol.10
, pp. 75-83
-
-
Pace, C.N.1
Shirley, B.A.2
McNutt, M.3
Gajiwala, K.4
-
2
-
-
0018588511
-
Stability of proteins: Small globular proteins
-
Privalov PL. Stability of proteins: small globular proteins. Adv Protein Chem 1979;33:167-241.
-
(1979)
Adv Protein Chem
, vol.33
, pp. 167-241
-
-
Privalov, P.L.1
-
3
-
-
0025370815
-
Dominant forces in protein folding
-
Dill KA. Dominant forces in protein folding. Biochemistry 1990;29:7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
4
-
-
0023368698
-
Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit
-
Yutani K, Ogasahara K, Tsujita T, Sugino Y. Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit. Proc Natl Acad Sci USA 1987;84:4441-4444.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 4441-4444
-
-
Yutani, K.1
Ogasahara, K.2
Tsujita, T.3
Sugino, Y.4
-
5
-
-
0023741058
-
Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile-3
-
Matsumura M, Becktel WJ, Matthews BW. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile-3. Nature 1988;334:406-410.
-
(1988)
Nature
, vol.334
, pp. 406-410
-
-
Matsumura, M.1
Becktel, W.J.2
Matthews, B.W.3
-
6
-
-
0024375463
-
Energetics of complementary side-chain packing in a protein hydrophobic core
-
Kellis JT, Nyberg K, Fersht AR. Energetics of complementary side-chain packing in a protein hydrophobic core. Biochemistry 1989;28:4914-4922.
-
(1989)
Biochemistry
, vol.28
, pp. 4914-4922
-
-
Kellis, J.T.1
Nyberg, K.2
Fersht, A.R.3
-
7
-
-
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
-
8
-
-
0026553768
-
The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
-
Serrano L, Kellis JT, Cann P, Matouschek A, Fersht AR. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability J Mol Biol 1992;224:783-804.
-
(1992)
J Mol Biol
, vol.224
, pp. 783-804
-
-
Serrano, L.1
Kellis, J.T.2
Cann, P.3
Matouschek, A.4
Fersht, A.R.5
-
9
-
-
0027016842
-
Dissection of protein structure and folding by directed mutagenesis
-
Baase WA, Eriksson AE, Zhang XJ, Heinz DW, Sauer U, Blaber M, Baldwin EP, Wozniak JA, Matthews BW. Dissection of protein structure and folding by directed mutagenesis. Faraday Discuss 1992;93:173-181.
-
(1992)
Faraday Discuss
, vol.93
, pp. 173-181
-
-
Baase, W.A.1
Eriksson, A.E.2
Zhang, X.J.3
Heinz, D.W.4
Sauer, U.5
Blaber, M.6
Baldwin, E.P.7
Wozniak, J.A.8
Matthews, B.W.9
-
10
-
-
0026567907
-
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
-
Eriksson AE, Baase WA, Zhang XJ, Heinz DW, Blaber M, Baldwin EP, Matthews BW. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 1992;255:178-183.
-
(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
-
11
-
-
0031050618
-
Contribution of the hydrophobic effect to the stability of human lysozyme: Calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants
-
Takano K, Yamagata Y, Fujii S, Yutani K. Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants. Biochemistry 1997;36:688-698.
-
(1997)
Biochemistry
, vol.36
, pp. 688-698
-
-
Takano, K.1
Yamagata, Y.2
Fujii, S.3
Yutani, K.4
-
12
-
-
0031893269
-
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
-
Xu J, Baase WA, Baldwin E, Matthews BW. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci 1998;7:158-177.
-
(1998)
Protein Sci
, vol.7
, pp. 158-177
-
-
Xu, J.1
Baase, W.A.2
Baldwin, E.3
Matthews, B.W.4
-
13
-
-
0035923433
-
Energetics of side chain packing in staphylococcal nuclease assessed by systematic double mutant cycles
-
Chen J, Stites WE. Energetics of side chain packing in staphylococcal nuclease assessed by systematic double mutant cycles. Biochemistry 2001;40:14004-14011.
-
(2001)
Biochemistry
, vol.40
, pp. 14004-14011
-
-
Chen, J.1
Stites, W.E.2
-
14
-
-
0035923436
-
Energetics of side chain packing in staphylococcal nuclease assessed by exchange of valines, isoleucines, and leucines
-
Holder JB, Bennett AF, Chen J, Spencer DS, Byrne MP, Stites WE. Energetics of side chain packing in staphylococcal nuclease assessed by exchange of valines, isoleucines, and leucines. Biochemistry 2001;40:13998-14003.
-
(2001)
Biochemistry
, vol.40
, pp. 13998-14003
-
-
Holder, J.B.1
Bennett, A.F.2
Chen, J.3
Spencer, D.S.4
Byrne, M.P.5
Stites, W.E.6
-
15
-
-
0036137007
-
A cavity-forming mutation in insulin induces segmental unfolding of a surrounding α-helix
-
Xu B, Hua QX, Nakagawa SH, Jia W, Chu YC, Katsoyannis PG, Weiss MA. A cavity-forming mutation in insulin induces segmental unfolding of a surrounding α-helix. Protein Sci 2002;11:104-116.
-
(2002)
Protein Sci
, vol.11
, pp. 104-116
-
-
Xu, B.1
Hua, Q.X.2
Nakagawa, S.H.3
Jia, W.4
Chu, Y.C.5
Katsoyannis, P.G.6
Weiss, M.A.7
-
17
-
-
0346458811
-
N-H·O, O-H·O, and C-H·O hydrogen bonds in protein-ligand complexes: Strong and weak interactions in molecular recognition
-
Sarkhel S, Desiraju GR. N-H·O, O-H·O, and C-H·O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition. Proteins 2004;54:247-259.
-
(2004)
Proteins
, vol.54
, pp. 247-259
-
-
Sarkhel, S.1
Desiraju, G.R.2
-
18
-
-
0028808533
-
Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease
-
Byrne MP, Manuel RL, Lowe LG, Stites WE. Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease. Biochemistry 1995;34:13949-13960.
-
(1995)
Biochemistry
, vol.34
, pp. 13949-13960
-
-
Byrne, M.P.1
Manuel, R.L.2
Lowe, L.G.3
Stites, W.E.4
-
19
-
-
0029843132
-
Hydrogen bonding stabilizes globular proteins
-
Myers JK, Pace CN. Hydrogen bonding stabilizes globular proteins. Biophys J 1996;71:2033-2039.
-
(1996)
Biophys J
, vol.71
, pp. 2033-2039
-
-
Myers, J.K.1
Pace, C.N.2
-
20
-
-
0035895356
-
Polar group burial contributes more to protein stability than nonpolar group burial
-
Pace CN. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry 2001;40:310-313.
-
(2001)
Biochemistry
, vol.40
, pp. 310-313
-
-
Pace, C.N.1
-
21
-
-
0028929583
-
Free energy balance in protein folding
-
Honig B, Yang AS. Free energy balance in protein folding. Adv Protein Chem 1995;46:27-58.
-
(1995)
Adv Protein Chem
, vol.46
, pp. 27-58
-
-
Honig, B.1
Yang, A.S.2
-
22
-
-
0029094346
-
Enthalpic contribution to protein stability: Insights from atom-based calculations and statistical mechanics
-
Lazaridis T, Archontis G, Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Adv Protein Chem 1995;47:231-306.
-
(1995)
Adv Protein Chem
, vol.47
, pp. 231-306
-
-
Lazaridis, T.1
Archontis, G.2
Karplus, M.3
-
23
-
-
0030342727
-
Helmholtz free energies of atom pair interactions in proteins
-
Sippl MJ, Ortner M, Jaritz M, Lackner P, Flockner H. Helmholtz free energies of atom pair interactions in proteins. Fold Des 1996;1:289-298.
-
(1996)
Fold Des
, vol.1
, pp. 289-298
-
-
Sippl, M.J.1
Ortner, M.2
Jaritz, M.3
Lackner, P.4
Flockner, H.5
-
24
-
-
21244467453
-
A double-deletion method to quantifying incremental binding energies in proteins from experiment. Example of a destabilizing hydrogen bonding pair
-
Campos LA, Cuesta-Lopez S, Lopez-Llano J, Falo F, Sancho J. A double-deletion method to quantifying incremental binding energies in proteins from experiment. Example of a destabilizing hydrogen bonding pair. Biophys J 2004;88:1311-1321.
-
(2004)
Biophys J
, vol.88
, pp. 1311-1321
-
-
Campos, L.A.1
Cuesta-Lopez, S.2
Lopez-Llano, J.3
Falo, F.4
Sancho, J.5
-
25
-
-
22244449669
-
Do all backbone polar groups in proteins form hydrogen bonds?
-
Fleming PJ, Rose GD. Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci 2005;14:1911-1917.
-
(2005)
Protein Sci
, vol.14
, pp. 1911-1917
-
-
Fleming, P.J.1
Rose, G.D.2
-
26
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000;10:139-145.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
27
-
-
0030777760
-
Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
-
Gilis D, Rooman M. Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J Mol Biol 1997;272:276-290.
-
(1997)
J Mol Biol
, vol.272
, pp. 276-290
-
-
Gilis, D.1
Rooman, M.2
-
28
-
-
0036948069
-
PoPMuSiC, rationally designing point mutations in protein structures
-
Kwasigroch JM, Gilis D, Dehouck Y, Rooman M. PoPMuSiC, rationally designing point mutations in protein structures. Bioinformatics 2002;18:1701-1702.
-
(2002)
Bioinformatics
, vol.18
, pp. 1701-1702
-
-
Kwasigroch, J.M.1
Gilis, D.2
Dehouck, Y.3
Rooman, M.4
-
29
-
-
25844482592
-
Prediction of protein thermostability with a direction-and distance-dependent knowledge-based potential
-
Hoppe C, Schomburg D. Prediction of protein thermostability with a direction-and distance-dependent knowledge-based potential. Protein Sci 2005;14:2682-2692.
-
(2005)
Protein Sci
, vol.14
, pp. 2682-2692
-
-
Hoppe, C.1
Schomburg, D.2
-
30
-
-
0025787845
-
Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the Ile-96 - Ala mutation in barnase
-
Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96 - Ala mutation in barnase. Proc Natl Acad Sci USA 1991;88:10880-10884.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 10880-10884
-
-
Prevost, M.1
Wodak, S.J.2
Tidor, B.3
Karplus, M.4
-
31
-
-
0034669841
-
Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides
-
Pitera JW, Kollman PA. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins 2000;41:385-397.
-
(2000)
Proteins
, vol.41
, pp. 385-397
-
-
Pitera, J.W.1
Kollman, P.A.2
-
32
-
-
0035037981
-
Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins?
-
Funahashi J, Takano K, Yutani K. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins? Protein Eng 2001;14:127-134.
-
(2001)
Protein Eng
, vol.14
, pp. 127-134
-
-
Funahashi, J.1
Takano, K.2
Yutani, K.3
-
33
-
-
3242879771
-
Computational alanine scanning of protein-protein interfaces
-
Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Sci STKE 2004;(219): p 12.
-
(2004)
Sci STKE
, vol.219
, pp. 12
-
-
Kortemme, T.1
Kim, D.E.2
Baker, D.3
-
35
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
36
-
-
23044487169
-
Statistical analysis and prediction of protein-protein interfaces
-
Bordner AJ, Abagyan R. Statistical analysis and prediction of protein-protein interfaces. Proteins 2005;60:353-366.
-
(2005)
Proteins
, vol.60
, pp. 353-366
-
-
Bordner, A.J.1
Abagyan, R.2
-
37
-
-
23144461249
-
I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure
-
Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 2005;33:W306-W310.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Capriotti, E.1
Fariselli, P.2
Casadio, R.3
-
38
-
-
11844281294
-
A neural-network-based method for predicting protein stability changes upon single point mutations
-
Capriotti E, Fariselli P, Casadio R. A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics 2004;20(Suppl. 1):163-168.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
, pp. 163-168
-
-
Capriotti, E.1
Fariselli, P.2
Casadio, R.3
-
39
-
-
0029414725
-
Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments
-
Vajda S, Weng Z, DeLisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Eng 1995;8:1081-1092.
-
(1995)
Protein Eng
, vol.8
, pp. 1081-1092
-
-
Vajda, S.1
Weng, Z.2
DeLisi, C.3
-
40
-
-
0036893044
-
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
-
Zhou H, Zhou Y. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins 2002;49:483-492.
-
(2002)
Proteins
, vol.49
, pp. 483-492
-
-
Zhou, H.1
Zhou, Y.2
-
41
-
-
0024362070
-
On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5
-
Novotny J, Bruccoleri RE, Saul FA. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry 1989;28:4735-4749.
-
(1989)
Biochemistry
, vol.28
, pp. 4735-4749
-
-
Novotny, J.1
Bruccoleri, R.E.2
Saul, F.A.3
-
42
-
-
0012227656
-
A comprehensive analytical treatment of continuum electrostatics
-
Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 1996;100:1578-1599.
-
(1996)
J Phys Chem
, vol.100
, pp. 1578-1599
-
-
Schaefer, M.1
Karplus, M.2
-
43
-
-
0032484151
-
Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
-
Schaefer M, Bartels C, Karplus M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol 1998;284:835-848.
-
(1998)
J Mol Biol
, vol.284
, pp. 835-848
-
-
Schaefer, M.1
Bartels, C.2
Karplus, M.3
-
44
-
-
0027058608
-
Residue solvent accessibilities in the unfolded polypeptide chain
-
Zielenkiewicz P, Saenger W. Residue solvent accessibilities in the unfolded polypeptide chain. Biophys J 1992;63:1483-1486.
-
(1992)
Biophys J
, vol.63
, pp. 1483-1486
-
-
Zielenkiewicz, P.1
Saenger, W.2
-
45
-
-
0025912338
-
Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors
-
Hubbard SJ, Campbell SF, Thornton JM. Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol 1991;220:507-530.
-
(1991)
J Mol Biol
, vol.220
, pp. 507-530
-
-
Hubbard, S.J.1
Campbell, S.F.2
Thornton, J.M.3
-
46
-
-
0343274684
-
Solvation: How to obtain microscopic energies from partitioning and solvation experiments
-
Chan HS, Dill KA. Solvation: how to obtain microscopic energies from partitioning and solvation experiments. Annu Rev Biophys Biomol Struct 1997;26:425-459.
-
(1997)
Annu Rev Biophys Biomol Struct
, vol.26
, pp. 425-459
-
-
Chan, H.S.1
Dill, K.A.2
-
47
-
-
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
-
48
-
-
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
-
49
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
50
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimisation, and dynamics calculations
-
Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimisation, and dynamics calculations. J Comp Chem 1983;4:187-217.
-
(1983)
J Comp Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
51
-
-
0032773941
-
Role of structural and sequence information in the prediction of protein stability changes: Comparison between buried and partially buried mutations
-
Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A. Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations. Protein Eng 1999;12:549-555.
-
(1999)
Protein Eng
, vol.12
, pp. 549-555
-
-
Gromiha, M.M.1
Oobatake, M.2
Kono, H.3
Uedaira, H.4
Sarai, A.5
-
52
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJ, Meyer EE, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer, E.E.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
53
-
-
0033976585
-
-
Gromiha MM, An J, Kono H, Oobatake M, Uedaira H, Prabakaran P, Sarai A. ProTherm, version 2.0: thermodynamic database for proteins and mutants. Nucleic Acids Res 2000;28:283-285.
-
Gromiha MM, An J, Kono H, Oobatake M, Uedaira H, Prabakaran P, Sarai A. ProTherm, version 2.0: thermodynamic database for proteins and mutants. Nucleic Acids Res 2000;28:283-285.
-
-
-
-
54
-
-
33746322440
-
Do proteins with similar folds have similar transition state structures? A diffuse transition state of the 169 residue apoflavodoxin
-
Bueno M, Ayuso-Tejedor S, Sancho J. Do proteins with similar folds have similar transition state structures? A diffuse transition state of the 169 residue apoflavodoxin. J Mol Biol 2006;359:813-824.
-
(2006)
J Mol Biol
, vol.359
, pp. 813-824
-
-
Bueno, M.1
Ayuso-Tejedor, S.2
Sancho, J.3
-
55
-
-
0028485627
-
Protein stability effects of a complete set of alanine substitutions in Arc repressor
-
Milla ME, Brown BM, Sauer RT. Protein stability effects of a complete set of alanine substitutions in Arc repressor. Nat Struct Biol 1994;1:518-523.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 518-523
-
-
Milla, M.E.1
Brown, B.M.2
Sauer, R.T.3
-
56
-
-
0027383834
-
Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease
-
Green SM, Shortle D. Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease. Biochemistry 1993;32:10131-10139.
-
(1993)
Biochemistry
, vol.32
, pp. 10131-10139
-
-
Green, S.M.1
Shortle, D.2
-
57
-
-
0034692882
-
Towards understanding a molecular switch mechanism: Thermodynamic and crystallographic studies of the signal transduction protein CheY
-
Sola M, Lopez-Hernandez E, Cronet P, Lacroix E, Serrano L, Coll M, Parraga A. Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY. J Mol Biol 2000;303:213-225.
-
(2000)
J Mol Biol
, vol.303
, pp. 213-225
-
-
Sola, M.1
Lopez-Hernandez, E.2
Cronet, P.3
Lacroix, E.4
Serrano, L.5
Coll, M.6
Parraga, A.7
-
58
-
-
0032574698
-
Context-dependent nature of destabilizing mutations on the stability of FKBP12
-
Main ER, Fulton KF, Jackson SE. Context-dependent nature of destabilizing mutations on the stability of FKBP12. Biochemistry 1998;37:6145-6153.
-
(1998)
Biochemistry
, vol.37
, pp. 6145-6153
-
-
Main, E.R.1
Fulton, K.F.2
Jackson, S.E.3
-
59
-
-
0034703474
-
Two proteins with the same structure respond very differently to mutation: The role of plasticity in protein stability
-
Cota E, Hamill SJ, Fowler SB, Clarke J. Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability. J Mol Biol 2000;302:713-725.
-
(2000)
J Mol Biol
, vol.302
, pp. 713-725
-
-
Cota, E.1
Hamill, S.J.2
Fowler, S.B.3
Clarke, J.4
-
60
-
-
0042360857
-
Energetics of a hydrogen bond (charged and neutral) and of a cation-π interaction in apoflavodoxin
-
Fernandez-Recio J, Romero A, Sancho J. Energetics of a hydrogen bond (charged and neutral) and of a cation-π interaction in apoflavodoxin. J Mol Biol 1999;290:319-330.
-
(1999)
J Mol Biol
, vol.290
, pp. 319-330
-
-
Fernandez-Recio, J.1
Romero, A.2
Sancho, J.3
-
61
-
-
0032560623
-
Hydrophobic core substitutions in calbindin D9k: Effects on stability and structure
-
Julenius K, Thulin E, Linse S, Finn BE. Hydrophobic core substitutions in calbindin D9k: effects on stability and structure. Biochemistry 1998;37:8915-8925.
-
(1998)
Biochemistry
, vol.37
, pp. 8915-8925
-
-
Julenius, K.1
Thulin, E.2
Linse, S.3
Finn, B.E.4
-
62
-
-
0035937261
-
Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1β: Does alteration in buried water play a role?
-
Covalt JC, Roy M, Jennings PA. Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1β: does alteration in buried water play a role? J Mol Biol 2001;307:657-669.
-
(2001)
J Mol Biol
, vol.307
, pp. 657-669
-
-
Covalt, J.C.1
Roy, M.2
Jennings, P.A.3
-
63
-
-
0027261309
-
Inclusion body formation and protein stability in sequence variants of interleukin-1β
-
Chrunyk BA, Evans J, Lillquist J, Young P, Wetzel R. Inclusion body formation and protein stability in sequence variants of interleukin-1β. J Biol Chem 1993;268:18053-18061.
-
(1993)
J Biol Chem
, vol.268
, pp. 18053-18061
-
-
Chrunyk, B.A.1
Evans, J.2
Lillquist, J.3
Young, P.4
Wetzel, R.5
-
64
-
-
0028988431
-
Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy
-
Hammen PK, Scholtz JM, Anderson JW, Waygood EB, Klevit RE. Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy. Protein Sci 1995;4:936-944.
-
(1995)
Protein Sci
, vol.4
, pp. 936-944
-
-
Hammen, P.K.1
Scholtz, J.M.2
Anderson, J.W.3
Waygood, E.B.4
Klevit, R.E.5
-
65
-
-
0024971012
-
Conformational stability and activity of ribonuclease T1 and mutants. Gln25-Lys,Glu58-Ala, and the double mutant
-
Shirley BA, Stanssens P, Steyaert J, Pace CN. Conformational stability and activity of ribonuclease T1 and mutants. Gln25-Lys,Glu58-Ala, and the double mutant. J Biol Chem 1989;264:11621-11625.
-
(1989)
J Biol Chem
, vol.264
, pp. 11621-11625
-
-
Shirley, B.A.1
Stanssens, P.2
Steyaert, J.3
Pace, C.N.4
-
66
-
-
0026755510
-
Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: Evidence for mutational effects on the free energy of the denatured state
-
Green SM, Meeker AK, Shortle D. Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: evidence for mutational effects on the free energy of the denatured state. Biochemistry 1992;31:5717-5728.
-
(1992)
Biochemistry
, vol.31
, pp. 5717-5728
-
-
Green, S.M.1
Meeker, A.K.2
Shortle, D.3
-
67
-
-
0029967068
-
Contributions of the ionizable amino acids to the stability of staphylococcal nuclease
-
Meeker AK, Garcia-Moreno B, Shortle D. Contributions of the ionizable amino acids to the stability of staphylococcal nuclease. Biochemistry 1996;35:6443-6449.
-
(1996)
Biochemistry
, vol.35
, pp. 6443-6449
-
-
Meeker, A.K.1
Garcia-Moreno, B.2
Shortle, D.3
-
68
-
-
0030057477
-
Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues
-
Khorasanizadeh S, Peters ID, Roder H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat Struct Biol 1996;3:193-205.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 193-205
-
-
Khorasanizadeh, S.1
Peters, I.D.2
Roder, H.3
-
69
-
-
0037133530
-
Role of the N-terminal helix I for dimerization and stability of the calcium-binding protein S100B
-
Ferguson PL, Shaw GS. Role of the N-terminal helix I for dimerization and stability of the calcium-binding protein S100B. Biochemistry 2002;41:3637-3646.
-
(2002)
Biochemistry
, vol.41
, pp. 3637-3646
-
-
Ferguson, P.L.1
Shaw, G.S.2
-
71
-
-
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 LS, Otzen DE, Fersht AR. 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 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
-
72
-
-
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
-
73
-
-
0032884925
-
Confirmation of the hierarchical folding of RNase H: A protein engineering study
-
Raschke TM, Kho J, Marqusee S. Confirmation of the hierarchical folding of RNase H: a protein engineering study. Nat Struct Biol 1999;6:825-831.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 825-831
-
-
Raschke, T.M.1
Kho, J.2
Marqusee, S.3
-
74
-
-
0026563455
-
Effect of cavity-modulating mutations on the stability of Escherichia coli ribonuclease HI
-
Kimura S, Oda Y, Nakai T, Katayanagi K, Kitakuni E, Nakai C, Nakamura H, Ikehara M, Kanaya S. Effect of cavity-modulating mutations on the stability of Escherichia coli ribonuclease HI. Eur J Biochem 1992;206:337-343.
-
(1992)
Eur J Biochem
, vol.206
, pp. 337-343
-
-
Kimura, S.1
Oda, Y.2
Nakai, T.3
Katayanagi, K.4
Kitakuni, E.5
Nakai, C.6
Nakamura, H.7
Ikehara, M.8
Kanaya, S.9
-
75
-
-
0015866154
-
Environment and exposure to solvent of protein atoms - lysozyme and insulin
-
Shrake A, Rupley JA. Environment and exposure to solvent of protein atoms - lysozyme and insulin. J Mol Biol 1973;79:351-371.
-
(1973)
J Mol Biol
, vol.79
, pp. 351-371
-
-
Shrake, A.1
Rupley, J.A.2
-
76
-
-
0035814880
-
Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding
-
Pan Y, Daggett V. Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding. Biochemistry 2001;40:2723-2731.
-
(2001)
Biochemistry
, vol.40
, pp. 2723-2731
-
-
Pan, Y.1
Daggett, V.2
-
77
-
-
0022412192
-
Hydrophobicity of amino acid residues in globular proteins
-
Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH. Hydrophobicity of amino acid residues in globular proteins. Science 1985;229:834-838.
-
(1985)
Science
, vol.229
, pp. 834-838
-
-
Rose, G.D.1
Geselowitz, A.R.2
Lesser, G.J.3
Lee, R.H.4
Zehfus, M.H.5
-
79
-
-
0029958659
-
Structure-based thermodynamic scale of α-helix propensities in amino acids
-
Luque I, Mayorga OL, Freire E. Structure-based thermodynamic scale of α-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
-
80
-
-
0029620316
-
Modeling unfolded states of peptides and proteins
-
Creamer TP, Srinivasan R, Rose GD. Modeling unfolded states of peptides and proteins. Biochemistry 1995;34:16245-16250.
-
(1995)
Biochemistry
, vol.34
, pp. 16245-16250
-
-
Creamer, T.P.1
Srinivasan, R.2
Rose, G.D.3
-
81
-
-
0030933329
-
Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
-
Creamer TP, Srinivasan R, Rose GD. Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility Biochemistry 1997;36:2832-2835.
-
(1997)
Biochemistry
, vol.36
, pp. 2832-2835
-
-
Creamer, T.P.1
Srinivasan, R.2
Rose, G.D.3
-
82
-
-
0033529861
-
Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone
-
Street AG, Mayo SL. Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone. Proc Natl Acad Sci USA 1999;96:9074-9076.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 9074-9076
-
-
Street, A.G.1
Mayo, S.L.2
-
83
-
-
0034663581
-
Side-chain conformational entropy in protein unfolded states
-
Creamer TP. Side-chain conformational entropy in protein unfolded states. Proteins 2000;40:443-450.
-
(2000)
Proteins
, vol.40
, pp. 443-450
-
-
Creamer, T.P.1
-
84
-
-
0028343413
-
Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy
-
Koehl P, Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 1994;239:249-275.
-
(1994)
J Mol Biol
, vol.239
, pp. 249-275
-
-
Koehl, P.1
Delarue, M.2
-
85
-
-
0028871798
-
Side-chain conformational entropy in protein folding
-
Doig AJ, Sternberg MJ. Side-chain conformational entropy in protein folding. Protein Sci 1995;4:2247-2251.
-
(1995)
Protein Sci
, vol.4
, pp. 2247-2251
-
-
Doig, A.J.1
Sternberg, M.J.2
-
86
-
-
11244318120
-
Computational protein design is a challenge for implicit solvation models
-
Jaramillo A, Wodak SJ. Computational protein design is a challenge for implicit solvation models. Biophys J 2005;88:156-171.
-
(2005)
Biophys J
, vol.88
, pp. 156-171
-
-
Jaramillo, A.1
Wodak, S.J.2
-
87
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu AA, Shelenkov AA, Dunbrack RL. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack, R.L.3
-
88
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
Zhang C, Vasmatzis G, Cornette JL, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
-
(1997)
J Mol Biol
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.L.3
DeLisi, C.4
-
89
-
-
0023051843
-
Internal cavities and buried waters in globular proteins
-
Rashin AA, Iofin M, Honig B. Internal cavities and buried waters in globular proteins. Biochemistry 1986;25:3619-3625.
-
(1986)
Biochemistry
, vol.25
, pp. 3619-3625
-
-
Rashin, A.A.1
Iofin, M.2
Honig, B.3
-
90
-
-
0028607523
-
Cavities and packing at protein interfaces
-
Hubbard SJ, Argos P. Cavities and packing at protein interfaces. Protein Sci 1994;3:2194-2206.
-
(1994)
Protein Sci
, vol.3
, pp. 2194-2206
-
-
Hubbard, S.J.1
Argos, P.2
-
91
-
-
0028095182
-
Buried waters and internal cavities in monomeric proteins
-
Williams MA, Goodfellow JM, Thornton JM. Buried waters and internal cavities in monomeric proteins. Protein Sci 1994;3:1224-1235.
-
(1994)
Protein Sci
, vol.3
, pp. 1224-1235
-
-
Williams, M.A.1
Goodfellow, J.M.2
Thornton, J.M.3
-
92
-
-
4644298947
-
Accelerated exchange of a buried water molecule in selectively disulfide-reduced bovine pancreatic trypsin inhibitor
-
Denisov VP, Peters J, Horlein HD, Halle B. Accelerated exchange of a buried water molecule in selectively disulfide-reduced bovine pancreatic trypsin inhibitor. Biochemistry 2004;43:12020-12027.
-
(2004)
Biochemistry
, vol.43
, pp. 12020-12027
-
-
Denisov, V.P.1
Peters, J.2
Horlein, H.D.3
Halle, B.4
-
93
-
-
4944233531
-
Dynamics of water molecules buried in cavities of apolipoprotein E studied by molecular dynamics simulations and continuum electrostatic calculations
-
Prevost M. Dynamics of water molecules buried in cavities of apolipoprotein E studied by molecular dynamics simulations and continuum electrostatic calculations. Biopolymers 2004;75:196-207.
-
(2004)
Biopolymers
, vol.75
, pp. 196-207
-
-
Prevost, M.1
-
95
-
-
0016352763
-
Hydrophobic bonding and accessible surface area in proteins
-
Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature 1974;248:338-339.
-
(1974)
Nature
, vol.248
, pp. 338-339
-
-
Chothia, C.1
-
96
-
-
0010661547
-
An estimate of shape-related contributions to hydrophobic Gibbs energies
-
Sanchez-Ruiz JM. An estimate of shape-related contributions to hydrophobic Gibbs energies. J Phys Chem 1995;99:12076-12030.
-
(1995)
J Phys Chem
, vol.99
, pp. 12076-12030
-
-
Sanchez-Ruiz, J.M.1
-
97
-
-
0014718113
-
Protein denaturation. C. Theoretical models for the mechanism of denaturation
-
Tanford C. Protein denaturation. C. Theoretical models for the mechanism of denaturation Adv Protein Chem 1970;24:1-95.
-
(1970)
Adv Protein Chem
, vol.24
, pp. 1-95
-
-
Tanford, C.1
-
98
-
-
0025271463
-
pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1
-
Pace CN, Laurents DV, Thomson JA. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry 1990;29:2564-2572.
-
(1990)
Biochemistry
, vol.29
, pp. 2564-2572
-
-
Pace, C.N.1
Laurents, D.V.2
Thomson, J.A.3
-
99
-
-
0037007485
-
Fifty years of solvent denaturation
-
Schellman JA. Fifty years of solvent denaturation. Biophys Chem 2002;96:91-101.
-
(2002)
Biophys Chem
, vol.96
, pp. 91-101
-
-
Schellman, J.A.1
-
100
-
-
4544334447
-
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
-
Bordner AJ, Abagyan RA. Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Proteins 2004;57:400-413.
-
(2004)
Proteins
, vol.57
, pp. 400-413
-
-
Bordner, A.J.1
Abagyan, R.A.2
-
101
-
-
0029873155
-
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
-
Gilis D, Rooman M. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J Mol Biol 1996;257:1112-1126.
-
(1996)
J Mol Biol
, vol.257
, pp. 1112-1126
-
-
Gilis, D.1
Rooman, M.2
-
102
-
-
0031023842
-
Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables
-
Topham CM, Srinivasan N, Blundell TL. Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables. Protein Eng 1997;10:7-21.
-
(1997)
Protein Eng
, vol.10
, pp. 7-21
-
-
Topham, C.M.1
Srinivasan, N.2
Blundell, T.L.3
|