-
1
-
-
0028048679
-
Core-packing constraints, hydrophobicity and protein design
-
Baldwin, E. P., and Matthews, B. W. (1994) Core-packing constraints, hydrophobicity and protein design, Curr. Opin. Biotechnol. 5, 396-402.
-
(1994)
Curr. Opin. Biotechnol.
, vol.5
, pp. 396-402
-
-
Baldwin, E.P.1
Matthews, B.W.2
-
4
-
-
0030059689
-
Forces contributing to the conformational stability of proteins
-
Pace, C. N., Shirley, B. A., McNutt, M., and Gajiwala, K. (1996) Forces contributing to the conformational stability of proteins, FASEB J. 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
-
5
-
-
27344449197
-
Progress in modeling of protein structures and interactions
-
Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., and Baker, D. (2005) Progress in modeling of protein structures and interactions, Science 310, 638-642.
-
(2005)
Science
, vol.310
, pp. 638-642
-
-
Schueler-Furman, O.1
Wang, C.2
Bradley, P.3
Misura, K.4
Baker, D.5
-
6
-
-
0036667732
-
Energy estimation in protein design
-
Mendes, J., Guerois, R., and Serrano, L. (2002) Energy estimation in protein design, Curr. Opin. Struct. Biol. 12, 441-446.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 441-446
-
-
Mendes, J.1
Guerois, R.2
Serrano, L.3
-
7
-
-
4143150944
-
Advances in computational protein design
-
Park, S., Yang, X., and Saven, J. G. (2004) Advances in computational protein design, Curr. Opin. Struct. Biol. 14, 487-494.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 487-494
-
-
Park, S.1
Yang, X.2
Saven, J.G.3
-
8
-
-
0032835617
-
De novo design and structural characterization of proteins and metalloproteins
-
DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., and Lombardi, A. (1999) De novo design and structural characterization of proteins and metalloproteins, Annu. Rev. Biochem. 68, 779-819.
-
(1999)
Annu. Rev. Biochem.
, vol.68
, pp. 779-819
-
-
DeGrado, W.F.1
Summa, C.M.2
Pavone, V.3
Nastri, F.4
Lombardi, A.5
-
10
-
-
0035782661
-
Review: Protein design - Where we were, where we are, where we're going
-
Pokala, N., and Handel, T. M. (2001) Review: Protein design-where we were, where we are, where we're going, J. Struct. Biol. 134, 269-281.
-
(2001)
J. Struct. Biol.
, vol.134
, pp. 269-281
-
-
Pokala, N.1
Handel, T.M.2
-
11
-
-
0041387567
-
A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins
-
Dantas, G., Kuhlman, B., Callender, D., Wong, M., and Baker, D. (2003) A large scale test of computational protein design: Folding and stability of nine completely redesigned globular proteins, J. Mol. Biol. 332, 449-460.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 449-460
-
-
Dantas, G.1
Kuhlman, B.2
Callender, D.3
Wong, M.4
Baker, D.5
-
12
-
-
0030334742
-
Stabilization of proteins by rational design of α-helix stability using helix/coil transition theory
-
Villegas, V., Viguera, A. R., Aviles, F. X., and Serrano, L. (1996) Stabilization of proteins by rational design of α-helix stability using helix/coil transition theory, Folding Des. 1, 29-34.
-
(1996)
Folding Des.
, vol.1
, pp. 29-34
-
-
Villegas, V.1
Viguera, A.R.2
Aviles, F.X.3
Serrano, L.4
-
13
-
-
0036307678
-
Electrostatics significantly affect the stability of designed homeodomain variants
-
Marshall, S. A., Morgan, C. S., and Mayo, S. L. (2002) Electrostatics significantly affect the stability of designed homeodomain variants, J. Mol. Biol. 316, 189-199.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 189-199
-
-
Marshall, S.A.1
Morgan, C.S.2
Mayo, S.L.3
-
14
-
-
0032872888
-
Increasing protein stability by altering long-range coulombic interactions
-
Grimsley, G. R., Shaw, K. L., Fee, L. R., Alston, R. W., Huyghues-Despointes, B. M., Thurlkill, R. L., Scholtz, J. M., and Pace, C. N. (1999) Increasing protein stability by altering long-range coulombic interactions, Protein Sci. 8, 1843-1849.
-
(1999)
Protein Sci.
, vol.8
, pp. 1843-1849
-
-
Grimsley, G.R.1
Shaw, K.L.2
Fee, L.R.3
Alston, R.W.4
Huyghues-Despointes, B.M.5
Thurlkill, R.L.6
Scholtz, J.M.7
Pace, C.N.8
-
15
-
-
0033554840
-
Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface
-
Loladze, V. V., Ibarra-Molero, B., Sanchez-Ruiz, J. M., and Makhatadze, G. I. (1999) Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface, Biochemistry 38, 16419-16423.
-
(1999)
Biochemistry
, vol.38
, pp. 16419-16423
-
-
Loladze, V.V.1
Ibarra-Molero, B.2
Sanchez-Ruiz, J.M.3
Makhatadze, G.I.4
-
16
-
-
0034620528
-
Rational modification of protein stability by the mutation of charged surface residues
-
Spector, S., Wang, M., Carp, S. A., Robblee, J., Hendsch, Z. S., Fairman, R., Tidor, B., and Raleigh, D. P. (2000) Rational modification of protein stability by the mutation of charged surface residues, Biochemistry 39, 872-879.
-
(2000)
Biochemistry
, vol.39
, pp. 872-879
-
-
Spector, S.1
Wang, M.2
Carp, S.A.3
Robblee, J.4
Hendsch, Z.S.5
Fairman, R.6
Tidor, B.7
Raleigh, D.P.8
-
17
-
-
0034100848
-
Two exposed amino acid residues confer thermostability on a cold shock protein
-
Perl, D., Mueller, U., Heinemann, U., and Schmid, F. X. (2000) Two exposed amino acid residues confer thermostability on a cold shock protein, Nat. Struct. Biol. 7, 380-383.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 380-383
-
-
Perl, D.1
Mueller, U.2
Heinemann, U.3
Schmid, F.X.4
-
18
-
-
0035964254
-
Stabilization of a fibronectin type III domain by the removal of unfavorable electrostatic interactions on the protein surface
-
Koide, A., Jordan, M. R., Horner, S. R., Batori, V., and Koide, S. (2001) Stabilization of a fibronectin type III domain by the removal of unfavorable electrostatic interactions on the protein surface, Biochemistry 40, 10326-10333.
-
(2001)
Biochemistry
, vol.40
, pp. 10326-10333
-
-
Koide, A.1
Jordan, M.R.2
Horner, S.R.3
Batori, V.4
Koide, S.5
-
19
-
-
0036228118
-
Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein
-
Lee, K. K., Fitch, C. A., and Garcia-Moreno, E. B. (2002) Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein, Protein Sci. 11, 1004-1016.
-
(2002)
Protein Sci.
, vol.11
, pp. 1004-1016
-
-
Lee, K.K.1
Fitch, C.A.2
Garcia-Moreno, E.B.3
-
20
-
-
0347298770
-
Changes in stability upon charge reversal and neutralization substitution in staphylococcal nuclease are dominated by favorable electrostatic effects
-
Schwehm, J. M., Fitch, C. A., Dang, B. N., Garcia-Moreno, E. B., and Stites, W. E. (2003) Changes in stability upon charge reversal and neutralization substitution in staphylococcal nuclease are dominated by favorable electrostatic effects, Biochemistry 42, 1118-1128.
-
(2003)
Biochemistry
, vol.42
, pp. 1118-1128
-
-
Schwehm, J.M.1
Fitch, C.A.2
Dang, B.N.3
Garcia-Moreno, E.B.4
Stites, W.E.5
-
21
-
-
24044547376
-
How to improve nature: Study of the electrostatic properties of the surface of α-lactalbumin
-
Permyakov, S. E., Makhatadze, G. I., Owenius, R., Uversky, V. N., Brooks, C. L., Permyakov, E. A., and Berliner, L. J. (2005) How to improve nature: Study of the electrostatic properties of the surface of α-lactalbumin, Protein Eng., Des. Sel. 18, 425-433.
-
(2005)
Protein Eng., Des. Sel.
, vol.18
, pp. 425-433
-
-
Permyakov, S.E.1
Makhatadze, G.I.2
Owenius, R.3
Uversky, V.N.4
Brooks, C.L.5
Permyakov, E.A.6
Berliner, L.J.7
-
22
-
-
29344472867
-
Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer
-
Lee, C. F., Makhatadze, G. I., and Wong, K. B. (2005) Effects of Charge-to-Alanine Substitutions on the Stability of Ribosomal Protein L30e from Thermococcus celer, Biochemistry 44, 16817-16825.
-
(2005)
Biochemistry
, vol.44
, pp. 16817-16825
-
-
Lee, C.F.1
Makhatadze, G.I.2
Wong, K.B.3
-
23
-
-
0036303785
-
The effects of ionic strength on protein stability: The cold shock protein family
-
Dominy, B. N., Perl, D., Schmid, F. X., and Brooks, C. L., III (2002) The effects of ionic strength on protein stability: The cold shock protein family, J. Mol. Biol. 319, 541-554.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 541-554
-
-
Dominy, B.N.1
Perl, D.2
Schmid, F.X.3
Brooks III, C.L.4
-
24
-
-
0037380834
-
Electrostatic contributions to the stability of a thermophilic cold shock protein
-
Zhou, H. X., and Dong, F. (2003) Electrostatic contributions to the stability of a thermophilic cold shock protein, Biophys. J. 84, 2216-2222.
-
(2003)
Biophys. J.
, vol.84
, pp. 2216-2222
-
-
Zhou, H.X.1
Dong, F.2
-
25
-
-
0037474539
-
Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI = 3.5) and a basic variant (pI = 10.2)
-
Laurents, D. V., Huyghues-Despointes, B. M., Bruix, M., Thurlkill, R. L., Schell, D., Newsom, S., Grimsley, G. R., Shaw, K. L., Trevino, S., Rico, M., Briggs, J. M., Antosiewicz, J. M., Scholtz, J. M., and Pace, C. N. (2003) Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI = 3.5) and a basic variant (pI = 10.2), J. Mol. Biol. 325, 1077-1092.
-
(2003)
J. Mol. Biol.
, vol.325
, pp. 1077-1092
-
-
Laurents, D.V.1
Huyghues-Despointes, B.M.2
Bruix, M.3
Thurlkill, R.L.4
Schell, D.5
Newsom, S.6
Grimsley, G.R.7
Shaw, K.L.8
Trevino, S.9
Rico, M.10
Briggs, J.M.11
Antosiewicz, J.M.12
Scholtz, J.M.13
Pace, C.N.14
-
27
-
-
0035951083
-
Molecular characterization and tissue distribution of a novel member of the S100 family of EF-hand proteins
-
Gribenko, A. V., Hopper, J. E., and Makhatadze, G. I. (2001) Molecular characterization and tissue distribution of a novel member of the S100 family of EF-hand proteins, Biochemistry 40, 15538-15548.
-
(2001)
Biochemistry
, vol.40
, pp. 15538-15548
-
-
Gribenko, A.V.1
Hopper, J.E.2
Makhatadze, G.I.3
-
28
-
-
0037432563
-
Contribution of surface salt bridges to protein stability: Guidelines for protein engineering
-
Makhatadze, G. I., Loladze, V. V., Ermolenko, D. N., Chen, X., and Thomas, S. T. (2003) Contribution of surface salt bridges to protein stability: Guidelines for protein engineering, J. Mol. Biol. 327, 1135-1148.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 1135-1148
-
-
Makhatadze, G.I.1
Loladze, V.V.2
Ermolenko, D.N.3
Chen, X.4
Thomas, S.T.5
-
29
-
-
1042298814
-
Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions
-
Makhatadze, G. I., Loladze, V. V., Gribenko, A. V., and Lopez, M. M. (2004) Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions, J. Mol. Biol. 336, 929-942.
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 929-942
-
-
Makhatadze, G.I.1
Loladze, V.V.2
Gribenko, A.V.3
Lopez, M.M.4
-
30
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F., and Sali, A. (2000) Comparative protein structure modeling of genes and genomes, Annu. Rev. Biophys. Biomol. Struct. 29, 291-325.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
31
-
-
25144470141
-
Mutational analysis demonstrates that specific electrostatic interactions can play a key role in the denatured state ensemble of proteins
-
Cho, J. H., and Raleigh, D. P. (2005) Mutational Analysis Demonstrates that Specific Electrostatic Interactions can Play a Key Role in the Denatured State Ensemble of Proteins, J. Mol. Biol. 353, 174-185.
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 174-185
-
-
Cho, J.H.1
Raleigh, D.P.2
-
32
-
-
22244458003
-
Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa
-
Trefethen, J. M., Pace, C. N., Scholtz, J. M., and Brems, D. N. (2005) Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa, Protein Sci. 14, 1934-1938.
-
(2005)
Protein Sci.
, vol.14
, pp. 1934-1938
-
-
Trefethen, J.M.1
Pace, C.N.2
Scholtz, J.M.3
Brems, D.N.4
-
33
-
-
0028983182
-
a values of the denatured state are on average 0.4 units lower than those of model compounds
-
a values of the denatured state are on average 0.4 units lower than those of model compounds, Biochemistry 34, 9424-9433.
-
(1995)
Biochemistry
, vol.34
, pp. 9424-9433
-
-
Oliveberg, M.1
Arcus, V.L.2
Fersht, A.R.3
-
34
-
-
0033551039
-
a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions
-
a values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions, Biochemistry 38, 4896-4903.
-
(1999)
Biochemistry
, vol.38
, pp. 4896-4903
-
-
Kuhlman, B.1
Luisi, D.L.2
Young, P.3
Raleigh, D.P.4
-
35
-
-
0033852796
-
Charge-charge interactions influence the denatured state ensemble and contribute to protein stability
-
Pace, C. N., Alston, R. W., and Shaw, K. L. (2000) Charge-charge interactions influence the denatured state ensemble and contribute to protein stability, Protein Sci. 9, 1395-1398.
-
(2000)
Protein Sci
, vol.9
, pp. 1395-1398
-
-
Pace, C.N.1
Alston, R.W.2
Shaw, K.L.3
-
36
-
-
0033544710
-
Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability
-
Elcock, A. H. (1999) Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability, J. Mol. Biol. 294, 1051-1062.
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 1051-1062
-
-
Elcock, A.H.1
-
37
-
-
0037133605
-
A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins
-
Zhou, H. X. (2002) A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins, Proc. Natl. Acad. Sci. U.S.A. 99, 3569-3574.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 3569-3574
-
-
Zhou, H.X.1
-
38
-
-
14744281316
-
Empirical parametrization of pK values for carboxylic acids in proteins using a genetic algorithm
-
Godoy-Ruiz, R., Perez-Jimenez, R., Garcia-Mira, M. M., Plaza del Pino, I. M., and Sanchez-Ruiz, J. M. (2005) Empirical parametrization of pK values for carboxylic acids in proteins using a genetic algorithm, Biophys. Chem. 115, 263-266.
-
(2005)
Biophys. Chem.
, vol.115
, pp. 263-266
-
-
Godoy-Ruiz, R.1
Perez-Jimenez, R.2
Garcia-Mira, M.M.3
Plaza Del Pino, I.M.4
Sanchez-Ruiz, J.M.5
-
39
-
-
0030018338
-
Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain
-
Kranz, J. K., Lu, J., and Hall, K. B. (1996) Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain, Protein Sci. 5, 1567-1583.
-
(1996)
Protein Sci.
, vol.5
, pp. 1567-1583
-
-
Kranz, J.K.1
Lu, J.2
Hall, K.B.3
-
40
-
-
0033573838
-
Thermodynamics and kinetics of folding of common-type acylphosphatase: Comparison to the highly homologous muscle isoenzyme
-
Taddei, N., Chiti, F., Paoli, P., Fiaschi, T., Bucciantini, M., Stefani, M., Dobson, C. M., and Ramponi, G. (1999) Thermodynamics and kinetics of folding of common-type acylphosphatase: Comparison to the highly homologous muscle isoenzyme, Biochemistry 38, 2135-2142.
-
(1999)
Biochemistry
, vol.38
, pp. 2135-2142
-
-
Taddei, N.1
Chiti, F.2
Paoli, P.3
Fiaschi, T.4
Bucciantini, M.5
Stefani, M.6
Dobson, C.M.7
Ramponi, G.8
-
41
-
-
0031214818
-
Folding and stability of a fibronectin type III domain of human tenascin
-
Clarke, J., Hamill, S. J., and Johnson, C. M. (1997) Folding and stability of a fibronectin type III domain of human tenascin, J. Mol. Biol. 270, 771-778.
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 771-778
-
-
Clarke, J.1
Hamill, S.J.2
Johnson, C.M.3
-
42
-
-
0036902235
-
Close-range electrostatic interactions in proteins
-
Kumar, S., and Nussinov, R. (2002) Close-range electrostatic interactions in proteins, ChemBioChem 3, 604-617.
-
(2002)
ChemBioChem
, vol.3
, pp. 604-617
-
-
Kumar, S.1
Nussinov, R.2
-
43
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B., and Nicholls, A. (1995) Classical electrostatics in biology and chemistry, Science 268, 1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
44
-
-
0035451052
-
What are the dielectric "constants" of proteins and how to validate electrostatic models?
-
Schutz, C. N., and Warshel, A. (2001) What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44, 400-417.
-
(2001)
Proteins
, vol.44
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
45
-
-
1542320003
-
Structural interpretation of pH and salt-dependent processes in proteins with computational methods
-
Garcia-Moreno, E. B., and Fitch, C. A. (2004) Structural interpretation of pH and salt-dependent processes in proteins with computational methods, Methods Enzymol. 380, 20-51.
-
(2004)
Methods Enzymol.
, vol.380
, pp. 20-51
-
-
Garcia-Moreno, E.B.1
Fitch, C.A.2
|