-
1
-
-
23944490117
-
Missense meanderings in sequence space: A biophysical view of protein evolution
-
DOI 10.1038/nrg1672
-
DePristo, M.A., Weinreich, D.M. & Hartl, D.L. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat. Rev. Genet. 6, 678-687 (2005 (Pubitemid 41192319)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.9
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
2
-
-
70349901079
-
Stability effects of mutations and protein evolvability
-
Tokuriki, N. & Tawfik, D.S. Stability effects of mutations and protein evolvability. Curr. Opin. Struct. Biol. 19, 596-604 (2009
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 596-604
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
3
-
-
35148875679
-
Genetic constraints on protein evolution
-
DOI 10.1080/10409230701597642, PII 782796873
-
Camps, M., Herman, A., Loh, E. & Loeb, L.A. Genetic constraints on protein evolution. Crit. Rev. Biochem. Mol. Biol. 42, 313-326 (2007 (Pubitemid 47537270)
-
(2007)
Critical Reviews in Biochemistry and Molecular Biology
, vol.42
, Issue.5
, pp. 313-326
-
-
Camps, M.1
Herman, A.2
Loh, E.3
Loeb, L.A.4
-
4
-
-
28044467526
-
Mutagenesis-based definitions and probes of residue burial in proteins
-
DOI 10.1073/pnas.0505089102
-
Bajaj, K., Chakrabarti, P. & Varadarajan, R. Mutagenesis-based definitions and probes of residue burial in proteins. Proc. Natl. Acad. Sci. USA 102, 16221-16226 (2005 (Pubitemid 41688895)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.45
, pp. 16221-16226
-
-
Bajaj, K.1
Chakrabarti, P.2
Varadarajan, R.3
-
5
-
-
51149203927
-
Canalization of development and the inheritance of acquired characters
-
Waddington, C. Canalization of development and the inheritance of acquired characters. Nature 150, 563-565 (1942
-
(1942)
Nature
, vol.150
, pp. 563-565
-
-
Waddington, C.1
-
6
-
-
40149099484
-
How protein stability and new functions trade off
-
Tokuriki, N., Stricher, F., Serrano, L. & Tawfik, D.S. How protein stability and new functions trade off. PLOS Comput. Biol. 4, e1000002 (2008
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Tokuriki, N.1
Stricher, F.2
Serrano, L.3
Tawfik, D.S.4
-
7
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
DOI 10.1016/S0022-2836(02)00400-X
-
Wang, X., Minasov, G. & Shoichet, B.K. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J. Mol. Biol. 320, 85-95 (2002 (Pubitemid 34722236)
-
(2002)
Journal of Molecular Biology
, vol.320
, Issue.1
, pp. 85-95
-
-
Wang, X.1
Minasov, G.2
Shoichet, B.K.3
-
8
-
-
42549144579
-
On the origins of novelty in development and evolution
-
DOI 10.1002/bies.20754
-
Moczek, A.P. On the origins of novelty in development and evolution. Bioessays 30, 432-447 (2008 (Pubitemid 351588925)
-
(2008)
BioEssays
, vol.30
, Issue.5
, pp. 432-447
-
-
Moczek, A.P.1
-
9
-
-
77953718211
-
Sequence space and the ongoing expansion of the protein universe
-
Povolotskaya, I.S. & Kondrashov, F.A. Sequence space and the ongoing expansion of the protein universe. Nature 465, 922-926 (2010
-
(2010)
Nature
, vol.465
, pp. 922-926
-
-
Povolotskaya, I.S.1
Kondrashov, F.A.2
-
10
-
-
0032569851
-
Hsp90 as a capacitor for morphological evolution
-
DOI 10.1038/24550
-
Rutherford, S.L. & Lindquist, S. Hsp90 as a capacitor for morphological evolution. Nature 396, 336-342 (1998 (Pubitemid 28557387)
-
(1998)
Nature
, vol.396
, Issue.6709
, pp. 336-342
-
-
Rutherford, S.L.1
Lindquist, S.2
-
11
-
-
77957740228
-
Protein folding sculpting evolutionary change
-
Lindquist, S. Protein folding sculpting evolutionary change. Cold Spring Harb. Symp. Quant. Biol. 74, 103-108 (2010
-
(2010)
Cold Spring Harb. Symp. Quant. Biol.
, vol.74
, pp. 103-108
-
-
Lindquist, S.1
-
12
-
-
0037030713
-
Hsp90 as a capacitor of phenotypic variation
-
DOI 10.1038/nature749
-
Queitsch, C., Sangster, T.A. & Lindquist, S. Hsp90 as a capacitor of phenotypic variation. Nature 417, 618-624 (2002). (Pubitemid 34614814)
-
(2002)
Nature
, vol.417
, Issue.6889
, pp. 618-624
-
-
Queitsch, C.1
Sangstert, T.A.2
Lindquist, S.3
-
14
-
-
55949106049
-
Modulation of the activity of newly synthesized human phenylalanine hydroxylase mutant proteins by low-molecular-weight compounds
-
Nascimento, C., Leandro, J., Tavares de Almeida, I. & Leandro, P. Modulation of the activity of newly synthesized human phenylalanine hydroxylase mutant proteins by low-molecular-weight compounds. Protein J. 27, 392-400 (2008
-
(2008)
Protein J.
, vol.27
, pp. 392-400
-
-
Nascimento, C.1
Leandro, J.2
Tavares De Almeida, I.3
Leandro, P.4
-
15
-
-
33847226970
-
The solubility of recombinant proteins expressed in Escherichia coli is increased by otsA and otsB co-transformation
-
Schultz, T., Liu, J., Capasso, P. & de Marco, A. The solubility of recombinant proteins expressed in Escherichia coli is increased by otsA and otsB co-transformation. Biochem. Biophys. Res. Commun. 355, 234-239 (2007
-
(2007)
Biochem. Biophys. Res. Commun.
, vol.355
, pp. 234-239
-
-
Schultz, T.1
Liu, J.2
Capasso, P.3
De Marco, A.4
-
16
-
-
75149172037
-
Osmolyte-induced conformational changes in the Hsp90 molecular chaperone
-
Street, T.O., Krukenberg, K.A., Rosgen, J., Bolen, D.W. & Agard, D.A. Osmolyte-induced conformational changes in the Hsp90 molecular chaperone. Protein Sci. 19, 57-65 (2010
-
(2010)
Protein Sci.
, vol.19
, pp. 57-65
-
-
Street, T.O.1
Krukenberg, K.A.2
Rosgen, J.3
Bolen, D.W.4
Agard, D.A.5
-
17
-
-
0035955743
-
Chemical chaperones regulate molecular chaperones in vitro and in cells under combined salt and heat stresses
-
Diamant, S., Eliahu, N., Rosenthal, D. & Goloubinoff, P. Chemical chaperones regulate molecular chaperones in vitro and in cells under combined salt and heat stresses. J. Biol. Chem. 276, 39586-39591 (2001
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 39586-39591
-
-
Diamant, S.1
Eliahu, N.2
Rosenthal, D.3
Goloubinoff, P.4
-
18
-
-
0035958656
-
The osmophobic effect: Natural selection of a thermodynamic force in protein folding
-
DOI 10.1006/jmbi.2001.4819
-
Bolen, D.W. & Baskakov, I.V. The osmophobic effect: natural selection of a thermodynamic force in protein folding. J. Mol. Biol. 310, 955-963 (2001 (Pubitemid 32738368)
-
(2001)
Journal of Molecular Biology
, vol.310
, Issue.5
, pp. 955-963
-
-
Bolen, D.W.1
Baskakov, I.V.2
-
19
-
-
33749018832
-
Crowding and confinement effects on protein diffusion in vivo
-
DOI 10.1128/JB.01982-05
-
Konopka, M.C., Shkel, I.A., Cayley, S., Record, M.T. & Weisshaar, J.C. Crowding and confinement effects on protein diffusion in vivo. J. Bacteriol. 188, 6115-6123 (2006 (Pubitemid 44448553)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.17
, pp. 6115-6123
-
-
Konopka, M.C.1
Shkel, I.A.2
Cayley, S.3
Record, M.T.4
Weisshaar, J.C.5
-
20
-
-
0035824871
-
Crowding and hydration effects on protein conformation: A study with sol-gel encapsulated proteins
-
DOI 10.1006/jmbi.2001.5166
-
Eggers, D.K. & Valentine, J.S. Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins. J. Mol. Biol. 314, 911-922 (2001 (Pubitemid 34087857)
-
(2001)
Journal of Molecular Biology
, vol.314
, Issue.4
, pp. 911-922
-
-
Eggers, D.K.1
Valentine, J.S.2
-
21
-
-
78649876151
-
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
-
Ando, T. & Skolnick, J. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc. Natl. Acad. Sci. USA 107, 18457-18462 (2010
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 18457-18462
-
-
Ando, T.1
Skolnick, J.2
-
22
-
-
22744447508
-
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli
-
DOI 10.1016/j.cell.2005.05.028, PII S0092867405005441
-
Kerner, M.J. et al. Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122, 209-220 (2005 (Pubitemid 41032985)
-
(2005)
Cell
, vol.122
, Issue.2
, pp. 209-220
-
-
Kerner, M.J.1
Naylor, D.J.2
Ishihama, Y.3
Maier, T.4
Chang, H.-C.5
Stines, A.P.6
Georgopoulos, C.7
Frishman, D.8
Hayer-Hartl, M.9
Mann, M.10
Hartl, F.U.11
-
23
-
-
0032514615
-
GroEL-GroES-mediated protein folding requires an intact central cavity
-
DOI 10.1073/pnas.95.21.12163
-
Wang, J.D., Michelitsch, M.D. & Weissman, J.S. GroEL-GroES-mediated protein folding requires an intact central cavity. Proc. Natl. Acad. Sci. USA 95, 12163-12168 (1998 (Pubitemid 28483736)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.21
, pp. 12163-12168
-
-
Wang, J.D.1
Michelitsch, M.D.2
Weissman, J.S.3
-
24
-
-
0020336190
-
Living with water stress: evolution of osmolyte systems
-
Yancey, P.H., Clark, M.E., Hand, S.C., Bowlus, R.D. & Somero, G.N. Living with water stress: evolution of osmolyte systems. Science 217, 1214-1222 (1982 (Pubitemid 13283134)
-
(1982)
Science
, vol.217
, Issue.4566
, pp. 1214-1222
-
-
Yancey, P.H.1
Clark, M.E.2
Hand, S.C.3
Bowlus, R.D.4
Somero, G.N.5
-
25
-
-
77954277524
-
Chaperonin-catalyzed rescue of kinetically trapped states in protein folding
-
Chakraborty, K. et al. Chaperonin-catalyzed rescue of kinetically trapped states in protein folding. Cell 9, 112-122 (2010
-
(2010)
Cell
, vol.9
, pp. 112-122
-
-
Chakraborty, K.1
-
26
-
-
79954426601
-
Endoplasmic reticulum stress-sensing mechanisms in yeast and mammalian cells
-
Kimata, Y. & Kohno, K. Endoplasmic reticulum stress-sensing mechanisms in yeast and mammalian cells. Curr. Opin. Cell Biol. 23, 135-142 (2011
-
(2011)
Curr. Opin. Cell Biol.
, vol.23
, pp. 135-142
-
-
Kimata, Y.1
Kohno, K.2
-
27
-
-
63449128473
-
Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum
-
Jonikas, M.C. et al. Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science 323, 1693-1697 (2009
-
(2009)
Science
, vol.323
, pp. 1693-1697
-
-
Jonikas, M.C.1
-
28
-
-
77955044557
-
Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state
-
Hong, J. & Gierasch, L.M. Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state. J. Am. Chem. Soc. 132, 10445-10452 (2010
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 10445-10452
-
-
Hong, J.1
Gierasch, L.M.2
-
29
-
-
76749109966
-
Hydrogen bonding progressively strengthens upon transfer of the protein urea-denatured state to water and protecting osmolytes
-
Holthauzen, L.M., Rosgen, J. & Bolen, D.W. Hydrogen bonding progressively strengthens upon transfer of the protein urea-denatured state to water and protecting osmolytes. Biochemistry 49, 1310-1318 (2010
-
(2010)
Biochemistry
, vol.49
, pp. 1310-1318
-
-
Holthauzen, L.M.1
Rosgen, J.2
Bolen, D.W.3
-
30
-
-
0032555691
-
Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase
-
Wolf, E. et al. Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell 94, 439-449 (1998 (Pubitemid 28391860)
-
(1998)
Cell
, vol.94
, Issue.4
, pp. 439-449
-
-
Wolf, E.1
Vassilev, A.2
Makino, Y.3
Sali, A.4
Nakatani, Y.5
Burley, S.K.6
-
31
-
-
0013815214
-
Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units
-
Ramakrishnan, C. & Ramachandran, G.N. Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909-933 (1965
-
(1965)
Biophys. J.
, vol.5
, pp. 909-933
-
-
Ramakrishnan, C.1
Ramachandran, G.N.2
-
32
-
-
23144436398
-
The FoldX web server: An online force field
-
DOI 10.1093/nar/gki387
-
Schymkowitz, J. et al. The FoldX web server: an online force field. Nucleic Acids Res. 33, W382-W388 (2005 (Pubitemid 44529948)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
33
-
-
45749102914
-
The Zyggregator method for predicting protein aggregation propensities
-
Tartaglia, G.G. & Vendruscolo, M. The Zyggregator method for predicting protein aggregation propensities. Chem. Soc. Rev. 37, 1395-1401 (2008
-
(2008)
Chem. Soc. Rev.
, vol.37
, pp. 1395-1401
-
-
Tartaglia, G.G.1
Vendruscolo, M.2
-
34
-
-
0027142978
-
The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase
-
DOI 10.1006/jmbi.1993.1609
-
Bernard, P. et al. The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase. J. Mol. Biol. 234, 534-541 (1993 (Pubitemid 24007784)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 534-541
-
-
Bernard, P.1
Kezdy, K.E.2
Van Melderen, L.3
Steyaert, J.4
Wyns, L.5
Pato, M.L.6
Higgins, P.N.7
Couturier, M.8
-
35
-
-
57449092721
-
Structural correlates of the temperature sensitive phenotype derived from saturation mutagenesis studies of CcdB
-
Bajaj, K. et al. Structural correlates of the temperature sensitive phenotype derived from saturation mutagenesis studies of CcdB. Biochemistry 47, 12964-12973 (2008
-
(2008)
Biochemistry
, vol.47
, pp. 12964-12973
-
-
Bajaj, K.1
-
36
-
-
18044374122
-
Molecular basis of gyrase poisoning by the addiction toxin CcdB
-
Dao-Thi, M.H. et al. Molecular basis of gyrase poisoning by the addiction toxin CcdB. J. Mol. Biol. 348, 1091-1102 (2005
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 1091-1102
-
-
Dao-Thi, M.H.1
-
37
-
-
47049104940
-
Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses
-
Gunasekera, T.S., Csonka, L.N. & Paliy, O. Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses. J. Bacteriol. 190, 3712-3720 (2008
-
(2008)
J. Bacteriol.
, vol.190
, pp. 3712-3720
-
-
Gunasekera, T.S.1
Csonka, L.N.2
Paliy, O.3
-
38
-
-
0025769565
-
Role of heat shock protein DnaK in osmotic adaptation of Escherichia coli
-
Meury, J. & Kohiyama, M. Role of heat shock protein DnaK in osmotic adaptation of Escherichia coli. J. Bacteriol. 173, 4404-4410 (1991
-
(1991)
J. Bacteriol.
, vol.173
, pp. 4404-4410
-
-
Meury, J.1
Kohiyama, M.2
-
39
-
-
0032039542
-
Multiple effects of trehalose on protein folding in vitro and in vivo
-
Singer, M.A. & Lindquist, S. Multiple effects of trehalose on protein folding in vitro and in vivo. Mol. Cell 1, 639-648 (1998 (Pubitemid 128379242)
-
(1998)
Molecular Cell
, vol.1
, Issue.5
, pp. 639-648
-
-
Singer, M.A.1
Lindquist, S.2
-
40
-
-
0023801241
-
Accumulation of trehalose by Escherichia coli K-12 at high osmotic pressure depends on the presence of amber suppressors
-
Rod, M.L., Alam, K.Y., Cunningham, P.R. & Clark, D.P. Accumulation of trehalose by Escherichia coli K-12 at high osmotic pressure depends on the presence of amber suppressors. J. Bacteriol. 170, 3601-3610 (1988
-
(1988)
J. Bacteriol.
, vol.170
, pp. 3601-3610
-
-
Rod, M.L.1
Alam, K.Y.2
Cunningham, P.R.3
Clark, D.P.4
-
41
-
-
3142742712
-
Trehalose is required for growth of Mycobacterium smegmatis
-
DOI 10.1074/jbc.M313103200
-
Woodruff, P.J. et al. Trehalose is required for growth of Mycobacterium smegmatis. J. Biol. Chem. 279, 28835-28843 (2004 (Pubitemid 38915750)
-
(2004)
Journal of Biological Chemistry
, vol.279
, Issue.28
, pp. 28835-28843
-
-
Woodruff, P.J.1
Carlson, B.L.2
Siridechadilok, B.3
Pratt, M.R.4
Senaratne, R.H.5
Mougous, J.D.6
Riley, L.W.7
Williams, S.J.8
Bertozzi, C.R.9
-
42
-
-
78049437929
-
Trehalose extends longevity in the nematode Caenorhabditis elegans
-
Honda, Y., Tanaka, M. & Honda, S. Trehalose extends longevity in the nematode Caenorhabditis elegans. Aging Cell 9, 558-569 (2010
-
(2010)
Aging Cell
, vol.9
, pp. 558-569
-
-
Honda, Y.1
Tanaka, M.2
Honda, S.3
-
43
-
-
70349266064
-
Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging
-
Ben-Zvi, A., Miller, E.A. & Morimoto, R.I. Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging. Proc. Natl. Acad. Sci. USA 106, 14914-14919 (2009
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 14914-14919
-
-
Ben-Zvi, A.1
Miller, E.A.2
Morimoto, R.I.3
-
44
-
-
50249175120
-
Chemical and biological approaches synergize to ameliorate protein-folding diseases
-
Mu, T.W. et al. Chemical and biological approaches synergize to ameliorate protein-folding diseases. Cell 134, 769-781 (2008
-
(2008)
Cell
, vol.134
, pp. 769-781
-
-
Mu, T.W.1
-
45
-
-
77952501011
-
Endoplasmic reticulum Ca2+ increases enhance mutant glucocerebrosidase proteostasis
-
Ong, D.S., Mu, T.W., Palmer, A.E. & Kelly, J.W. Endoplasmic reticulum Ca2+ increases enhance mutant glucocerebrosidase proteostasis. Nat. Chem. Biol. 6, 424-432 (2010
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 424-432
-
-
Ong, D.S.1
Mu, T.W.2
Palmer, A.E.3
Kelly, J.W.4
-
46
-
-
33646897305
-
Structural features of the GroEL-GroES nano-cage required for rapid folding of encapsulated protein
-
Tang, Y.C. et al. Structural features of the GroEL-GroES nano-cage required for rapid folding of encapsulated protein. Cell 125, 903-914 (2006
-
(2006)
Cell
, vol.125
, pp. 903-914
-
-
Tang, Y.C.1
-
47
-
-
0033614009
-
Crystal structure of CcdB, a topoisomerase poison from E. coli
-
DOI 10.1006/jmbi.1998.2395
-
Loris, R. et al. Crystal structure of CcdB, a topoisomerase poison from E. coli. J. Mol. Biol. 285, 1667-1677 (1999 (Pubitemid 29060463)
-
(1999)
Journal of Molecular Biology
, vol.285
, Issue.4
, pp. 1667-1677
-
-
Loris, R.1
Dao-Thi, M.-H.2
Bahassi, E.M.3
Van Melderen, L.4
Poortmans, F.5
Liddington, R.6
Couturier, M.7
Wyns, L.8
|