-
1
-
-
84864645362
-
Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling
-
L. Afriat-Jurnou, C.J. Jackson, and D.S. Tawfik Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling Biochemistry 51 2012 6047 6055
-
(2012)
Biochemistry
, vol.51
, pp. 6047-6055
-
-
Afriat-Jurnou, L.1
Jackson, C.J.2
Tawfik, D.S.3
-
2
-
-
84864439921
-
FastML: A web server for probabilistic reconstruction of ancestral sequences
-
H. Ashkenazy, O. Penn, A. Doron-Faigenboim, O. Cohen, G. Cannarozzi, O. Zomer, and T. Pupko FastML: a web server for probabilistic reconstruction of ancestral sequences Nucleic Acids Res. 40 2012 W580 W584
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W580-W584
-
-
Ashkenazy, H.1
Penn, O.2
Doron-Faigenboim, A.3
Cohen, O.4
Cannarozzi, G.5
Zomer, O.6
Pupko, T.7
-
3
-
-
84935005249
-
Internal symmetry in protein structures: Prevalence, functional relevance and evolution
-
S. Balaji Internal symmetry in protein structures: prevalence, functional relevance and evolution Curr. Opin. Struct. Biol. 32 2015 156 166
-
(2015)
Curr. Opin. Struct. Biol.
, vol.32
, pp. 156-166
-
-
Balaji, S.1
-
4
-
-
84948438701
-
Assessing the prediction fidelity of ancestral reconstruction by a library approach
-
H. Bar-Rogovsky, A. Stern, O. Penn, I. Kobl, T. Pupko, and D.S. Tawfik Assessing the prediction fidelity of ancestral reconstruction by a library approach Protein Eng. Des. Sel. 28 2015 507 518
-
(2015)
Protein Eng. Des. Sel.
, vol.28
, pp. 507-518
-
-
Bar-Rogovsky, H.1
Stern, A.2
Penn, O.3
Kobl, I.4
Pupko, T.5
Tawfik, D.S.6
-
5
-
-
84872272432
-
Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness
-
S. Bershtein, W. Mu, A.W. Serohijos, J. Zhou, and E.I. Shakhnovich Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness Mol. Cell 49 2013 133 144
-
(2013)
Mol. Cell
, vol.49
, pp. 133-144
-
-
Bershtein, S.1
Mu, W.2
Serohijos, A.W.3
Zhou, J.4
Shakhnovich, E.I.5
-
6
-
-
79959830883
-
Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins
-
M.B. Borgia, A. Borgia, R.B. Best, A. Steward, D. Nettels, B. Wunderlich, B. Schuler, and J. Clarke Single-molecule fluorescence reveals sequence-specific misfolding in multidomain proteins Nature 474 2011 662 665
-
(2011)
Nature
, vol.474
, pp. 662-665
-
-
Borgia, M.B.1
Borgia, A.2
Best, R.B.3
Steward, A.4
Nettels, D.5
Wunderlich, B.6
Schuler, B.7
Clarke, J.8
-
7
-
-
70349464621
-
An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
-
J.T. Bridgham, E.A. Ortlund, and J.W. Thornton An epistatic ratchet constrains the direction of glucocorticoid receptor evolution Nature 461 2009 515 519
-
(2009)
Nature
, vol.461
, pp. 515-519
-
-
Bridgham, J.T.1
Ortlund, E.A.2
Thornton, J.W.3
-
8
-
-
84855771724
-
Modular evolution and the origins of symmetry: Reconstruction of a three-fold symmetric globular protein
-
A. Broom, A.C. Doxey, Y.D. Lobsanov, L.G. Berthin, D.R. Rose, P.L. Howell, B.J. McConkey, and E.M. Meiering Modular evolution and the origins of symmetry: reconstruction of a three-fold symmetric globular protein Structure 20 2012 161 171
-
(2012)
Structure
, vol.20
, pp. 161-171
-
-
Broom, A.1
Doxey, A.C.2
Lobsanov, Y.D.3
Berthin, L.G.4
Rose, D.R.5
Howell, P.L.6
McConkey, B.J.7
Meiering, E.M.8
-
9
-
-
84948393948
-
Protein unfolding rates correlate as strongly as folding rates with native structure
-
A. Broom, S. Gosavi, and E.M. Meiering Protein unfolding rates correlate as strongly as folding rates with native structure Protein Sci. 24 2015 580 587
-
(2015)
Protein Sci.
, vol.24
, pp. 580-587
-
-
Broom, A.1
Gosavi, S.2
Meiering, E.M.3
-
10
-
-
84882340111
-
New genes as drivers of phenotypic evolution
-
S. Chen, B.H. Krinsky, and M. Long New genes as drivers of phenotypic evolution Nat. Rev. Genet. 14 2013 645 660
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 645-660
-
-
Chen, S.1
Krinsky, B.H.2
Long, M.3
-
11
-
-
62649123200
-
Establishing wild-type levels of catalytic activity on natural and artificial (β α)8-barrel protein scaffolds
-
J. Claren, C. Malisi, B. Höcker, and R. Sterner Establishing wild-type levels of catalytic activity on natural and artificial (β α)8-barrel protein scaffolds Proc. Natl. Acad. Sci. USA 106 2009 3704 3709
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 3704-3709
-
-
Claren, J.1
Malisi, C.2
Höcker, B.3
Sterner, R.4
-
12
-
-
0034710944
-
Nonglassy kinetics in the folding of a simple single-domain protein
-
B. Gillespie, and K.W. Plaxco Nonglassy kinetics in the folding of a simple single-domain protein Proc. Natl. Acad. Sci. USA 97 2000 12014 12019
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 12014-12019
-
-
Gillespie, B.1
Plaxco, K.W.2
-
13
-
-
0034333196
-
Rapid automatic detection and alignment of repeats in protein sequences
-
A. Heger, and L. Holm Rapid automatic detection and alignment of repeats in protein sequences Proteins 41 2000 224 237
-
(2000)
Proteins
, vol.41
, pp. 224-237
-
-
Heger, A.1
Holm, L.2
-
14
-
-
84892475033
-
Comparing protein folding in vitro and in vivo: Foldability meets the fitness challenge
-
K.S. Hingorani, and L.M. Gierasch Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge Curr. Opin. Struct. Biol. 24 2014 81 90
-
(2014)
Curr. Opin. Struct. Biol.
, vol.24
, pp. 81-90
-
-
Hingorani, K.S.1
Gierasch, L.M.2
-
15
-
-
84901378640
-
Design of proteins from smaller fragments-learning from evolution
-
B. Höcker Design of proteins from smaller fragments-learning from evolution Curr. Opin. Struct. Biol. 27 2014 56 62
-
(2014)
Curr. Opin. Struct. Biol.
, vol.27
, pp. 56-62
-
-
Höcker, B.1
-
16
-
-
84885439160
-
β-propeller blades as ancestral peptides in protein evolution
-
K.O. Kopec, and A.N. Lupas β-propeller blades as ancestral peptides in protein evolution PLoS ONE 8 2014 e77074
-
(2014)
PLoS ONE
, vol.8
, pp. e77074
-
-
Kopec, K.O.1
Lupas, A.N.2
-
17
-
-
0041734982
-
Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein
-
S.M. Larson, and V.S. Pande Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein J. Mol. Biol. 332 2003 275 286
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 275-286
-
-
Larson, S.M.1
Pande, V.S.2
-
18
-
-
78651068037
-
Experimental support for the evolution of symmetric protein architecture from a simple peptide motif
-
J. Lee, and M. Blaber Experimental support for the evolution of symmetric protein architecture from a simple peptide motif Proc. Natl. Acad. Sci. USA 108 2011 126 130
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 126-130
-
-
Lee, J.1
Blaber, M.2
-
19
-
-
84921804046
-
Symmetric protein architecture in protein design: Top-down symmetric deconstruction
-
L.M. Longo, and M. Blaber Symmetric protein architecture in protein design: top-down symmetric deconstruction Methods Mol. Biol. 1216 2014 161 182
-
(2014)
Methods Mol. Biol.
, vol.1216
, pp. 161-182
-
-
Longo, L.M.1
Blaber, M.2
-
20
-
-
84887408868
-
Alternative folding nuclei definitions facilitate the evolution of a symmetric protein fold from a smaller peptide motif
-
L.M. Longo, J. Lee, C.A. Tenorio, and M. Blaber Alternative folding nuclei definitions facilitate the evolution of a symmetric protein fold from a smaller peptide motif Structure 21 2013 2042 2050
-
(2013)
Structure
, vol.21
, pp. 2042-2050
-
-
Longo, L.M.1
Lee, J.2
Tenorio, C.A.3
Blaber, M.4
-
21
-
-
0029008590
-
A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil
-
K.J. Lumb, and P.S. Kim A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil Biochemistry 34 1995 8642 8648
-
(1995)
Biochemistry
, vol.34
, pp. 8642-8648
-
-
Lumb, K.J.1
Kim, P.S.2
-
22
-
-
84950135105
-
Ancestral protein reconstruction: Techniques and applications
-
R. Merkl, and R. Sterner Ancestral protein reconstruction: techniques and applications Biol. Chem. 396 2015 1 21
-
(2015)
Biol. Chem.
, vol.396
, pp. 1-21
-
-
Merkl, R.1
Sterner, R.2
-
24
-
-
84860013075
-
Structure of an intermediate state in protein folding and aggregation
-
P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundström, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo, and L.E. Kay Structure of an intermediate state in protein folding and aggregation Science 336 2012 362 366
-
(2012)
Science
, vol.336
, pp. 362-366
-
-
Neudecker, P.1
Robustelli, P.2
Cavalli, A.3
Walsh, P.4
Lundström, P.5
Zarrine-Afsar, A.6
Sharpe, S.7
Vendruscolo, M.8
Kay, L.E.9
-
25
-
-
84926289262
-
Control of repeat-protein curvature by computational protein design
-
K. Park, B.W. Shen, F. Parmeggiani, P.-S. Huang, B.L. Stoddard, and D. Baker Control of repeat-protein curvature by computational protein design Nat. Struct. Mol. Biol. 22 2015 167 174
-
(2015)
Nat. Struct. Mol. Biol.
, vol.22
, pp. 167-174
-
-
Park, K.1
Shen, B.W.2
Parmeggiani, F.3
Huang, P.-S.4
Stoddard, B.L.5
Baker, D.6
-
26
-
-
31744450975
-
Evolution of new protein topologies through multistep gene rearrangements
-
S.G. Peisajovich, L. Rockah, and D.S. Tawfik Evolution of new protein topologies through multistep gene rearrangements Nat. Genet. 38 2006 168 174
-
(2006)
Nat. Genet.
, vol.38
, pp. 168-174
-
-
Peisajovich, S.G.1
Rockah, L.2
Tawfik, D.S.3
-
27
-
-
0023697408
-
Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants
-
M.M. Santoro, and D.W. Bolen Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants Biochemistry 27 1988 8063 8068
-
(1988)
Biochemistry
, vol.27
, pp. 8063-8068
-
-
Santoro, M.M.1
Bolen, D.W.2
-
28
-
-
34248674895
-
The stability effects of protein mutations appear to be universally distributed
-
N. Tokuriki, F. Stricher, J. Schymkowitz, L. Serrano, and D.S. Tawfik The stability effects of protein mutations appear to be universally distributed J. Mol. Biol. 369 2007 1318 1332
-
(2007)
J. Mol. Biol.
, vol.369
, pp. 1318-1332
-
-
Tokuriki, N.1
Stricher, F.2
Schymkowitz, J.3
Serrano, L.4
Tawfik, D.S.5
-
29
-
-
0035029482
-
Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol
-
T. Tomoyasu, A. Mogk, H. Langen, P. Goloubinoff, and B. Bukau Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol Mol. Microbiol. 40 2001 397 413
-
(2001)
Mol. Microbiol.
, vol.40
, pp. 397-413
-
-
Tomoyasu, T.1
Mogk, A.2
Langen, H.3
Goloubinoff, P.4
Bukau, B.5
-
30
-
-
0024711839
-
Structure of quinoprotein methylamine dehydrogenase at 2.25 A resolution
-
F.M. Vellieux, F. Huitema, H. Groendijk, K.H. Kalk, J.F. Jzn, J.A. Jongejan, J.A. Duine, K. Petratos, J. Drenth, and W.G. Hol Structure of quinoprotein methylamine dehydrogenase at 2.25 A resolution EMBO J. 8 1989 2171 2178
-
(1989)
EMBO J.
, vol.8
, pp. 2171-2178
-
-
Vellieux, F.M.1
Huitema, F.2
Groendijk, H.3
Kalk, K.H.4
Jzn, J.F.5
Jongejan, J.A.6
Duine, J.A.7
Petratos, K.8
Drenth, J.9
Hol, W.G.10
-
32
-
-
84908072118
-
Computational design of a self-assembling symmetrical β-propeller protein
-
A.R. Voet, H. Noguchi, C. Addy, D. Simoncini, D. Terada, S. Unzai, S.Y. Park, K.Y. Zhang, and J.R. Tame Computational design of a self-assembling symmetrical β-propeller protein Proc. Natl. Acad. Sci. USA 111 2014 15102 15107
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 15102-15107
-
-
Voet, A.R.1
Noguchi, H.2
Addy, C.3
Simoncini, D.4
Terada, D.5
Unzai, S.6
Park, S.Y.7
Zhang, K.Y.8
Tame, J.R.9
-
33
-
-
28644437048
-
The importance of sequence diversity in the aggregation and evolution of proteins
-
C.F. Wright, S.A. Teichmann, J. Clarke, and C.M. Dobson The importance of sequence diversity in the aggregation and evolution of proteins Nature 438 2005 878 881
-
(2005)
Nature
, vol.438
, pp. 878-881
-
-
Wright, C.F.1
Teichmann, S.A.2
Clarke, J.3
Dobson, C.M.4
-
34
-
-
33751415081
-
Reconstruction of functional β-propeller lectins via homo-oligomeric assembly of shorter fragments
-
I. Yadid, and D.S. Tawfik Reconstruction of functional β-propeller lectins via homo-oligomeric assembly of shorter fragments J. Mol. Biol. 365 2007 10 17
-
(2007)
J. Mol. Biol.
, vol.365
, pp. 10-17
-
-
Yadid, I.1
Tawfik, D.S.2
-
35
-
-
78650425278
-
Functional β-propeller lectins by tandem duplications of repetitive units
-
I. Yadid, and D.S. Tawfik Functional β-propeller lectins by tandem duplications of repetitive units Protein Eng. Des. Sel. 24 2011 185 195
-
(2011)
Protein Eng. Des. Sel.
, vol.24
, pp. 185-195
-
-
Yadid, I.1
Tawfik, D.S.2
-
36
-
-
77952163331
-
Metamorphic proteins mediate evolutionary transitions of structure
-
I. Yadid, N. Kirshenbaum, M. Sharon, O. Dym, and D.S. Tawfik Metamorphic proteins mediate evolutionary transitions of structure Proc. Natl. Acad. Sci. USA 107 2010 7287 7292
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 7287-7292
-
-
Yadid, I.1
Kirshenbaum, N.2
Sharon, M.3
Dym, O.4
Tawfik, D.S.5
-
37
-
-
84873105668
-
Frustration in the energy landscapes of multidomain protein misfolding
-
W. Zheng, N.P. Schafer, and P.G. Wolynes Frustration in the energy landscapes of multidomain protein misfolding Proc. Natl. Acad. Sci. USA 110 2013 1680 1685
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 1680-1685
-
-
Zheng, W.1
Schafer, N.P.2
Wolynes, P.G.3
|