-
2
-
-
0028342845
-
The evolution of functionally novel proteins after gene duplication
-
A.L. Hughes The evolution of functionally novel proteins after gene duplication Proc. Biol. Sci. 256 1994 119 124
-
(1994)
Proc. Biol. Sci.
, vol.256
, pp. 119-124
-
-
Hughes, A.L.1
-
3
-
-
0017272554
-
Enzyme recruitment in evolution of new function
-
R.A. Jensen Enzyme recruitment in evolution of new function Annu. Rev. Microbiol. 30 1976 409 425
-
(1976)
Annu. Rev. Microbiol.
, vol.30
, pp. 409-425
-
-
Jensen, R.A.1
-
4
-
-
0015980083
-
On earlier states of the biochemical system
-
M. Ycas On earlier states of the biochemical system J. Theor. Biol. 44 1974 145 160
-
(1974)
J. Theor. Biol.
, vol.44
, pp. 145-160
-
-
Ycas, M.1
-
5
-
-
0033117461
-
Catalytic promiscuity and the evolution of new enzymatic activities
-
P.J. O'Brien, and D. Herschlag Catalytic promiscuity and the evolution of new enzymatic activities Chem. Biol. 6 1999 R91 R105
-
(1999)
Chem. Biol.
, vol.6
-
-
O'Brien, P.J.1
Herschlag, D.2
-
6
-
-
77953623874
-
Enzyme promiscuity: A mechanistic and evolutionary perspective
-
O. Khersonsky, and D.S. Tawfik Enzyme promiscuity: a mechanistic and evolutionary perspective Annu. Rev. Biochem. 79 2010 471 505
-
(2010)
Annu. Rev. Biochem.
, vol.79
, pp. 471-505
-
-
Khersonsky, O.1
Tawfik, D.S.2
-
7
-
-
0032477286
-
Sulfatase activity of E coli alkaline phosphatase demonstrates a functional link to arylsulfatases, an evolutionarily related enzyme family
-
P.J. O'Brien, and D. Herschlag Sulfatase activity of E. coli alkaline phosphatase demonstrates a functional link to arylsulfatases, an evolutionarily related enzyme family J. Am. Chem. Soc. 120 1998 12369 12370
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 12369-12370
-
-
O'Brien, P.J.1
Herschlag, D.2
-
8
-
-
0344012191
-
The 4-oxalocrotonate tautomerase- and YwhB-catalyzed hydration of 3E-haloacrylates: Implications for the evolution of new enzymatic activities
-
S.C. Wang, W.H. Johnson Jr., and C.P. Whitman The 4-oxalocrotonate tautomerase- and YwhB-catalyzed hydration of 3E-haloacrylates: implications for the evolution of new enzymatic activities J. Am. Chem. Soc. 125 2003 14282 14283
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 14282-14283
-
-
Wang, S.C.1
Johnson, Jr.W.H.2
Whitman, C.P.3
-
10
-
-
78649857195
-
Three serendipitous pathways in E coli can bypass a block in pyridoxal-5'-phosphate synthesis
-
J. Kim, J.P. Kershner, Y. Novikov, R.K. Shoemaker, and S.D. Copley Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis Mol. Syst. Biol. 6 2010 436
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 436
-
-
Kim, J.1
Kershner, J.P.2
Novikov, Y.3
Shoemaker, R.K.4
Copley, S.D.5
-
11
-
-
0035846958
-
In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates
-
I. Matsumura, and A.D. Ellington In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates J. Mol. Biol. 305 2001 331 339
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 331-339
-
-
Matsumura, I.1
Ellington, A.D.2
-
12
-
-
10044248344
-
Catalytic promiscuity in biocatalysis: Using old enzymes to form new bonds and follow new pathways
-
U.T. Bornscheuer, and R.J. Kazlauskas Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways Angew. Chem. Int. Ed. Engl. 43 2004 6032 6040
-
(2004)
Angew. Chem. Int. Ed. Engl.
, vol.43
, pp. 6032-6040
-
-
Bornscheuer, U.T.1
Kazlauskas, R.J.2
-
13
-
-
84960296241
-
Mechanisms of protein evolution and their application to protein engineering
-
E.A. Toone, Wiley & Sons
-
M.E. Glasner, J.A. Gerlt, and P.C. Babbitt Mechanisms of protein evolution and their application to protein engineering E.A. Toone, Advances in Enzymology and Related Areas of Molecular Biology, Volume 75: Protein Evolution 2007 Wiley & Sons 193 239
-
(2007)
Advances in Enzymology and Related Areas of Molecular Biology, Volume 75: Protein Evolution
, pp. 193-239
-
-
Glasner, M.E.1
Gerlt, J.A.2
Babbitt, P.C.3
-
14
-
-
11244281311
-
The 'evolvability' of promiscuous protein functions
-
A. Aharoni, L. Gaidukov, O. Khersonsky, Q.G.S. Mc, C. Roodveldt, and D.S. Tawfik The 'evolvability' of promiscuous protein functions Nat. Genet. 37 2005 73 76
-
(2005)
Nat. Genet.
, vol.37
, pp. 73-76
-
-
Aharoni, A.1
Gaidukov, L.2
Khersonsky, O.3
Mc, Q.G.S.4
Roodveldt, C.5
Tawfik, D.S.6
-
15
-
-
33745229352
-
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily
-
M.E. Glasner, N. Fayazmanesh, R.A. Chiang, A. Sakai, M.P. Jacobson, J.A. Gerlt, and P.C. Babbitt Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily J. Mol. Biol. 360 2006 228 250
-
(2006)
J. Mol. Biol.
, vol.360
, pp. 228-250
-
-
Glasner, M.E.1
Fayazmanesh, N.2
Chiang, R.A.3
Sakai, A.4
Jacobson, M.P.5
Gerlt, J.A.6
Babbitt, P.C.7
-
16
-
-
0035219809
-
2) and ubiquinone (coenzyme Q): A perspective on enzymatic mechanisms
-
2) and ubiquinone (coenzyme Q): a perspective on enzymatic mechanisms Vitam. Horm. 61 2001 173 218
-
(2001)
Vitam. Horm.
, vol.61
, pp. 173-218
-
-
Meganathan, R.1
-
17
-
-
0033528659
-
Unexpected divergence of enzyme function and sequence. "n-acylamino acid racemase" is o-succinylbenzoate synthase
-
D.R. Palmer, J.B. Garrett, V. Sharma, R. Meganathan, P.C. Babbitt, and J.A. Gerlt Unexpected divergence of enzyme function and sequence. "N-acylamino acid racemase" is o-succinylbenzoate synthase Biochemistry 38 1999 4252 4258
-
(1999)
Biochemistry
, vol.38
, pp. 4252-4258
-
-
Palmer, D.R.1
Garrett, J.B.2
Sharma, V.3
Meganathan, R.4
Babbitt, P.C.5
Gerlt, J.A.6
-
18
-
-
33645677238
-
Evolution of enzymatic activities in the enolase superfamily: N-succinylamino acid racemase and a new pathway for the irreversible conversion of d- to l-amino acids
-
A. Sakai, D.F. Xiang, C. Xu, L. Song, W.S. Yew, F.M. Raushel, and J.A. Gerlt Evolution of enzymatic activities in the enolase superfamily: N-succinylamino acid racemase and a new pathway for the irreversible conversion of d- to l-amino acids Biochemistry 45 2006 4455 4462
-
(2006)
Biochemistry
, vol.45
, pp. 4455-4462
-
-
Sakai, A.1
Xiang, D.F.2
Xu, C.3
Song, L.4
Yew, W.S.5
Raushel, F.M.6
Gerlt, J.A.7
-
19
-
-
84902134541
-
Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family
-
(Epub date May 28, 2014)
-
D. Odokonyero, A. Sakai, Y. Patskovsky, V.N. Malashkevich, A.A. Fedorov, J.B. Bonanno, E.V. Fedorov, R. Toro, R. Agarwal, C. Wang, N.D.S. Ozerova, W.S. Yew, J.M. Sauder, S. Swaminathan, S.K. Burley, S.C. Almo, and M.E. Glasner Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family Proc. Natl. Acad. Sci. 2014 (Epub date May 28, 2014)
-
(2014)
Proc. Natl. Acad. Sci.
-
-
Odokonyero, D.1
Sakai, A.2
Patskovsky, Y.3
Malashkevich, V.N.4
Fedorov, A.A.5
Bonanno, J.B.6
Fedorov, E.V.7
Toro, R.8
Agarwal, R.9
Wang, C.10
Ozerova, N.D.S.11
Yew, W.S.12
Sauder, J.M.13
Swaminathan, S.14
Burley, S.K.15
Almo, S.C.16
Glasner, M.E.17
-
20
-
-
84855286291
-
Divergent evolution in enolase superfamily: Strategies for assigning functions
-
J.A. Gerlt, P.C. Babbitt, M.P. Jacobson, and S.C. Almo Divergent evolution in enolase superfamily: strategies for assigning functions J. Biol. Chem. 287 2012 29 34
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 29-34
-
-
Gerlt, J.A.1
Babbitt, P.C.2
Jacobson, M.P.3
Almo, S.C.4
-
21
-
-
0346096856
-
Evolution of enzymatic activity in the enolase superfamily: Functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis
-
E.A. Taylor Ringia, J.B. Garrett, J.B. Thoden, H.M. Holden, I. Rayment, and J.A. Gerlt Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis Biochemistry 43 2004 224 229
-
(2004)
Biochemistry
, vol.43
, pp. 224-229
-
-
Taylor Ringia, E.A.1
Garrett, J.B.2
Thoden, J.B.3
Holden, H.M.4
Rayment, I.5
Gerlt, J.A.6
-
22
-
-
84934441968
-
A family of LIC vectors for high-throughput cloning and purification of proteins
-
W.H. Eschenfeldt, S. Lucy, C.S. Millard, A. Joachimiak, and I.D. Mark A family of LIC vectors for high-throughput cloning and purification of proteins Methods Mol. Biol. 498 2009 105 115
-
(2009)
Methods Mol. Biol.
, vol.498
, pp. 105-115
-
-
Eschenfeldt, W.H.1
Lucy, S.2
Millard, C.S.3
Joachimiak, A.4
Mark, I.D.5
-
23
-
-
84864720657
-
Residues required for activity in Escherichia coli o-succinylbenzoate synthase (OSBS) are not conserved in all OSBS enzymes
-
W.W. Zhu, C. Wang, J. Jipp, L. Ferguson, S.N. Lucas, M.A. Hicks, and M.E. Glasner Residues required for activity in Escherichia coli o-succinylbenzoate synthase (OSBS) are not conserved in all OSBS enzymes Biochemistry 51 2012 6171 6181
-
(2012)
Biochemistry
, vol.51
, pp. 6171-6181
-
-
Zhu, W.W.1
Wang, C.2
Jipp, J.3
Ferguson, L.4
Lucas, S.N.5
Hicks, M.A.6
Glasner, M.E.7
-
24
-
-
41149132407
-
Comparative protein structure modeling using MODELLER
-
(John Wiley & Sons, Inc.)
-
N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.-Y. Shen, U. Pieper, and A. Sali Comparative protein structure modeling using MODELLER Curr. Protoc. Protein Sci. 2001 (John Wiley & Sons, Inc.)
-
(2001)
Curr. Protoc. Protein Sci.
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.-Y.6
Pieper, U.7
Sali, A.8
-
25
-
-
2442612271
-
Evolution of enzymatic activity in the enolase superfamily: Structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis
-
J.B. Thoden, E.A. Taylor Ringia, J.B. Garrett, J.A. Gerlt, H.M. Holden, and I. Rayment Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis Biochemistry 43 2004 5716 5727
-
(2004)
Biochemistry
, vol.43
, pp. 5716-5727
-
-
Thoden, J.B.1
Taylor Ringia, E.A.2
Garrett, J.B.3
Gerlt, J.A.4
Holden, H.M.5
Rayment, I.6
-
26
-
-
4143121187
-
Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans
-
W.C. Wang, W.C. Chiu, S.K. Hsu, C.L. Wu, C.Y. Chen, J.S. Liu, and W.H. Hsu Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans J. Mol. Biol. 342 2004 155 169
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 155-169
-
-
Wang, W.C.1
Chiu, W.C.2
Hsu, S.K.3
Wu, C.L.4
Chen, C.Y.5
Liu, J.S.6
Hsu, W.H.7
-
27
-
-
0033810049
-
Modeling of loops in protein structures
-
A. Fiser, R.K. Do, and A. Sali Modeling of loops in protein structures Protein Sci. 9 2000 1753 1773
-
(2000)
Protein Sci.
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
28
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
M.-Y. Shen, and A. Sali Statistical potential for assessment and prediction of protein structures Protein Sci. 15 2006 2507 2524
-
(2006)
Protein Sci.
, vol.15
, pp. 2507-2524
-
-
Shen, M.-Y.1
Sali, A.2
-
29
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
O. Trott, and A.J. Olson AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem. 31 2010 455 461
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
30
-
-
77954286682
-
Opal web services for biomedical applications
-
J.Y. Ren, N. Williams, L. Clementi, S. Krishnan, and W.W. Li Opal web services for biomedical applications Nucleic Acids Res. 38 2010 W724 W731
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Ren, J.Y.1
Williams, N.2
Clementi, L.3
Krishnan, S.4
Li, W.W.5
-
31
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
32
-
-
84867288643
-
Avogadro: An advanced semantic chemical editor, visualization, and analysis platform
-
M.D. Hanwell, D.E. Curtis, D.C. Lonie, T. Vandermeersch, E. Zurek, and G.R. Hutchison Avogadro: an advanced semantic chemical editor, visualization, and analysis platform J. Cheminform. 4 2012 17
-
(2012)
J. Cheminform.
, vol.4
, pp. 17
-
-
Hanwell, M.D.1
Curtis, D.E.2
Lonie, D.C.3
Vandermeersch, T.4
Zurek, E.5
Hutchison, G.R.6
-
33
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate, 1000 genomes
-
R. Overbeek, T. Begley, R.M. Butler, J.V. Choudhuri, H.Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E.D. Frank, S. Gerdes, E.M. Glass, A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M. Kubal, N. Larsen, B. Linke, A.C. McHardy, F. Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman, V. Portnoy, G.D. Pusch, D.A. Rodionov, C. Ruckert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, and V. Vonstein The subsystems approach to genome annotation and its use in the project to annotate, 1000 genomes Nucleic Acids Res. 33 2005 5691 5702
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
De Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
Fonstein, M.11
Frank, E.D.12
Gerdes, S.13
Glass, E.M.14
Goesmann, A.15
Hanson, A.16
Iwata-Reuyl, D.17
Jensen, R.18
Jamshidi, N.19
Krause, L.20
Kubal, M.21
Larsen, N.22
Linke, B.23
McHardy, A.C.24
Meyer, F.25
Neuweger, H.26
Olsen, G.27
Olson, R.28
Osterman, A.29
Portnoy, V.30
Pusch, G.D.31
Rodionov, D.A.32
Ruckert, C.33
Steiner, J.34
Stevens, R.35
Thiele, I.36
Vassieva, O.37
Ye, Y.38
Zagnitko, O.39
Vonstein, V.40
more..
-
34
-
-
84904741648
-
-
submitted for publication
-
A.W. McMillan, M.S. Lopez, M. Zhu, B.C. Morse, I.-C. Yeo, J. Amos, K. Hull, D. Romo, M.E. Glasner, Role of an active site loop in the promiscuous activities of amycolatopsis sp. T-1-60 NSAR/OSBS, submitted for publication.
-
Role of An Active Site Loop in the Promiscuous Activities of Amycolatopsis Sp. T-1-60 NSAR/OSBS
-
-
McMillan, A.W.1
Lopez, M.S.2
Zhu, M.3
Morse, B.C.4
Yeo, I.-C.5
Amos, J.6
Hull, K.7
Romo, D.8
Glasner, M.E.9
-
35
-
-
78651290702
-
ModBase, a database of annotated comparative protein structure models, and associated resources
-
U. Pieper, B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E.C. Meng, E.F. Pettersen, C.C. Huang, R.S. Datta, P. Sampathkumar, M.S. Madhusudhan, K. Sjolander, T.E. Ferrin, S.K. Burley, and A. Sali ModBase, a database of annotated comparative protein structure models, and associated resources Nucleic Acids Res. 39 2011 D465 D474
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Pieper, U.1
Webb, B.M.2
Barkan, D.T.3
Schneidman-Duhovny, D.4
Schlessinger, A.5
Braberg, H.6
Yang, Z.7
Meng, E.C.8
Pettersen, E.F.9
Huang, C.C.10
Datta, R.S.11
Sampathkumar, P.12
Madhusudhan, M.S.13
Sjolander, K.14
Ferrin, T.E.15
Burley, S.K.16
Sali, A.17
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