-
1
-
-
0035783063
-
Fold change in evolution of protein structures
-
Grishin N.V. Fold change in evolution of protein structures. J Struct Biol 2001, 134:167-185.
-
(2001)
J Struct Biol
, vol.134
, pp. 167-185
-
-
Grishin, N.V.1
-
2
-
-
1642325936
-
Evolutionary history and higher order classification of AAA+ ATPases
-
Iyer L.M., Leipe D.D., Koonin E.V., Aravind L. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol 2004, 146:11-31.
-
(2004)
J Struct Biol
, vol.146
, pp. 11-31
-
-
Iyer, L.M.1
Leipe, D.D.2
Koonin, E.V.3
Aravind, L.4
-
4
-
-
33751415081
-
Reconstruction of functional beta-propeller lectins via homo-oligomeric assembly of shorter fragments
-
Yadid I., Tawfik D.S. Reconstruction of functional beta-propeller lectins via homo-oligomeric assembly of shorter fragments. J Mol Biol 2007, 365:10-17.
-
(2007)
J Mol Biol
, vol.365
, pp. 10-17
-
-
Yadid, I.1
Tawfik, D.S.2
-
5
-
-
77952163331
-
Metamorphic proteins mediate evolutionary transitions of structure
-
Yadid I., Kirshenbaum N., Sharon M., Dym O., Tawfik D.S. Metamorphic proteins mediate evolutionary transitions of structure. Proc Natl Acad Sci U S A 2010, 107:7287-7292.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 7287-7292
-
-
Yadid, I.1
Kirshenbaum, N.2
Sharon, M.3
Dym, O.4
Tawfik, D.S.5
-
6
-
-
84862830777
-
The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms
-
Kim K.M., Caetano-Anolles G. The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms. BMC Evol Biol 2012, 12:13.
-
(2012)
BMC Evol Biol
, vol.12
, pp. 13
-
-
Kim, K.M.1
Caetano-Anolles, G.2
-
7
-
-
84869082987
-
Emergence of symmetric protein architecture from a simple peptide motif: evolutionary models
-
[Epub ahead of print]
-
Blaber M., Lee J., Longo L. Emergence of symmetric protein architecture from a simple peptide motif: evolutionary models. Cell Mol Life Sci 2012, [Epub ahead of print].
-
(2012)
Cell Mol Life Sci
-
-
Blaber, M.1
Lee, J.2
Longo, L.3
-
8
-
-
70349461173
-
The continuity of protein structure space is an intrinsic property of proteins
-
Skolnick J., Arakaki A.K., Lee S.Y., Brylinski M. The continuity of protein structure space is an intrinsic property of proteins. Proc Natl Acad Sci U S A 2009, 106:15690-15695.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 15690-15695
-
-
Skolnick, J.1
Arakaki, A.K.2
Lee, S.Y.3
Brylinski, M.4
-
9
-
-
22244450719
-
Protein families and their evolution-a structural perspective
-
Orengo C.A., Thornton J.M. Protein families and their evolution-a structural perspective. Annu Rev Biochem 2005, 74:867-900.
-
(2005)
Annu Rev Biochem
, vol.74
, pp. 867-900
-
-
Orengo, C.A.1
Thornton, J.M.2
-
10
-
-
80052969570
-
The evolutionary origin of orphan genes
-
Tautz D., Domazet-Loso T. The evolutionary origin of orphan genes. Nat Rev Genet 2011, 12:692-702.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 692-702
-
-
Tautz, D.1
Domazet-Loso, T.2
-
11
-
-
70349645640
-
Recent de novo origin of human protein-coding genes
-
Knowles D.G., McLysaght A. Recent de novo origin of human protein-coding genes. Genome Res 2009, 19:1752-1759.
-
(2009)
Genome Res
, vol.19
, pp. 1752-1759
-
-
Knowles, D.G.1
McLysaght, A.2
-
12
-
-
78649231644
-
Origins, evolution, and phenotypic impact of new genes
-
Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res 2013, 20:1313-1326.
-
(2013)
Genome Res
, vol.20
, pp. 1313-1326
-
-
Kaessmann, H.1
-
13
-
-
84869060468
-
Evolution of viral proteins originated de novo by overprinting
-
Sabath N., Wagner A., Karlin D. Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol 2012, 29:3767-3780.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 3767-3780
-
-
Sabath, N.1
Wagner, A.2
Karlin, D.3
-
14
-
-
84881103245
-
Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes
-
Carter J.J., Daugherty M.D., Qi X., Bheda-Malge A., Wipf G.C., Robinson K., Roman A., Malik H.S., Galloway D.A. Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. Proc Natl Acad Sci U S A 2013, 110:12744-12749.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 12744-12749
-
-
Carter, J.J.1
Daugherty, M.D.2
Qi, X.3
Bheda-Malge, A.4
Wipf, G.C.5
Robinson, K.6
Roman, A.7
Malik, H.S.8
Galloway, D.A.9
-
15
-
-
33745899357
-
The crystal structure of ORF-9b, a lipid binding protein from the SARS coronavirus
-
Meier C., Aricescu A.R., Assenberg R., Aplin R.T., Gilbert R.J., Grimes J.M., Stuart D.I. The crystal structure of ORF-9b, a lipid binding protein from the SARS coronavirus. Structure 2006, 14:1157-1165.
-
(2006)
Structure
, vol.14
, pp. 1157-1165
-
-
Meier, C.1
Aricescu, A.R.2
Assenberg, R.3
Aplin, R.T.4
Gilbert, R.J.5
Grimes, J.M.6
Stuart, D.I.7
-
16
-
-
70349737853
-
Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation
-
Rancurel C., Khosravi M., Dunker A.K., Romero P.R., Karlin D. Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J Virol 2009, 83:10719-10736.
-
(2009)
J Virol
, vol.83
, pp. 10719-10736
-
-
Rancurel, C.1
Khosravi, M.2
Dunker, A.K.3
Romero, P.R.4
Karlin, D.5
-
17
-
-
78650476811
-
A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation
-
Wang M., Jiang Y.Y., Kim K.M., Qu G., Ji H.F., Mittenthal J.E., Zhang H.Y., Caetano-Anolles G. A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation. Mol Biol Evol 2011, 28:567-582.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 567-582
-
-
Wang, M.1
Jiang, Y.Y.2
Kim, K.M.3
Qu, G.4
Ji, H.F.5
Mittenthal, J.E.6
Zhang, H.Y.7
Caetano-Anolles, G.8
-
18
-
-
33846059668
-
The generation of new protein functions by the combination of domains
-
Bashton M., Chothia C. The generation of new protein functions by the combination of domains. Structure 2007, 15:85-99.
-
(2007)
Structure
, vol.15
, pp. 85-99
-
-
Bashton, M.1
Chothia, C.2
-
19
-
-
58149196295
-
The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world
-
Wang M., Caetano-Anolles G. The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 2009, 17:66-78.
-
(2009)
Structure
, vol.17
, pp. 66-78
-
-
Wang, M.1
Caetano-Anolles, G.2
-
20
-
-
84862907907
-
Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny
-
Wu Y.C., Rasmussen M.D., Kellis M. Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. Mol Biol Evol 2012, 29:689-705.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 689-705
-
-
Wu, Y.C.1
Rasmussen, M.D.2
Kellis, M.3
-
21
-
-
84860138819
-
Evolution of protein domain architectures
-
Forslund K., Sonnhammer E.L. Evolution of protein domain architectures. Methods Mol Biol 2012, 856:187-216.
-
(2012)
Methods Mol Biol
, vol.856
, pp. 187-216
-
-
Forslund, K.1
Sonnhammer, E.L.2
-
22
-
-
77958156358
-
How do proteins gain new domains?
-
Marsh J.A., Teichmann S.A. How do proteins gain new domains?. Genome Biol 2010, 11:126.
-
(2010)
Genome Biol
, vol.11
, pp. 126
-
-
Marsh, J.A.1
Teichmann, S.A.2
-
23
-
-
84864645362
-
Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling
-
Afriat-Jurnou L., Jackson C.J., Tawfik D.S. Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling. Biochemistry 2012, 51:6047-6055.
-
(2012)
Biochemistry
, vol.51
, pp. 6047-6055
-
-
Afriat-Jurnou, L.1
Jackson, C.J.2
Tawfik, D.S.3
-
24
-
-
84875601072
-
Protein insertions and deletions enabled by neutral roaming in sequence space
-
Toth-Petroczy A., Tawfik D.S. Protein insertions and deletions enabled by neutral roaming in sequence space. Mol Biol Evol 2013, 30:761-771.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 761-771
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
25
-
-
33746922036
-
Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes
-
Burroughs A.M., Allen K.N., Dunaway-Mariano D., Aravind L. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol 2006, 361:1003-1034.
-
(2006)
J Mol Biol
, vol.361
, pp. 1003-1034
-
-
Burroughs, A.M.1
Allen, K.N.2
Dunaway-Mariano, D.3
Aravind, L.4
-
26
-
-
84880659609
-
Evolutionary diversification of the multimeric states of proteins
-
Lynch M. Evolutionary diversification of the multimeric states of proteins. Proc Natl Acad Sci U S A 2013, 110:E2821-E2828.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
-
-
Lynch, M.1
-
27
-
-
79961038718
-
Maps of protein structure space reveal a fundamental relationship between protein structure and function
-
Osadchy M., Kolodny R. Maps of protein structure space reveal a fundamental relationship between protein structure and function. Proc Natl Acad Sci U S A 2011, 108:12301-12306.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 12301-12306
-
-
Osadchy, M.1
Kolodny, R.2
-
28
-
-
78651338019
-
Extending CATH: increasing coverage of the protein structure universe and linking structure with function
-
Cuff A.L., Sillitoe I., Lewis T., Clegg A.B., Rentzsch R., Furnham N., Pellegrini-Calace M., Jones D., Thornton J., Orengo C.A. Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res 2011, 39:D420-D426.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cuff, A.L.1
Sillitoe, I.2
Lewis, T.3
Clegg, A.B.4
Rentzsch, R.5
Furnham, N.6
Pellegrini-Calace, M.7
Jones, D.8
Thornton, J.9
Orengo, C.A.10
-
29
-
-
84858077472
-
The Pfam protein families database
-
Punta M., Coggill P.C., Eberhardt R.Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., Clements J., et al. The Pfam protein families database. Nucleic Acids Res 2012, 40:D290-D301.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
-
34
-
-
0014935646
-
Natural selection and the concept of a protein space
-
Smith J.M. Natural selection and the concept of a protein space. Nature 1970, 225:563-564.
-
(1970)
Nature
, vol.225
, pp. 563-564
-
-
Smith, J.M.1
-
35
-
-
13044269058
-
Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space
-
Bornberg-Bauer E., Chan H.S. Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. Proc Natl Acad Sci U S A 1999, 96:10689-10694.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 10689-10694
-
-
Bornberg-Bauer, E.1
Chan, H.S.2
-
36
-
-
23944490117
-
Missense meanderings in sequence space: a biophysical view of protein evolution
-
DePristo M.A., Weinreich D.M., Hartl D.L. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 2005, 6:678-687.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 678-687
-
-
DePristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
37
-
-
15544390249
-
Protein structure and evolutionary history determine sequence space topology
-
Shakhnovich B.E., Deeds E., Delisi C., Shakhnovich E. Protein structure and evolutionary history determine sequence space topology. Genome Res 2005, 15:385-392.
-
(2005)
Genome Res
, vol.15
, pp. 385-392
-
-
Shakhnovich, B.E.1
Deeds, E.2
Delisi, C.3
Shakhnovich, E.4
-
38
-
-
70349901079
-
Stability effects of mutations and protein evolvability
-
Tokuriki N., Tawfik D.S. Stability effects of mutations and protein evolvability. Curr Opin Struct Biol 2009, 19:596-604.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 596-604
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
39
-
-
67650287695
-
In the light of directed evolution: pathways of adaptive protein evolution
-
Bloom J.D., Arnold F.H. In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 2009, 106(Suppl. 1):9995-10000.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.SUPPL 1
, pp. 9995-10000
-
-
Bloom, J.D.1
Arnold, F.H.2
-
40
-
-
84880563504
-
Evolvability of thermophilic proteins from archaea and bacteria
-
Takano K., Aoi A., Koga Y., Kanaya S. Evolvability of thermophilic proteins from archaea and bacteria. Biochemistry 2013, 52:4774-4780.
-
(2013)
Biochemistry
, vol.52
, pp. 4774-4780
-
-
Takano, K.1
Aoi, A.2
Koga, Y.3
Kanaya, S.4
-
41
-
-
84891761205
-
Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure
-
Yeh S.W., Liu J.W., Yu S.H., Shih C.H., Hwang J.K., Echave J. Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Mol Biol Evol 2014, 31:135-139.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 135-139
-
-
Yeh, S.W.1
Liu, J.W.2
Yu, S.H.3
Shih, C.H.4
Hwang, J.K.5
Echave, J.6
-
42
-
-
33748143748
-
Structural determinants of the rate of protein evolution in yeast
-
Bloom J.D., Drummond D.A., Arnold F.H., Wilke C.O. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 2006, 23:1751-1761.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1751-1761
-
-
Bloom, J.D.1
Drummond, D.A.2
Arnold, F.H.3
Wilke, C.O.4
-
43
-
-
80055069190
-
Protein structural modularity and robustness are associated with evolvability
-
Rorick M.M., Wagner G.P. Protein structural modularity and robustness are associated with evolvability. Genome Biol Evol 2011, 3:456-475.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 456-475
-
-
Rorick, M.M.1
Wagner, G.P.2
-
44
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
Bershtein S., Segal M., Bekerman R., Tokuriki N., Tawfik D.S. Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 2006, 444:929-932.
-
(2006)
Nature
, vol.444
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
45
-
-
59649108762
-
Do viral proteins posses unique biophysical features?
-
Tokuriki N. Do viral proteins posses unique biophysical features?. Trends Biochem Sci 2008, 34:53-59.
-
(2008)
Trends Biochem Sci
, vol.34
, pp. 53-59
-
-
Tokuriki, N.1
-
46
-
-
0036017388
-
Evolutionary rate heterogeneity in proteins with long disordered regions
-
Brown C.J., Takayama S., Campen A.M., Vise P., Marshall T.W., Oldfield C.J., Williams C.J., Dunker A.K. Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 2002, 55:104-110.
-
(2002)
J Mol Evol
, vol.55
, pp. 104-110
-
-
Brown, C.J.1
Takayama, S.2
Campen, A.M.3
Vise, P.4
Marshall, T.W.5
Oldfield, C.J.6
Williams, C.J.7
Dunker, A.K.8
-
47
-
-
79960601166
-
Slow protein evolutionary rates are dictated by surface-core association
-
Toth-Petroczy A., Tawfik D.S. Slow protein evolutionary rates are dictated by surface-core association. Proc Natl Acad Sci U S A 2011, 108:11151-11156.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 11151-11156
-
-
Toth-Petroczy, A.1
Tawfik, D.S.2
-
48
-
-
84879549646
-
What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs
-
Dellus-Gur E., Toth-Petroczy A., Elias M., Tawfik D.S. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J Mol Biol 2013, 425:2609-2621.
-
(2013)
J Mol Biol
, vol.425
, pp. 2609-2621
-
-
Dellus-Gur, E.1
Toth-Petroczy, A.2
Elias, M.3
Tawfik, D.S.4
-
49
-
-
84866060981
-
The role of local backrub motions in evolved and designed mutations
-
Keedy D.A., Georgiev I., Triplett E.B., Donald B.R., Richardson D.C., Richardson J.S. The role of local backrub motions in evolved and designed mutations. PLoS Comput Biol 2012, 8:e1002629.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Keedy, D.A.1
Georgiev, I.2
Triplett, E.B.3
Donald, B.R.4
Richardson, D.C.5
Richardson, J.S.6
-
50
-
-
84874036318
-
Flexible backbone sampling methods to model and design protein alternative conformations
-
Ollikainen N., Smith C.A., Fraser J.S., Kortemme T. Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol 2013, 523:61-85.
-
(2013)
Methods Enzymol
, vol.523
, pp. 61-85
-
-
Ollikainen, N.1
Smith, C.A.2
Fraser, J.S.3
Kortemme, T.4
-
51
-
-
43149112799
-
Contact density affects protein evolutionary rate from bacteria to animals
-
Zhou T., Drummond D.A., Wilke C.O. Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol 2008, 66:395-404.
-
(2008)
J Mol Evol
, vol.66
, pp. 395-404
-
-
Zhou, T.1
Drummond, D.A.2
Wilke, C.O.3
-
52
-
-
84892475033
-
Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge
-
Hingorani K.S., Gierasch L.M. Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge. Curr Opin Struct Biol 2014, 24C:81-90.
-
(2014)
Curr Opin Struct Biol
, vol.24 C
, pp. 81-90
-
-
Hingorani, K.S.1
Gierasch, L.M.2
-
54
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
Wang X., Minasov G., Shoichet B.K. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 2002, 320:85-95.
-
(2002)
J Mol Biol
, vol.320
, pp. 85-95
-
-
Wang, X.1
Minasov, G.2
Shoichet, B.K.3
-
55
-
-
33645811495
-
Protein stability promotes evolvability
-
Bloom J.D., Labthavikul S.T., Otey C.R., Arnold F.H. Protein stability promotes evolvability. Proc Natl Acad Sci U S A 2006, 103:5869-5874.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 5869-5874
-
-
Bloom, J.D.1
Labthavikul, S.T.2
Otey, C.R.3
Arnold, F.H.4
-
56
-
-
44949206468
-
Protein robustness promotes evolutionary innovations on large evolutionary time-scales
-
Ferrada E., Wagner A. Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proc Biol Sci 2008, 275:1595-1602.
-
(2008)
Proc Biol Sci
, vol.275
, pp. 1595-1602
-
-
Ferrada, E.1
Wagner, A.2
-
57
-
-
0023557882
-
Relationship of protein flexibility to thermostability
-
Vihinen M. Relationship of protein flexibility to thermostability. Protein Eng 1987, 1:477-480.
-
(1987)
Protein Eng
, vol.1
, pp. 477-480
-
-
Vihinen, M.1
-
58
-
-
33845288649
-
Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability
-
Reetz M.T., Carballeira J.D., Vogel A. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 2006, 45:7745-7751.
-
(2006)
Angew Chem Int Ed Engl
, vol.45
, pp. 7745-7751
-
-
Reetz, M.T.1
Carballeira, J.D.2
Vogel, A.3
-
59
-
-
41649116075
-
A structural model of latent evolutionary potentials underlying neutral networks in proteins
-
Wroe R., Chan H.S., Bornberg-Bauer E. A structural model of latent evolutionary potentials underlying neutral networks in proteins. HFSP J 2007, 1:79-87.
-
(2007)
HFSP J
, vol.1
, pp. 79-87
-
-
Wroe, R.1
Chan, H.S.2
Bornberg-Bauer, E.3
-
60
-
-
64849101493
-
Protein dynamism and evolvability
-
Tokuriki N., Tawfik D.S. Protein dynamism and evolvability. Science 2009, 324:203-207.
-
(2009)
Science
, vol.324
, pp. 203-207
-
-
Tokuriki, N.1
Tawfik, D.S.2
-
61
-
-
84875443183
-
Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme
-
Ben-David M., Wieczorek G., Elias M., Silman I., Sussman J.L., Tawfik D.S. Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme. J Mol Biol 2013, 425:1028-1038.
-
(2013)
J Mol Biol
, vol.425
, pp. 1028-1038
-
-
Ben-David, M.1
Wieczorek, G.2
Elias, M.3
Silman, I.4
Sussman, J.L.5
Tawfik, D.S.6
-
62
-
-
84859267247
-
Catalytic versatility and backups in enzyme active sites: the case of serum paraoxonase 1
-
Ben-David M., Elias M., Filippi J.J., Dunach E., Silman I., Sussman J.L., Tawfik D.S. Catalytic versatility and backups in enzyme active sites: the case of serum paraoxonase 1. J Mol Biol 2012, 418:181-196.
-
(2012)
J Mol Biol
, vol.418
, pp. 181-196
-
-
Ben-David, M.1
Elias, M.2
Filippi, J.J.3
Dunach, E.4
Silman, I.5
Sussman, J.L.6
Tawfik, D.S.7
-
64
-
-
0041673352
-
Structural determinant of protein designability
-
England J.L., Shakhnovich E.I. Structural determinant of protein designability. Phys Rev Lett 2003, 90:218101.
-
(2003)
Phys Rev Lett
, vol.90
, pp. 218101
-
-
England, J.L.1
Shakhnovich, E.I.2
-
65
-
-
77955844575
-
Robustness and evolvability
-
Masel J., Trotter M.V. Robustness and evolvability. Trends Genet 2010, 26:406-414.
-
(2010)
Trends Genet
, vol.26
, pp. 406-414
-
-
Masel, J.1
Trotter, M.V.2
-
66
-
-
84896691834
-
Intrinsic disorder in proteins involved in the innate antiviral immunity: another flexible side of a molecular arms race
-
Xue B., Uversky V.N. Intrinsic disorder in proteins involved in the innate antiviral immunity: another flexible side of a molecular arms race. J Mol Biol 2013, 426:1322-1350.
-
(2013)
J Mol Biol
, vol.426
, pp. 1322-1350
-
-
Xue, B.1
Uversky, V.N.2
-
67
-
-
84877896151
-
Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding
-
Hsu W.L., Oldfield C.J., Xue B., Meng J., Huang F., Romero P., Uversky V.N., Dunker A.K. Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding. Protein Sci 2013, 22:258-273.
-
(2013)
Protein Sci
, vol.22
, pp. 258-273
-
-
Hsu, W.L.1
Oldfield, C.J.2
Xue, B.3
Meng, J.4
Huang, F.5
Romero, P.6
Uversky, V.N.7
Dunker, A.K.8
-
69
-
-
79958023248
-
Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies
-
Meng E.C., Babbitt P.C. Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Curr Opin Struct Biol 2011, 21:391-397.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 391-397
-
-
Meng, E.C.1
Babbitt, P.C.2
-
70
-
-
0036435882
-
Analysis of catalytic residues in enzyme active sites
-
Bartlett G.J., Porter C.T., Borkakoti N., Thornton J.M. Analysis of catalytic residues in enzyme active sites. J Mol Biol 2002, 324:105-121.
-
(2002)
J Mol Biol
, vol.324
, pp. 105-121
-
-
Bartlett, G.J.1
Porter, C.T.2
Borkakoti, N.3
Thornton, J.M.4
-
71
-
-
79960696816
-
Exploring the structure-function loop adaptability of a (beta/alpha)(8)-barrel enzyme through loop swapping and hinge variability
-
Ochoa-Leyva A., Barona-Gomez F., Saab-Rincon G., Verdel-Aranda K., Sanchez F., Soberon X. Exploring the structure-function loop adaptability of a (beta/alpha)(8)-barrel enzyme through loop swapping and hinge variability. J Mol Biol 2011, 411:143-157.
-
(2011)
J Mol Biol
, vol.411
, pp. 143-157
-
-
Ochoa-Leyva, A.1
Barona-Gomez, F.2
Saab-Rincon, G.3
Verdel-Aranda, K.4
Sanchez, F.5
Soberon, X.6
-
72
-
-
33747892053
-
Relative contributions of structural designability and functional diversity in molecular evolution of duplicates
-
Shakhnovich B.E. Relative contributions of structural designability and functional diversity in molecular evolution of duplicates. Bioinformatics 2006, 22:e440-e445.
-
(2006)
Bioinformatics
, vol.22
-
-
Shakhnovich, B.E.1
-
73
-
-
0017227120
-
Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins
-
Zuckerkandl E. Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins. J Mol Evol 1976, 7:167-183.
-
(1976)
J Mol Evol
, vol.7
, pp. 167-183
-
-
Zuckerkandl, E.1
-
74
-
-
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 2010, 465:922-926.
-
(2010)
Nature
, vol.465
, pp. 922-926
-
-
Povolotskaya, I.S.1
Kondrashov, F.A.2
-
75
-
-
84867781208
-
Epistasis as the primary factor in molecular evolution
-
Breen M.S., Kemena C., Vlasov P.K., Notredame C., Kondrashov F.A. Epistasis as the primary factor in molecular evolution. Nature 2012, 490:535-538.
-
(2012)
Nature
, vol.490
, pp. 535-538
-
-
Breen, M.S.1
Kemena, C.2
Vlasov, P.K.3
Notredame, C.4
Kondrashov, F.A.5
-
76
-
-
79953738501
-
Initial mutations direct alternative pathways of protein evolution
-
Salverda M.L., Dellus E., Gorter F.A., Debets A.J., van der Oost J., Hoekstra R.F., Tawfik D.S., de Visser J.A. Initial mutations direct alternative pathways of protein evolution. PLoS Genet 2011, 7:e1001321.
-
(2011)
PLoS Genet
, vol.7
-
-
Salverda, M.L.1
Dellus, E.2
Gorter, F.A.3
Debets, A.J.4
van der Oost, J.5
Hoekstra, R.F.6
Tawfik, D.S.7
de Visser, J.A.8
-
77
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich D.M., Delaney N.F., Depristo M.A., Hartl D.L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 2006, 312:111-114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
78
-
-
44349161622
-
Intense neutral drifts yield robust and evolvable consensus proteins
-
Bershtein S., Goldin K., Tawfik D.S. Intense neutral drifts yield robust and evolvable consensus proteins. J Mol Biol 2008, 379:1029-1044.
-
(2008)
J Mol Biol
, vol.379
, pp. 1029-1044
-
-
Bershtein, S.1
Goldin, K.2
Tawfik, D.S.3
-
79
-
-
84879943516
-
Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors
-
Harms M.J., Eick G.N., Goswami D., Colucci J.K., Griffin P.R., Ortlund E.A., Thornton J.W. Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors. Proc Natl Acad Sci U S A 2013, 110:11475-11480.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 11475-11480
-
-
Harms, M.J.1
Eick, G.N.2
Goswami, D.3
Colucci, J.K.4
Griffin, P.R.5
Ortlund, E.A.6
Thornton, J.W.7
-
80
-
-
71149120194
-
Optimizing protein stability in vivo
-
Foit L., Morgan G.J., Kern M.J., Steimer L.R., von Hacht A.A., Titchmarsh J., Warriner S.L., Radford S.E., Bardwell J.C. Optimizing protein stability in vivo. Mol Cell 2009, 36:861-871.
-
(2009)
Mol Cell
, vol.36
, pp. 861-871
-
-
Foit, L.1
Morgan, G.J.2
Kern, M.J.3
Steimer, L.R.4
von Hacht, A.A.5
Titchmarsh, J.6
Warriner, S.L.7
Radford, S.E.8
Bardwell, J.C.9
-
81
-
-
79959834622
-
Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor
-
Carroll S.M., Ortlund E.A., Thornton J.W. Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PLoS Genet 2011, 7:e1002117.
-
(2011)
PLoS Genet
, vol.7
-
-
Carroll, S.M.1
Ortlund, E.A.2
Thornton, J.W.3
-
82
-
-
84887894373
-
Evolution of protein structures and interactions from the perspective of residue contact networks
-
Zhang X., Perica T., Teichmann S.A. Evolution of protein structures and interactions from the perspective of residue contact networks. Curr Opin Struct Biol 2013, 23:954-963.
-
(2013)
Curr Opin Struct Biol
, vol.23
, pp. 954-963
-
-
Zhang, X.1
Perica, T.2
Teichmann, S.A.3
-
83
-
-
84862992463
-
Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
-
Buljan M., Chalancon G., Eustermann S., Wagner G.P., Fuxreiter M., Bateman A., Babu M.M. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 2012, 46:871-883.
-
(2012)
Mol Cell
, vol.46
, pp. 871-883
-
-
Buljan, M.1
Chalancon, G.2
Eustermann, S.3
Wagner, G.P.4
Fuxreiter, M.5
Bateman, A.6
Babu, M.M.7
-
84
-
-
84866463338
-
Structural biology. Versatility from protein disorder
-
Babu M.M., Kriwacki R.W., Pappu R.V. Structural biology. Versatility from protein disorder. Science 2012, 337:1460-1461.
-
(2012)
Science
, vol.337
, pp. 1460-1461
-
-
Babu, M.M.1
Kriwacki, R.W.2
Pappu, R.V.3
-
85
-
-
66249092825
-
An analytically solvable model for rapid evolution of modular structure
-
Kashtan N., Mayo A.E., Kalisky T., Alon U. An analytically solvable model for rapid evolution of modular structure. PLoS Comput Biol 2009, 5:e1000355.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Kashtan, N.1
Mayo, A.E.2
Kalisky, T.3
Alon, U.4
|