-
1
-
-
34347383961
-
Evolutionary transitions in protein fold space
-
Taylor W.R. Evolutionary transitions in protein fold space. Curr Opin Struct Biol 17 (2007) 354-361
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 354-361
-
-
Taylor, W.R.1
-
2
-
-
40849118252
-
Moonlighting proteins in yeasts
-
[table of contents]
-
Gancedo C., and Flores C.-L. Moonlighting proteins in yeasts. Microbiol Mol Biol Rev 72 (2008) 197-210 [table of contents]
-
(2008)
Microbiol Mol Biol Rev
, vol.72
, pp. 197-210
-
-
Gancedo, C.1
Flores, C.-L.2
-
3
-
-
38449095243
-
Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression
-
Commichau F.M., and Stulke J. Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression. Mol Microbiol 67 (2008) 692-702
-
(2008)
Mol Microbiol
, vol.67
, pp. 692-702
-
-
Commichau, F.M.1
Stulke, J.2
-
4
-
-
33745727120
-
Structural diversity of domain superfamilies in the CATH database
-
•], describes the surprising amount of structural diversity that can arise in proteins that are related evolutionarily as a result of variations in functional necessities, such as novel oligomeric states or binding of ligands with different moieties.
-
•], describes the surprising amount of structural diversity that can arise in proteins that are related evolutionarily as a result of variations in functional necessities, such as novel oligomeric states or binding of ligands with different moieties.
-
(2006)
J Mol Biol
, vol.360
, pp. 725-741
-
-
Reeves, G.A.1
Dallman, T.J.2
Redfern, O.C.3
Akpor, A.4
Orengo, C.A.5
-
6
-
-
0034682881
-
An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
-
Yang A.S., and Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J Mol Biol 301 (2000) 665-678
-
(2000)
J Mol Biol
, vol.301
, pp. 665-678
-
-
Yang, A.S.1
Honig, B.2
-
8
-
-
33744805069
-
Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction
-
Kolodny R., Petrey D., and Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 16 (2006) 393-398
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 393-398
-
-
Kolodny, R.1
Petrey, D.2
Honig, B.3
-
9
-
-
66549120700
-
-
note
-
•] discusses an array of functional relationship between proteins that would normally be considered structurally dissimilar and evolutionarily unrelated, and highlights the potential for remote structural relationships to reveal useful functional information.
-
-
-
-
11
-
-
42949090435
-
A folding space odyssey
-
•] which demonstrate an unambiguous evolutionary link between proteins that would normally be classified differently in terms of their overall structure, that is an all-α protein and an α/β protein.
-
•] which demonstrate an unambiguous evolutionary link between proteins that would normally be classified differently in terms of their overall structure, that is an all-α protein and an α/β protein.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 2759-2760
-
-
Davidson, A.R.1
-
12
-
-
0033555717
-
Exploring the conformational properties of the sequence space between two proteins with different folds: an experimental study
-
Blanco F.J., Angrand I., and Serrano L. Exploring the conformational properties of the sequence space between two proteins with different folds: an experimental study. J Mol Biol 285 (1999) 741-753
-
(1999)
J Mol Biol
, vol.285
, pp. 741-753
-
-
Blanco, F.J.1
Angrand, I.2
Serrano, L.3
-
13
-
-
55749108537
-
NMR structures of two designed proteins with high sequence identity but different fold and function
-
He Y., Chen Y., Alexander P., Bryan P.N., and Orban J. NMR structures of two designed proteins with high sequence identity but different fold and function. Proc Natl Acad Sci U S A 105 (2008) 14412-14417
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 14412-14417
-
-
He, Y.1
Chen, Y.2
Alexander, P.3
Bryan, P.N.4
Orban, J.5
-
14
-
-
33846209932
-
Continuous molecular evolution of protein-domain structures by single amino acid changes
-
Meier S., Jensen P.R., David C.N., Chapman J., Holstein T.W., Grzesiek S., and Ozbek S. Continuous molecular evolution of protein-domain structures by single amino acid changes. Curr Biol 17 (2007) 173-178
-
(2007)
Curr Biol
, vol.17
, pp. 173-178
-
-
Meier, S.1
Jensen, P.R.2
David, C.N.3
Chapman, J.4
Holstein, T.W.5
Grzesiek, S.6
Ozbek, S.7
-
15
-
-
35848935407
-
A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution?
-
Meier S., and Ozbek S. A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution?. BioEssays: News Rev Mol Cell Dev Biol 29 (2007) 1095-1104
-
(2007)
BioEssays: News Rev Mol Cell Dev Biol
, vol.29
, pp. 1095-1104
-
-
Meier, S.1
Ozbek, S.2
-
16
-
-
1842420626
-
The Mad2 spindle checkpoint protein has two distinct natively folded states
-
Luo X., Tang Z., Xia G., Wassmann K., Matsumoto T., Rizo J., and Yu H. The Mad2 spindle checkpoint protein has two distinct natively folded states. Nat Struct Mol Biol 11 (2004) 338-345
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 338-345
-
-
Luo, X.1
Tang, Z.2
Xia, G.3
Wassmann, K.4
Matsumoto, T.5
Rizo, J.6
Yu, H.7
-
17
-
-
42449084477
-
Interconversion between two unrelated protein folds in the lymphotactin native state
-
Tuinstra R.L., Peterson F.C., Kutlesa S., Elgin E.S., Kron M.A., and Volkman B.F. Interconversion between two unrelated protein folds in the lymphotactin native state. Proc Natl Acad Sci U S A 105 (2008) 5057-5062
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 5057-5062
-
-
Tuinstra, R.L.1
Peterson, F.C.2
Kutlesa, S.3
Elgin, E.S.4
Kron, M.A.5
Volkman, B.F.6
-
18
-
-
33646472273
-
A tale of two ferredoxins: sequence similarity and structural differences
-
Krishna S.S., Sadreyev R.I., and Grishin N.V. A tale of two ferredoxins: sequence similarity and structural differences. BMC Struct Biol 6 (2006) 8
-
(2006)
BMC Struct Biol
, vol.6
, pp. 8
-
-
Krishna, S.S.1
Sadreyev, R.I.2
Grishin, N.V.3
-
19
-
-
33846059668
-
The generation of new protein functions by the combination of domains
-
Bashton M., and Chothia C. The generation of new protein functions by the combination of domains. Structure (London, England: 1993) 15 (2007) 85-99
-
(2007)
Structure (London, England: 1993)
, vol.15
, pp. 85-99
-
-
Bashton, M.1
Chothia, C.2
-
20
-
-
50849114838
-
Arrangements in the modular evolution of proteins
-
Moore A.D., Bjorklund A.K., Ekman D., Bornberg-Bauer E., and Elofsson A. Arrangements in the modular evolution of proteins. Trends Biochem Sci 33 (2008) 444-451
-
(2008)
Trends Biochem Sci
, vol.33
, pp. 444-451
-
-
Moore, A.D.1
Bjorklund, A.K.2
Ekman, D.3
Bornberg-Bauer, E.4
Elofsson, A.5
-
21
-
-
38349030530
-
Selecting folded proteins from a library of secondary structural elements
-
Graziano J.J., Liu W., Perera R., Geierstanger B.H., Lesley S.A., and Schultz P.G. Selecting folded proteins from a library of secondary structural elements. J Am Chem Soc 130 (2008) 176-185
-
(2008)
J Am Chem Soc
, vol.130
, pp. 176-185
-
-
Graziano, J.J.1
Liu, W.2
Perera, R.3
Geierstanger, B.H.4
Lesley, S.A.5
Schultz, P.G.6
-
22
-
-
34547762712
-
Probing the structural plasticity of an archaeal primordial cobaltochelatase CbiX(S)
-
Pisarchik A., Petri R., and Schmidt-Dannert C. Probing the structural plasticity of an archaeal primordial cobaltochelatase CbiX(S). Protein Eng Des Select 20 (2007) 257-265
-
(2007)
Protein Eng Des Select
, vol.20
, pp. 257-265
-
-
Pisarchik, A.1
Petri, R.2
Schmidt-Dannert, C.3
-
23
-
-
31744450975
-
Evolution of new protein topologies through multistep gene rearrangements
-
Peisajovich S.G., Rockah L., and Tawfik D.S. 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
-
24
-
-
33749262632
-
Common evolutionary origin of swapped-hairpin and double-psi beta barrels
-
•].
-
•].
-
(2006)
Structure (London, England: 1993)
, vol.14
, pp. 1489-1498
-
-
Coles, M.1
Hulko, M.2
Djuranovic, S.3
Truffault, V.4
Koretke, K.5
Martin, J.6
Lupas, A.N.7
-
28
-
-
44949143819
-
Cradle-loop barrels and the concept of metafolds in protein classification by natural descent
-
Alva V., Koretke K.K., Coles M., and Lupas A.N. Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol 18 (2008) 358-365
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 358-365
-
-
Alva, V.1
Koretke, K.K.2
Coles, M.3
Lupas, A.N.4
-
29
-
-
36749073976
-
A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels
-
Ammelburg M., Hartmann M.D., Djuranovic S., Alva V., Koretke K.K., Martin J., Sauer G., Truffault V., Zeth K., Lupas A.N., et al. A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure (London, England: 1993) 15 (2007) 1577-1590
-
(2007)
Structure (London, England: 1993)
, vol.15
, pp. 1577-1590
-
-
Ammelburg, M.1
Hartmann, M.D.2
Djuranovic, S.3
Alva, V.4
Koretke, K.K.5
Martin, J.6
Sauer, G.7
Truffault, V.8
Zeth, K.9
Lupas, A.N.10
-
30
-
-
0035116837
-
A garlic lectin exerted an antitumor activity and induced apoptosis in human tumor cells
-
Karasaki Y., Tsukamoto S., Mizusaki K., Sugiura T., and Gotoh S. A garlic lectin exerted an antitumor activity and induced apoptosis in human tumor cells. Food Res Int 34 (2001) 7-13
-
(2001)
Food Res Int
, vol.34
, pp. 7-13
-
-
Karasaki, Y.1
Tsukamoto, S.2
Mizusaki, K.3
Sugiura, T.4
Gotoh, S.5
-
31
-
-
44449139387
-
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
-
Xie L., and Bourne P.E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105 (2008) 5441-5446
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 5441-5446
-
-
Xie, L.1
Bourne, P.E.2
-
32
-
-
36949009488
-
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
-
This paper is an illustration of how useful biological information with important clinical applications can be derived from structures whose global similarity is remote but which have local similarities.
-
Xie L., Wang J., and Bourne P.E. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol 3 (2007) e217. This paper is an illustration of how useful biological information with important clinical applications can be derived from structures whose global similarity is remote but which have local similarities.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Xie, L.1
Wang, J.2
Bourne, P.E.3
-
33
-
-
33744982063
-
Time for a change
-
Pace N.R. Time for a change. Nature 441 (2006) 289
-
(2006)
Nature
, vol.441
, pp. 289
-
-
Pace, N.R.1
-
34
-
-
33847790997
-
Pattern pluralism and the Tree of Life hypothesis
-
Doolittle W.F., and Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci U S A 104 (2007) 2043-2049
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 2043-2049
-
-
Doolittle, W.F.1
Bapteste, E.2
-
35
-
-
57149085868
-
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
-
Koonin E.V., and Wolf Y.I. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36 (2008) 6688-6719
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 6688-6719
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
36
-
-
3042658652
-
Plant glutaredoxins: still mysterious reducing systems
-
Rouhier N., Gelhaye E., and Jacquot J.P. Plant glutaredoxins: still mysterious reducing systems. Cell Mol Life Sci 61 (2004) 1266-1277
-
(2004)
Cell Mol Life Sci
, vol.61
, pp. 1266-1277
-
-
Rouhier, N.1
Gelhaye, E.2
Jacquot, J.P.3
-
37
-
-
13444280436
-
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
-
Tian W., Arakaki A.K., and Skolnick J. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res 32 (2004) 6226-6239
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6226-6239
-
-
Tian, W.1
Arakaki, A.K.2
Skolnick, J.3
-
38
-
-
6944227836
-
Automated prediction of protein function and detection of functional sites from structure
-
Pazos F., and Sternberg M.J. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A 101 (2004) 14754-14759
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 14754-14759
-
-
Pazos, F.1
Sternberg, M.J.2
-
39
-
-
45549109966
-
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments
-
Manikandan K., Pal D., Ramakumar S., Brener N.E., Iyengar S.S., and Seetharaman G. Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. Genome Biol 9 (2008) R52
-
(2008)
Genome Biol
, vol.9
-
-
Manikandan, K.1
Pal, D.2
Ramakumar, S.3
Brener, N.E.4
Iyengar, S.S.5
Seetharaman, G.6
-
40
-
-
33748684383
-
Identification of function-associated loop motifs and application to protein function prediction
-
Espadaler J., Querol E., Aviles F.X., and Oliva B. Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics (Oxford, England) 22 (2006) 2237-2243
-
(2006)
Bioinformatics (Oxford, England)
, vol.22
, pp. 2237-2243
-
-
Espadaler, J.1
Querol, E.2
Aviles, F.X.3
Oliva, B.4
|