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Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme
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Cites
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000865 · Cited by 7,334
Scaling and assessment of data quality
Evans, P. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444905036693 · Cited by 4,374
Enzyme promiscuity: A mechanistic and evolutionary perspective
Tawfik, O. K. A. D. S. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-030409-143718 · Cited by 1,355
Exploring protein fitness landscapes by directed evolution
Romero, P. A., & Arnold, F. H. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2805 · Cited by 1,161
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters
Bar-Even, A., Noor, E., Savir, Y., Liebermeister, W., Davidi, D., Tawfik, D. S., & Milo, R. (2011) · Biochemistry · doi:10.1021/bi2002289 · Cited by 1,050
Self-citationProtein Dynamism and Evolvability
Tokuriki, N., & Tawfik, D. S. (2009) · Science · doi:10.1126/science.1169375 · Cited by 940
Self-citationStability effects of mutations and protein evolvability
Tokuriki, N., & Tawfik, D. S. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.08.003 · Cited by 834
Self-citationThe 'evolvability' of promiscuous protein functions
Aharoni, A., Gaidukov, L., Khersonsky, O., Gould, S. M., Roodveldt, C., & Tawfik, D. S. (2005) · Nature Genetics · doi:10.1038/ng1482 · Cited by 832
Self-citationCatalytic promiscuity and the evolution of new enzymatic activities
O'Brien, P. J., & Herschlag, D. (1999) · Chemistry & Biology · doi:10.1016/s1074-5521(99)80033-7 · Cited by 738
The evolution of trade‐offs: where are we?
ROFF, D. A., & FAIRBAIRN, D. J. (2007) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2006.01255.x · Cited by 697
Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
Khan, A. I., Dinh, D. M., Schneider, D., Lenski, R. E., & Cooper, T. F. (2011) · Science · doi:10.1126/science.1203801 · Cited by 580
How Protein Stability and New Functions Trade Off
Tokuriki, N., Stricher, F., Serrano, L., & Tawfik, D. S. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000002 · Cited by 580
Self-citationDiminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
Chou, H.-H., Chiu, H.-C., Delaney, N. F., Segrè, D., & Marx, C. J. (2011) · Science · doi:10.1126/science.1203799 · Cited by 510
In the light of directed evolution: Pathways of adaptive protein evolution
Bloom, J. D., & Arnold, F. H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901522106 · Cited by 468
Improving enzyme properties: when are closer mutations better?
Morley, K. L., & Kazlauskas, R. J. (2005) · Trends in Biotechnology · doi:10.1016/j.tibtech.2005.03.005 · Cited by 438
The Rise of Chemodiversity in Plants
Weng, J.-K., Philippe, R. N., & Noel, J. P. (2012) · Science · doi:10.1126/science.1217411 · Cited by 428
How enzymes adapt: lessons from directed evolution
Arnold, F. H., Wintrode, P. L., Miyazaki, K., & Gershenson, A. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01755-2 · Cited by 389
Diminishing Returns from Mutation Supply Rate in Asexual Populations
Arjan G., J., Visser, M. D., Zeyl, C. W., Gerrish, P. J., Blanchard, J. L., & Lenski, R. E. (1999) · Science · doi:10.1126/science.283.5400.404 · Cited by 374
Chaperonin overexpression promotes genetic variation and enzyme evolution
Tokuriki, N., & Tawfik, D. S. (2009) · Nature · doi:10.1038/nature08009 · Cited by 352
Self-citationCharacterization of the zinc binding site of bacterial phosphotriesterase.
Omburo, G. A., Kuo, J. M., Mullins, L. S., & Raushel, F. M. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)42207-7 · Cited by 325
Directed enzyme evolution: climbing fitness peaks one amino acid at a time
Tracewell, C. A., & Arnold, F. H. (2009) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.01.017 · Cited by 321
Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase
Aubert, S. D., Li, Y., & Raushel, F. M. (2004) · Biochemistry · doi:10.1021/bi0497805 · Cited by 316
Network Context and Selection in the Evolution to Enzyme Specificity
Nam, H., Lewis, N. E., Lerman, J. A., Lee, D.-H., Chang, R. L., Kim, D., & Palsson, B. O. (2012) · Science · doi:10.1126/science.1216861 · Cited by 277
LIMITS OF ADAPTATION: THE EVOLUTION OF SELECTIVE NEUTRALITY
Hartl, D. L., Dykhuizen, D. E., & Dean, A. M. (1985) · Genetics · doi:10.1093/genetics/111.3.655 · Cited by 277
Minimalist Active‐Site Redesign: Teaching Old Enzymes New Tricks
Toscano, M. D., Woycechowsky, K. J., & Hilvert, D. (2007) · Angewandte Chemie International Edition · doi:10.1002/anie.200604205 · Cited by 262
The neutral theory of molecular evolution and the world view of the neutralists
Kimura, M. (1989) · Genome · doi:10.1139/g89-009 · Cited by 220
Evolutionary History of a Specialized P450 Propane Monooxygenase
Fasan, R., Meharenna, Y. T., Snow, C. D., Poulos, T. L., & Arnold, F. H. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.06.060 · Cited by 211
What makes an enzyme promiscuous?
Babtie, A., Tokuriki, N., & Hollfelder, F. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.11.028 · Cited by 208
Self-citationO'Maille, P. E., Malone, A., Dellas, N., Andes Hess, B., Smentek, L., Sheehan, I., Greenhagen, B. T., Chappell, J., Manning, G., & Noel, J. P. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.113 · Cited by 205
Functional plasticity of paralogous diterpene synthases involved in conifer defense
Keeling, C. I., Weisshaar, S., Lin, R. P. C., & Bohlmann, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709466105 · Cited by 199
Strategy and success for the directed evolution of enzymes
Dalby, P. A. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.05.003 · Cited by 193
MacLean, R. C., Perron, G. G., & Gardner, A. (2010) · Genetics · doi:10.1534/genetics.110.123083 · Cited by 181
Khersonsky, O., Röthlisberger, D., Wollacott, A. M., Murphy, P., Dym, O., Albeck, S., Kiss, G., Houk, K. N., Baker, D., & Tawfik, D. S. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.01.041 · Cited by 177
Self-citationCaldwell, S. R., Newcomb, J. R., Schlecht, K. A., & Raushel, F. M. (1991) · Biochemistry · doi:10.1021/bi00244a010 · Cited by 170
Wang, Q., Hillwig, M. L., Okada, K., Yamazaki, K., Wu, Y., Swaminathan, S., Yamane, H., & Peters, R. J. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.305599 · Cited by 154
Protein engineers turned evolutionists
Peisajovich, S. G., & Tawfik, D. S. (2007) · Nature Methods · doi:10.1038/nmeth1207-991 · Cited by 154
Self-citationRoodveldt, C., & Tawfik, D. S. (2005) · Biochemistry · doi:10.1021/bi051021e · Cited by 135
Self-citationTradeoffs and Optimality in the Evolution of Gene Regulation
Poelwijk, F. J., de Vos, M. G. J., & Tans, S. J. (2011) · Cell · doi:10.1016/j.cell.2011.06.035 · Cited by 121
Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
Jackson, C. J., Foo, J.-L., Tokuriki, N., Afriat, L., Carr, P. D., Kim, H.-K., Schenk, G., Tawfik, D. S., & Ollis, D. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907548106 · Cited by 119
Self-citationRoodveldt, C., & Tawfik, D. S. (2005) · Protein Engineering Design and Selection · doi:10.1093/protein/gzi005 · Cited by 107
Self-citationNear Neutrality: Leading Edge of the Neutral Theory of Molecular Evolution
Hughes, A. L. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1438.001 · Cited by 100
Jackson, C. J., Foo, J. L., Kim, H. K., Carr, P. D., Liu, J., Salem, G., & Ollis, D. L. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.10.061 · Cited by 92
Self-citationDiminishing Returns of Population Size in the Rate of RNA Virus Adaptation
Miralles, R., Moyá, A., & Elena, S. F. (2000) · Journal of Virology · doi:10.1128/jvi.74.8.3566-3571.2000 · Cited by 79
Engineering specialized metabolic pathways—is there a room for enzyme improvements?
Bar‐Even, A., & Tawfik, D. S. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.10.006 · Cited by 71
Self-citationJackson, C. J., Carr, P. D., Kim, H. K., Liu, J., Herrald, P., Mitić, N., Schenk, G., Smith, C. A., & Ollis, D. L. (2006) · Biochemical Journal · doi:10.1042/bj20060276 · Cited by 61
Self-citationGrimsley, J. K., Calamini, B., Wild, J. R., & Mesecar, A. D. (2005) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2005.08.012 · Cited by 49
Stability for function trade-offs in the enolase superfamily "catalytic module".
Nagatani, R., González, A., Shoichet, B., Brinen, L., & Babbitt, P. (2007) · Biochemistry · doi:10.1021/bi700507d · Cited by 46
In search of the limits of evolution
Kondrashov, F. A. (2004) · Nature Genetics · doi:10.1038/ng0105-9 · Cited by 28
The Law of Diminishing Returns
Stebbins, J. (1944) · Science · doi:10.1126/science.99.2571.267 · Cited by 16
Cited by
Sun, Z., Liu, Q., Qu, G., Feng, Y., & Reetz, M. T. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00290 · Cited by 526
Currin, A., Swainston, N., Day, P. J., & Kell, D. B. (2015) · Chemical Society Reviews · doi:10.1039/c4cs00351a · Cited by 388
Evolutionary biochemistry: revealing the historical and physical causes of protein properties
Harms, M. J., & Thornton, J. W. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3540 · Cited by 330
Ferreiro, D. U., Komives, E. A., & Wolynes, P. G. (2014) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583514000092 · Cited by 314
The role of protein dynamics in the evolution of new enzyme function
Campbell, E., Kaltenbach, M., Correy, G. J., Carr, P. D., Porebski, B. T., Livingstone, E. K., Afriat-Jurnou, L., Buckle, A. M., Weik, M., Hollfelder, F., et al. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2175 · Cited by 311
Self-citation
Metadata
- Authors
- Tokuriki, N., Jackson, C. J., Afriat-Jurnou, L., Wyganowski, K. T., Tang, R., & Tawfik, D. S.
- Venue
- Nature Communications
- Published
- 2012-12-04
- Volume
- 3
- Issue
- 1
- Pages
- 1257-1257
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2000054450
- Cited by
- 253
- References
- 52
- FWCI
- 10.10
- Type
- journal article
- Language
- en
- Open access
- bronze
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