Dynamics and hydration explain failed functional transformation in dehalogenase design

Nature Chemical Biology

Volumn 10, Issue 6, 2014, Pages 428-430

  Sykora, Jan ^a   Brezovsky, Jan ^b   Koudelakova, Tana ^b   Lahoda, Maryna ^c,d   Fortova, Andrea ^b   Chernovets, Tatsiana ^a   Chaloupkova, Radka ^b   Stepankova, Veronika ^b   Prokop, Zbynek ^b,e   Smatanova, Ivana Kuta ^c,d   Hof, Martin ^a   Damborsky, Jiri ^b,e  

^a J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

^b MASARYK UNIVERSITY   (Czech Republic)

^c UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^d Institute of Nanobiology and Structural Biology of GCRC   (Czech Republic)

^e ST ANNE S UNIVERSITY HOSPITAL   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ACRYLAMIDE; ORGANOHALOGEN DERIVATIVE;

ARTICLE; BRADYRHIZOBIUM JAPONICUM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DYNAMICS; ENANTIOSELECTIVITY; ENZYME ACTIVITY; FLUORESCENCE; GEOMETRY; HYDRATION; MOLECULAR DYNAMICS; MUTATIONAL ANALYSIS; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RHODOCOCCUS RHODOCHROUS; THERMODYNAMICS;

AMINO ACID SEQUENCE; CATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; HYDROCARBONS, BROMINATED; HYDROLASES; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEIN ENGINEERING; SPECTROMETRY, FLUORESCENCE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; STEREOISOMERISM; WATER;

EID: 84901203399     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1502     Document Type: Article

References (34)

1. Damborsky, J. & Brezovsky, J. Curr. Opin. Chem. Biol. 19, 8-16 (2014).
2. Koehl, P. & Levitt, M. J. Mol. Biol. 293, 1161-1181 (1999).
3. Siegel, J.B. et al. Science 329, 309-313 (2010).
4. Röthlisberger, D. et al. Nature 453, 190-195 (2008).
5. Jiang, L. et al. Science 319, 1387-1391 (2008).
6. Kries, H., Blomberg, R. & Hilvert, D. Curr. Opin. Chem. Biol. 17, 221-228 (2013).
7. Khersonsky, O. et al. Proc. Natl. Acad. Sci. USA 109, 10358-10363 (2012).
8. Khare, S.D. et al. Nat. Chem. Biol. 8, 294-300 (2012).
9. Giger, L. et al. Nat. Chem. Biol. 9, 494-498 (2013).
10. Blomberg, R. et al. Nature 503, 418-421 (2013).
11. Sato, Y. et al. Appl. Environ. Microbiol. 71, 4372-4379 (2005).
12. Kulakova, A.N., Larkin, M.J. & Kulakov, L.A. Microbiology 143, 109-115 (1997).
13. Chovancová, E., Kosinski, J., Bujnicki, J.M. & Damborsky, J. Proteins 67, 305-316 (2007).
14. Prokop, Z. et al. Angew. Chem. Int. Edn Engl. 49, 6111-6115 (2010).
15. Eisenmesser, E.Z. et al. Nature 438, 117-121 (2005).
16. Henzler-Wildman, K. & Kern, D. Nature 450, 964-972 (2007).
17. Bhabha, G. et al. Science 332, 234-238 (2011).
18. Jimenez, R., Fleming, G.R., Kumar, P.V. & Maroncelli, M. Nature 369, 471-473 (1994).
19. Halle, B. & Nilsson, L. J. Phys. Chem. B 113, 8210-8213 (2009).
20. Jesenská, A. et al. J. Am. Chem. Soc. 131, 494-501 (2009).
21. Chang, C-W. et al. Proc. Natl. Acad. Sci. USA 107, 2914-2919 (2010).
22. Jurkiewicz, P., Cwiklik, L., Jungwirth, P. & Hof, M. Biochimie 94, 26-32 (2012).
23. Nilsson, L. & Halle, B. Proc. Natl. Acad. Sci. USA 102, 13867-13872 (2005).
24. Baker, D. Protein Sci. 19, 1817-1819 (2010).
25. Chovancova, E. et al. PLoS Comput. Biol. 8, e1002708 (2012).
26. Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor Laboratory Press, New York, 2001).
27. Iwasaki, I., Utsumi, S. & Ozawa, T. Bull. Chem. Soc. Jpn. 25, 226 (1952).
28. Furse, K.E. & Corcelli, S.A. J. Phys. Chem. Lett. 1, 1813-1820 (2010).
29. Ducruix, A. & Giegé, R. Crystallization of Nucleic Acids and Proteins: A Practical Approach. (Oxford University Press, New York, 1999).
30. Teng, T.Y. J. Appl. Crystallogr. 23, 387-391 (1990).
31. Vagin, A. & Teplyakov, A. J. Appl. Crystallogr. 30, 1022-1025 (1997).
32. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255 (1997).
33. Sheldrick, G.M. Acta Crystallogr. A 64, 112-122 (2008).
34. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).