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Items: 1 to 20 of 71

1.

Engineering enzyme access tunnels.

Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J.

Biotechnol Adv. 2019 Apr 23. pii: S0734-9750(19)30067-9. doi: 10.1016/j.biotechadv.2019.04.008. [Epub ahead of print] Review.

PMID:
31026496
2.

Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase.

Jindal G, Slanska K, Kolev V, Damborsky J, Prokop Z, Warshel A.

Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):389-394. doi: 10.1073/pnas.1804979115. Epub 2018 Dec 26.

PMID:
30587585
3.

Molecular Gating of an Engineered Enzyme Captured in Real Time.

Kokkonen P, Sykora J, Prokop Z, Ghose A, Bednar D, Amaro M, Beerens K, Bidmanova S, Slanska M, Brezovsky J, Damborsky J, Hof M.

J Am Chem Soc. 2018 Dec 26;140(51):17999-18008. doi: 10.1021/jacs.8b09848. Epub 2018 Dec 14.

PMID:
30501200
4.

Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips.

Pilát Z, Kizovský M, Ježek J, Krátký S, Sobota J, Šiler M, Samek O, Buryška T, Vaňáček P, Damborský J, Prokop Z, Zemánek P.

Sensors (Basel). 2018 Sep 23;18(10). pii: E3212. doi: 10.3390/s18103212.

5.

Development of Fluorescent Assay for Monitoring of Dehalogenase Activity.

Nevolova S, Manaskova E, Mazurenko S, Damborsky J, Prokop Z.

Biotechnol J. 2019 Mar;14(3):e1800144. doi: 10.1002/biot.201800144. Epub 2018 Aug 28.

PMID:
30052322
6.

Sensitive operation of enzyme-based biodevices by advanced signal processing.

Mazurenko S, Bidmanova S, Kotlanova M, Damborsky J, Prokop Z.

PLoS One. 2018 Jun 18;13(6):e0198913. doi: 10.1371/journal.pone.0198913. eCollection 2018.

7.

Haloalkane Dehalogenases From Marine Organisms.

Kunka A, Damborsky J, Prokop Z.

Methods Enzymol. 2018;605:203-251. doi: 10.1016/bs.mie.2018.03.005. Epub 2018 May 28. Review.

PMID:
29909825
8.

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site.

Kokkonen P, Bednar D, Dockalova V, Prokop Z, Damborsky J.

J Biol Chem. 2018 Jul 20;293(29):11505-11512. doi: 10.1074/jbc.RA117.000328. Epub 2018 Jun 1.

PMID:
29858243
9.

CalFitter: a web server for analysis of protein thermal denaturation data.

Mazurenko S, Stourac J, Kunka A, Nedeljkovic S, Bednar D, Prokop Z, Damborsky J.

Nucleic Acids Res. 2018 Jul 2;46(W1):W344-W349. doi: 10.1093/nar/gky358.

10.

Impact of the access tunnel engineering on catalysis is strictly ligand-specific.

Kaushik S, Marques SM, Khirsariya P, Paruch K, Libichova L, Brezovsky J, Prokop Z, Chaloupkova R, Damborsky J.

FEBS J. 2018 Apr;285(8):1456-1476. doi: 10.1111/febs.14418. Epub 2018 Mar 25.

11.

Computer-assisted engineering of hyperstable fibroblast growth factor 2.

Dvorak P, Bednar D, Vanacek P, Balek L, Eiselleova L, Stepankova V, Sebestova E, Kunova Bosakova M, Konecna Z, Mazurenko S, Kunka A, Vanova T, Zoufalova K, Chaloupkova R, Brezovsky J, Krejci P, Prokop Z, Dvorak P, Damborsky J.

Biotechnol Bioeng. 2018 Apr;115(4):850-862. doi: 10.1002/bit.26531. Epub 2018 Jan 24.

PMID:
29278409
12.

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating.

Mazurenko S, Kunka A, Beerens K, Johnson CM, Damborsky J, Prokop Z.

Sci Rep. 2017 Nov 24;7(1):16321. doi: 10.1038/s41598-017-16360-y.

13.

A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity.

Buryska T, Babkova P, Vavra O, Damborsky J, Prokop Z.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01684-17. doi: 10.1128/AEM.01684-17. Print 2018 Jan 15.

14.

Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.

Marques SM, Dunajova Z, Prokop Z, Chaloupkova R, Brezovsky J, Damborsky J.

J Chem Inf Model. 2017 Aug 28;57(8):1970-1989. doi: 10.1021/acs.jcim.7b00070. Epub 2017 Jul 28.

PMID:
28696117
15.

Metagenome-derived haloalkane dehalogenases with novel catalytic properties.

Kotik M, Vanacek P, Kunka A, Prokop Z, Damborsky J.

Appl Microbiol Biotechnol. 2017 Aug;101(16):6385-6397. doi: 10.1007/s00253-017-8393-3. Epub 2017 Jul 3.

PMID:
28674849
16.

Protection of Arabidopsis Blunt-Ended Telomeres Is Mediated by a Physical Association with the Ku Heterodimer.

Valuchova S, Fulnecek J, Prokop Z, Stolt-Bergner P, Janouskova E, Hofr C, Riha K.

Plant Cell. 2017 Jun;29(6):1533-1545. doi: 10.1105/tpc.17.00064. Epub 2017 Jun 5.

17.

FireProt: web server for automated design of thermostable proteins.

Musil M, Stourac J, Bendl J, Brezovsky J, Prokop Z, Zendulka J, Martinek T, Bednar D, Damborsky J.

Nucleic Acids Res. 2017 Jul 3;45(W1):W393-W399. doi: 10.1093/nar/gkx285.

18.

Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites.

Liskova V, Stepankova V, Bednar D, Brezovsky J, Prokop Z, Chaloupkova R, Damborsky J.

Angew Chem Int Ed Engl. 2017 Apr 18;56(17):4719-4723. doi: 10.1002/anie.201611193. Epub 2017 Mar 23.

PMID:
28334478
19.

Enzyme Tunnels and Gates As Relevant Targets in Drug Design.

Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J.

Med Res Rev. 2017 Sep;37(5):1095-1139. doi: 10.1002/med.21430. Epub 2016 Dec 13. Review.

PMID:
27957758
20.

Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels.

Kaushik S, Prokop Z, Damborsky J, Chaloupkova R.

FEBS J. 2017 Jan;284(1):134-148. doi: 10.1111/febs.13957. Epub 2016 Dec 7.

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