Jiri Damborsky

Jiri Damborsky

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Jiri Damborsky

Publications by authors named "Jiri Damborsky"

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Haloalkane Dehalogenases From Marine Organisms.

Methods Enzymol 2018 28;605:203-251. Epub 2018 May 28.

Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical for Research Center, St. Anne's University Hospital, Brno, Czech Republic. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00766879183013
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http://dx.doi.org/10.1016/bs.mie.2018.03.005DOI Listing
May 2019

Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5.

Acta Crystallogr F Struct Biol Commun 2019 May 24;75(Pt 5):324-331. Epub 2019 Apr 24.

Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.

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http://dx.doi.org/10.1107/S2053230X19002796DOI Listing
May 2019

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.

Nucleic Acids Res 2019 May 22. Epub 2019 May 22.

Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkz378DOI Listing
May 2019

Engineering enzyme access tunnels.

Biotechnol Adv 2019 Apr 23. Epub 2019 Apr 23.

Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S07349750193006
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http://dx.doi.org/10.1016/j.biotechadv.2019.04.008DOI Listing
April 2019

Development of Fluorescent Assay for Monitoring of Dehalogenase Activity.

Biotechnol J 2019 Mar 28;14(3):e1800144. Epub 2018 Aug 28.

Faculty of Science, Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX and Department of Experimental Biology, Masaryk University, Brno, 625 00, Czech Republic.

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http://doi.wiley.com/10.1002/biot.201800144
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http://dx.doi.org/10.1002/biot.201800144DOI Listing
March 2019

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

Proc Natl Acad Sci U S A 2019 01 26;116(2):389-394. Epub 2018 Dec 26.

Department of Chemistry, University of Southern California, Los Angeles, CA 90089;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1804979115
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http://dx.doi.org/10.1073/pnas.1804979115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329970PMC
January 2019

Computational Study of Protein-Ligand Unbinding for Enzyme Engineering.

Front Chem 2018 8;6:650. Epub 2019 Jan 8.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.

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http://dx.doi.org/10.3389/fchem.2018.00650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331733PMC
January 2019

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

PLoS One 2018 18;13(6):e0198913. Epub 2018 Jun 18.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198913PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005535PMC
December 2018

Molecular Gating of an Engineered Enzyme Captured in Real Time.

J Am Chem Soc 2018 Dec 14;140(51):17999-18008. Epub 2018 Dec 14.

J. Heyrovsky Institute of Physical Chemistry of the ASCR , v. v. i., Dolejskova 3 , 182 23 Prague 8 , Czech Republic.

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http://pubs.acs.org/doi/10.1021/jacs.8b09848
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http://dx.doi.org/10.1021/jacs.8b09848DOI Listing
December 2018

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

Sensors (Basel) 2018 Sep 23;18(10). Epub 2018 Sep 23.

Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.

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http://www.mdpi.com/1424-8220/18/10/3212
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http://dx.doi.org/10.3390/s18103212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6210807PMC
September 2018

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

Nucleic Acids Res 2018 Jul;46(W1):W344-W349

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1093/nar/gky358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031030PMC
July 2018

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

Nucleic Acids Res 2018 Jul;46(W1):W356-W362

Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, 62500 Brno, Czech Republic.

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https://academic.oup.com/nar/article/46/W1/W356/5001543
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http://dx.doi.org/10.1093/nar/gky417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030891PMC
July 2018

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

J Biol Chem 2018 07 1;293(29):11505-11512. Epub 2018 Jun 1.

From the Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic and

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA117.000328
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http://dx.doi.org/10.1074/jbc.RA117.000328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6065182PMC
July 2018

Computational Analysis of Protein Tunnels and Channels.

Methods Mol Biol 2018 ;1685:25-42

Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.

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http://link.springer.com/10.1007/978-1-4939-7366-8_3
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http://dx.doi.org/10.1007/978-1-4939-7366-8_3DOI Listing
June 2018

Computer-assisted engineering of hyperstable fibroblast growth factor 2.

Biotechnol Bioeng 2018 04 24;115(4):850-862. Epub 2018 Jan 24.

Faculty of Science, Department of Experimental Biology, Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1002/bit.26531DOI Listing
April 2018

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

FEBS J 2018 04 25;285(8):1456-1476. Epub 2018 Mar 25.

Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://doi.wiley.com/10.1111/febs.14418
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http://dx.doi.org/10.1111/febs.14418DOI Listing
April 2018

Gram-scale production of recombinant microbial enzymes in shake flasks.

FEMS Microbiol Lett 2018 Feb;365(2)

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, Brno 625 00, Czech Republic.

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http://dx.doi.org/10.1093/femsle/fnx265DOI Listing
February 2018

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

Appl Environ Microbiol 2018 01 2;84(2). Epub 2018 Jan 2.

Loschmidt Laboratories, Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic

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http://dx.doi.org/10.1128/AEM.01684-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5752856PMC
January 2018

Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

Biotechnol Adv 2017 Nov 5;35(7):845-866. Epub 2017 Aug 5.

Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.biotechadv.2017.08.001DOI Listing
November 2017

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating.

Sci Rep 2017 Nov 24;7(1):16321. Epub 2017 Nov 24.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.

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http://dx.doi.org/10.1038/s41598-017-16360-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701188PMC
November 2017

Enzyme Tunnels and Gates As Relevant Targets in Drug Design.

Med Res Rev 2017 09 13;37(5):1095-1139. Epub 2016 Dec 13.

Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.

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http://doi.wiley.com/10.1002/med.21430
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http://dx.doi.org/10.1002/med.21430DOI Listing
September 2017

Metagenome-derived haloalkane dehalogenases with novel catalytic properties.

Appl Microbiol Biotechnol 2017 Aug 3;101(16):6385-6397. Epub 2017 Jul 3.

Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic.

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http://dx.doi.org/10.1007/s00253-017-8393-3DOI Listing
August 2017

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

J Chem Inf Model 2017 08 28;57(8):1970-1989. Epub 2017 Jul 28.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/acs.jcim.7b00070DOI Listing
August 2017

Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity.

Chembiochem 2017 07 12;18(14):1448-1456. Epub 2017 Jun 12.

Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.

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http://dx.doi.org/10.1002/cbic.201700197DOI Listing
July 2017

FireProt: web server for automated design of thermostable proteins.

Nucleic Acids Res 2017 Jul;45(W1):W393-W399

Loschmidt Laboratories, Department of Experimental Biology, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkx285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570187PMC
July 2017

NewProt - a protein engineering portal.

Protein Eng Des Sel 2017 06;30(6):441-447

CMBI, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/protein/gzx024DOI Listing
June 2017

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

Angew Chem Int Ed Engl 2017 04 23;56(17):4719-4723. Epub 2017 Mar 23.

Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.

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http://dx.doi.org/10.1002/anie.201611193DOI Listing
April 2017

Wedelolactone Acts as Proteasome Inhibitor in Breast Cancer Cells.

Int J Mol Sci 2017 Mar 29;18(4). Epub 2017 Mar 29.

Laboratory of Cell Differentiation, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.3390/ijms18040729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5412315PMC
March 2017

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

FEBS J 2017 01 7;284(1):134-148. Epub 2016 Dec 7.

Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1111/febs.13957DOI Listing
January 2017

Fluorescence-based biosensor for monitoring of environmental pollutants: From concept to field application.

Biosens Bioelectron 2016 Oct 8;84:97-105. Epub 2015 Dec 8.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic; Enantis, spol. s r.o., Kamenice 34, 612 00 Brno, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.bios.2015.12.010DOI Listing
October 2016

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.

Nucleic Acids Res 2016 07 12;44(W1):W479-87. Epub 2016 May 12.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic

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http://dx.doi.org/10.1093/nar/gkw416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987947PMC
July 2016

Suppression of protein inactivation during freezing by minimizing pH changes using ionic cryoprotectants.

Int J Pharm 2016 Jul 17;509(1-2):41-49. Epub 2016 May 17.

Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5/A8, 625 00 Brno, Czech Republic; Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A29, 625 00 Brno, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.ijpharm.2016.05.031DOI Listing
July 2016

Enzyme-Based Test Strips for Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard.

Anal Chem 2016 06 9;88(11):6044-9. Epub 2016 May 9.

Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg , 93040 Regensburg, Germany.

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http://dx.doi.org/10.1021/acs.analchem.6b01272DOI Listing
June 2016

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.

PLoS Comput Biol 2016 05 25;12(5):e1004962. Epub 2016 May 25.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1371/journal.pcbi.1004962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880439PMC
May 2016

Discovery of Novel Haloalkane Dehalogenase Inhibitors.

Appl Environ Microbiol 2016 Jan 15;82(6):1958-1965. Epub 2016 Jan 15.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic

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http://dx.doi.org/10.1128/AEM.03916-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784020PMC
January 2016

Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway.

Microb Cell Fact 2015 Dec 21;14:201. Epub 2015 Dec 21.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.

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http://www.microbialcellfactories.com/content/14/1/201
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http://dx.doi.org/10.1186/s12934-015-0393-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687329PMC
December 2015

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

PLoS Comput Biol 2015 Nov 3;11(11):e1004556. Epub 2015 Nov 3.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic; Enantis, Ltd., Brno, Czech Republic.

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http://dx.doi.org/10.1371/journal.pcbi.1004556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631455PMC
November 2015

Instability restricts signaling of multiple fibroblast growth factors.

Cell Mol Life Sci 2015 Jun 18;72(12):2445-59. Epub 2015 Feb 18.

Department of Anatomy, Histology and Embryology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.

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http://dx.doi.org/10.1007/s00018-015-1856-8DOI Listing
June 2015

Site-specific analysis of protein hydration based on unnatural amino acid fluorescence.

J Am Chem Soc 2015 Apr 9;137(15):4988-92. Epub 2015 Apr 9.

‡Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/jacs.5b01681DOI Listing
April 2015

The PCNA interaction protein box sequence in Rad54 is an integral part of its ATPase domain and is required for efficient DNA repair and recombination.

PLoS One 2013 20;8(12):e82630. Epub 2013 Dec 20.

National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic ; Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic ; International Clinical Research Centre, Centre for Biomolecular and Cellular Engineering, Saint Anne's University Hospital, Brno, Czech Republic.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082630PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869717PMC
March 2015

Computational tools for designing smart libraries.

Methods Mol Biol 2014 ;1179:291-314

Loschmidt Laboratories, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.

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http://dx.doi.org/10.1007/978-1-4939-1053-3_20DOI Listing
March 2015

Mechanism-based discovery of novel substrates of haloalkane dehalogenases using in silico screening.

J Chem Inf Model 2015 Jan 30;55(1):54-62. Epub 2014 Dec 30.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/ci500486yDOI Listing
January 2015

Interfacing microwells with nanoliter compartments: a sampler generating high-resolution concentration gradients for quantitative biochemical analyses in droplets.

Anal Chem 2015 Jan 12;87(1):624-32. Epub 2014 Dec 12.

Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1021/ac503336gDOI Listing
January 2015

Lincomycin biosynthesis involves a tyrosine hydroxylating heme protein of an unusual enzyme family.

PLoS One 2013 4;8(12):e79974. Epub 2013 Dec 4.

Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic ; Central-European Technology Institute, Brno, Czech Republic ; Crop Research Institute, Drnovska Prague, Czech Republic.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079974PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851162PMC
September 2014

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.

Bioinformatics 2014 Sep 29;30(18):2684-5. Epub 2014 May 29.

Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic.

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http://dx.doi.org/10.1093/bioinformatics/btu364DOI Listing
September 2014

A Pseudomonas putida strain genetically engineered for 1,2,3-trichloropropane bioremediation.

Appl Environ Microbiol 2014 Sep 27;80(17):5467-76. Epub 2014 Jun 27.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands

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http://dx.doi.org/10.1128/AEM.01620-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136109PMC
September 2014

Maximizing the efficiency of multienzyme process by stoichiometry optimization.

Chembiochem 2014 Sep 5;15(13):1891-5. Epub 2014 Aug 5.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno (Czech Republic); International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno (Czech Republic).

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http://dx.doi.org/10.1002/cbic.201402265DOI Listing
September 2014

Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites.

Acta Crystallogr D Biol Crystallogr 2014 Jul 29;70(Pt 7):1884-97. Epub 2014 Jun 29.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1107/S1399004714009018DOI Listing
July 2014

Microscopic monitoring provides information on structure and properties during biocatalyst immobilization.

Biotechnol J 2014 Jun 16;9(6):852-60. Epub 2014 Apr 16.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Czech Republic.

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http://dx.doi.org/10.1002/biot.201300049DOI Listing
June 2014

Dynamics and hydration explain failed functional transformation in dehalogenase design.

Nat Chem Biol 2014 Jun 13;10(6):428-30. Epub 2014 Apr 13.

1] Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Brno, Czech Republic. [2] International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic.

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http://dx.doi.org/10.1038/nchembio.1502DOI Listing
June 2014

Immobilized synthetic pathway for biodegradation of toxic recalcitrant pollutant 1,2,3-trichloropropane.

Environ Sci Technol 2014 Jun 13;48(12):6859-66. Epub 2014 May 13.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/es500396rDOI Listing
June 2014

Fructose 1-phosphate is the one and only physiological effector of the Cra (FruR) regulator of Pseudomonas putida.

FEBS Open Bio 2014 4;4:377-86. Epub 2014 Apr 4.

Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid 28049, Spain.

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http://dx.doi.org/10.1016/j.fob.2014.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050194PMC
June 2014

Computational tools for designing and engineering enzymes.

Curr Opin Chem Biol 2014 Apr 31;19:8-16. Epub 2013 Dec 31.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://www.caver.cz/fil/publications/cochbi14.pdf
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http://dx.doi.org/10.1016/j.cbpa.2013.12.003DOI Listing
April 2014

Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant.

ACS Synth Biol 2014 Mar 17;3(3):172-81. Epub 2013 Dec 17.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/sb400147nDOI Listing
March 2014

Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.

Acta Crystallogr D Biol Crystallogr 2014 Feb 17;70(Pt 2):209-17. Epub 2014 Jan 17.

Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.

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http://dx.doi.org/10.1107/S1399004713026254DOI Listing
February 2014

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.

PLoS Comput Biol 2014 Jan 16;10(1):e1003440. Epub 2014 Jan 16.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic ; Center of Biomolecular and Cellular Engineering, International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic.

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http://dx.doi.org/10.1371/journal.pcbi.1003440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168PMC
January 2014

Interaction of organic solvents with protein structures at protein-solvent interface.

J Mol Model 2013 Nov 4;19(11):4701-11. Epub 2012 Jul 4.

Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 373 33, Nove Hrady, Czech Republic.

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http://dx.doi.org/10.1007/s00894-012-1507-zDOI Listing
November 2013

DspA from Strongylocentrotus purpuratus: The first biochemically characterized haloalkane dehalogenase of non-microbial origin.

Biochimie 2013 Nov 11;95(11):2091-6. Epub 2013 Aug 11.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1016/j.biochi.2013.07.025DOI Listing
November 2013

Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations.

J Phys Chem B 2013 Nov 8;117(46):14329-35. Epub 2013 Nov 8.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp409040uDOI Listing
November 2013

Software tools for identification, visualization and analysis of protein tunnels and channels.

Biotechnol Adv 2013 Jan-Feb;31(1):38-49. Epub 2012 Feb 10.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1016/j.biotechadv.2012.02.002DOI Listing
September 2013

Gates of enzymes.

Chem Rev 2013 Aug 25;113(8):5871-923. Epub 2013 Apr 25.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/cr300384wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744840PMC
August 2013

The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58.

FEBS J 2013 Jul 8;280(13):3149-59. Epub 2013 Apr 8.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1111/febs.12238DOI Listing
July 2013

Are time-dependent fluorescence shifts at the tunnel mouth of haloalkane dehalogenase enzymes dependent on the choice of the chromophore?

J Phys Chem B 2013 Jul 20;117(26):7898-906. Epub 2013 Jun 20.

J. Heyrovsky Institute of Physical Chemistry of the ASCR, v. v. i., Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Praha, Czech Republic.

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http://dx.doi.org/10.1021/jp403708cDOI Listing
July 2013

Organic co-solvents affect activity, stability and enantioselectivity of haloalkane dehalogenases.

Biotechnol J 2013 Jun 21;8(6):719-29. Epub 2013 Mar 21.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1002/biot.201200378DOI Listing
June 2013

Crystallographic analysis of new psychrophilic haloalkane dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2013 Jun 25;69(Pt 6):683-8. Epub 2013 May 25.

Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, CENAKVA and Institute of Complex Systems, Zamek 136, 373 33 Nove Hrady, Czech Republic.

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http://dx.doi.org/10.1107/S1744309113012979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668595PMC
June 2013

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

PLoS Comput Biol 2012 18;8(10):e1002708. Epub 2012 Oct 18.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1371/journal.pcbi.1002708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475669PMC
May 2013

Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.

Chembiochem 2013 May 5;14(7):890-7. Epub 2013 Apr 5.

Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1002/cbic.201200733DOI Listing
May 2013

Cation-specific effects on enzymatic catalysis driven by interactions at the tunnel mouth.

J Phys Chem B 2013 May 20;117(21):6394-402. Epub 2013 May 20.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1021/jp401506vDOI Listing
May 2013

Differences in crystallization of two LinB variants from Sphingobium japonicum UT26.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2013 Mar 22;69(Pt 3):284-7. Epub 2013 Feb 22.

South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses and Institute of Complex Systems, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic.

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http://dx.doi.org/10.1107/S1744309113002467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606575PMC
March 2013

Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site.

Int J Syst Evol Microbiol 2013 Feb 27;63(Pt 2):673-8. Epub 2012 Apr 27.

Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.

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http://dx.doi.org/10.1099/ijs.0.039834-0DOI Listing
February 2013

Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil.

Int J Syst Evol Microbiol 2013 Feb 27;63(Pt 2):667-72. Epub 2012 Apr 27.

Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.

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http://dx.doi.org/10.1099/ijs.0.039826-0DOI Listing
February 2013

Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site.

Int J Syst Evol Microbiol 2013 Feb 4;63(Pt 2):723-8. Epub 2012 May 4.

Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.

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http://dx.doi.org/10.1099/ijs.0.039396-0DOI Listing
February 2013

Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel.

Angew Chem Int Ed Engl 2013 Feb 9;52(7):1959-63. Epub 2013 Jan 9.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1002/anie.201206708DOI Listing
February 2013

Haloalkane dehalogenases: biotechnological applications.

Biotechnol J 2013 Jan 11;8(1):32-45. Epub 2012 Sep 11.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1002/biot.201100486DOI Listing
January 2013

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

J Biol Chem 2012 Aug 28;287(34):29062-74. Epub 2012 Jun 28.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany.

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http://dx.doi.org/10.1074/jbc.M112.377853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436548PMC
August 2012

Biochemical characterization of a novel haloalkane dehalogenase from a cold-adapted bacterium.

Appl Environ Microbiol 2012 Jul 11;78(14):4995-8. Epub 2012 May 11.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1128/AEM.00485-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416366PMC
July 2012

The new platinum-based anticancer agent LA-12 induces retinol binding protein 4 in vivo.

Proteome Sci 2011 Oct 31;9(1):68. Epub 2011 Oct 31.

Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 656 53 Brno, Czech Republic.

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http://dx.doi.org/10.1186/1477-5956-9-68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221626PMC
October 2011

Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature.

FEBS J 2011 Aug 27;278(15):2728-38. Epub 2011 Jun 27.

Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1111/j.1742-4658.2011.08203.xDOI Listing
August 2011

Substrate specificity of haloalkane dehalogenases.

Biochem J 2011 Apr;435(2):345-54

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 62500 Brno, Czech Republic.

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http://dx.doi.org/10.1042/BJ20101405DOI Listing
April 2011

Biochemical characteristics of the novel haloalkane dehalogenase DatA, isolated from the plant pathogen Agrobacterium tumefaciens C58.

Appl Environ Microbiol 2011 Mar 30;77(5):1881-4. Epub 2010 Dec 30.

oschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1128/AEM.02109-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067286PMC
March 2011

Elicitin-membrane interaction is driven by a positive charge on the protein surface: role of Lys13 residue in lipids loading and resistance induction.

Plant Physiol Biochem 2011 Mar 13;49(3):321-8. Epub 2011 Jan 13.

Department of Biochemistry and National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic.

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http://dx.doi.org/10.1016/j.plaphy.2011.01.008DOI Listing
March 2011

Crystallization and crystallographic analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA mutant DhaA31 and its complex with 1,2,3-trichloropropane.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2011 Mar 25;67(Pt 3):397-400. Epub 2011 Feb 25.

Institute of Physical Biology, University of South Bohemia, Ceske Budejovice, Zamek 136, 373 33 Nove Hrady, Czech Republic.

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http://dx.doi.org/10.1107/S1744309111001254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053171PMC
March 2011

Crystallization and preliminary X-ray diffraction analysis of the wild-type haloalkane dehalogenase DhaA and its variant DhaA13 complexed with different ligands.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2011 Feb 22;67(Pt 2):253-7. Epub 2011 Jan 22.

Institute of Physical Biology, University of South Bohemia Ceske Budejovice, Nove Hrady, Czech Republic.

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http://dx.doi.org/10.1107/S1744309110051286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3034621PMC
February 2011

Development of an enzymatic fiber-optic biosensor for detection of halogenated hydrocarbons.

Anal Bioanal Chem 2010 Nov 19;398(5):1891-8. Epub 2010 Aug 19.

Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1007/s00216-010-4083-zDOI Listing
November 2010

Rad52 SUMOylation affects the efficiency of the DNA repair.

Nucleic Acids Res 2010 Aug 5;38(14):4708-21. Epub 2010 Apr 5.

Department of Biology, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkq195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919706PMC
August 2010

Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering.

Angew Chem Int Ed Engl 2010 Aug;49(35):6111-5

Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1002/anie.201001753DOI Listing
August 2010

Systems biology at work.

Curr Opin Biotechnol 2010 Aug 19;21(4):498-501. Epub 2010 Aug 19.

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http://dx.doi.org/10.1016/j.copbio.2010.08.001DOI Listing
August 2010

Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation.

Biol Chem 2010 Feb-Mar;391(2-3):197-205

Center of Molecular Biology and Gene Therapy, Department of Internal Medicine - Hematooncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Cernopolni 9, CZ-625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1515/BC.2010.027DOI Listing
June 2010

Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

J Mol Biol 2009 Oct 3;392(5):1339-56. Epub 2009 Jul 3.

Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1016/j.jmb.2009.06.076DOI Listing
October 2009

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

Nat Chem Biol 2009 Oct 23;5(10):727-33. Epub 2009 Aug 23.

Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1038/nchembio.205DOI Listing
October 2009

Biochemical characterization of haloalkane dehalogenases DrbA and DmbC, Representatives of a Novel Subfamily.

Appl Environ Microbiol 2009 Aug 5;75(15):5157-60. Epub 2009 Jun 5.

Institute of Experimental Biology and National Center for Biomolecular Research, Masaryk University, Brno, Czech Republic.

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http://dx.doi.org/10.1128/AEM.00199-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725514PMC
August 2009

HotSpot Wizard: a web server for identification of hot spots in protein engineering.

Nucleic Acids Res 2009 Jul 21;37(Web Server issue):W376-83. Epub 2009 May 21.

Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkp410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703904PMC
July 2009

Crystallization and preliminary X-ray analysis of a novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94.

Acta Crystallogr Sect F Struct Biol Cryst Commun 2009 Apr 21;65(Pt 4):353-6. Epub 2009 Mar 21.

Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic.

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http://dx.doi.org/10.1107/S1744309109007039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664758PMC
April 2009

Editorial: Protein design and engineering for biocatalysis.

Authors:
Jiri Damborsky

Biotechnol J 2009 Apr;4(4):439

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http://dx.doi.org/10.1002/biot.200900080DOI Listing
April 2009