Jan Brezovsky

Jan Brezovsky

UNVERIFIED PROFILE

Are you Jan Brezovsky?   Register this Author

Register author
Jan Brezovsky

Jan Brezovsky

Publications by authors named "Jan Brezovsky"

Are you Jan Brezovsky?   Register this Author

42Publications

536Reads

-Profile Views

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/978-1-4939-7366-8_3
Publisher Site
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/med.21430
Publisher Site
http://dx.doi.org/10.1002/med.21430DOI Listing
September 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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

Tools and data services registry: a community effort to document bioinformatics resources.

Nucleic Acids Res 2016 Jan 3;44(D1):D38-47. Epub 2015 Nov 3.

Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv1116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702812PMC
January 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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

Wedelolactone induces growth of breast cancer cells by stimulation of estrogen receptor signalling.

J Steroid Biochem Mol Biol 2015 Aug 28;152:76-83. Epub 2015 Apr 28.

Laboratory of Cellular Differentiation, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5/A36, 625 00 Brno, Czech Republic; International Clinical Research Center, Center for Biological and Cellular Engineering, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jsbmb.2015.04.019DOI Listing
August 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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btu364DOI Listing
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).

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nchembio.1502DOI 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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
http://www.caver.cz/fil/publications/cochbi14.pdf
Web Search
http://swift.cmbi.ru.nl/gv/newprot/articlelist/cochbi14.pdf
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S136759311300235
Publisher Site
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00894-012-1507-zDOI 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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

Toxic effects of nine polycyclic aromatic compounds on Enchytraeus crypticus in artificial soil in relation to their properties.

Ecotoxicol Environ Saf 2011 Sep 29;74(6):1727-33. Epub 2011 Apr 29.

Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Kamenice 126/3, Brno, CZ-62500, Czech Republic.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ecoenv.2011.04.013DOI Listing
September 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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

Computational tools for designing and engineering biocatalysts.

Curr Opin Chem Biol 2009 Feb 16;13(1):26-34. Epub 2009 Mar 16.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cbpa.2009.02.021DOI Listing
February 2009

Nanosecond time-dependent Stokes shift at the tunnel mouth of haloalkane dehalogenases.

J Am Chem Soc 2009 Jan;131(2):494-501

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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja804020qDOI Listing
January 2009