Home

Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design

Sykora, J., Brezovsky, J., Koudelakova, T., Lahoda, M., Fortova, A., Chernovets, T., Chaloupkova, R., Stepankova, Prokop, Z., Kuta Smatanova, I., Hof, M., Damborsky, J., 2014, Nature Chemical Biology XX: XXX-XXX.

Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design

We emphasize the importance of dynamics and hydration for enzymatic catalysis and protein design by transplanting the active site from a haloalkane dehalogenase with high enantioselectivity to nonselective dehalogenase. Protein crystallography confirms that the active site geometry of the redesigned dehalogenase matches that of the target, but its enantioselectivity remains low. Time-dependent fluorescence shifts and computer simulations revealed that dynamics and hydration at the tunnel mouth differ substantially between the redesigned and target dehalogenase.

Read more

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

Bendl J., Stourac J., Salanda O., Pavelka A., Wieben E.D., Zendulka J., Brezovsky J., Damborsky J., 2014, PLOS Computational Biology 10: e1003440.

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

We have constructed three independent datasets by removing duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance and robustness. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp.

Read more

Gates of Enzymes

Gora, A., Brezovsky, J., Damborsky, J., 2013, Chemical Reviews 113: 5871–5923.

The Gates of EnzymesThis review highlights the importance of gates in enzymes. The gates control substrate access to the active site and product release, restrict solvent access to specific protein regions, and synchronize processes occurring in distinct parts of the enzyme. Survey of 129 gates in 71 enzymes enabled a rigorous definition of gates and establishment of a new scheme for their classification. Gates were assigned to six distinct classes – wings, swinging doors, apertures, drawbridges, double drawbridges and shells. Presented are summary statistics describing the propensity of specific amino acid residues in particular gate classes. The proposed classification scheme provides guidance for the analysis and engineering of gates in biomolecular systems.

Read more

Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel

Koudelakova, T., Chaloupkova, R., Brezovsky, J., Prokop, Z., Sebestova, E., Hesseler, M., Khabiri, M., Plevaka, M., Kulik, D., Kuta Smatanova, I., Rezacova, P., Ettrich, R., Bornscheuer, U. T., Damborsky, J., 2013, Angewandte Chemie International Edition 52: 1959-1963.

Engineering Enzyme Stability and Resistance to Organic Co-solvent by Access Tunnel Modification photo

Mutations targeting as few as four residues lining the access tunnel extended enzyme’s half-life in 40% dimethyl sulfoxide from minutes to weeks (4,000-fold) and increased its melting temperature by 19 °C. Protein crystallography and molecular dynamics revealed that the tunnel residue packing is a key determinant of protein stability and the active-site accessibility for co-solvent molecules (red dots). The broad applicability of this concept was verified by analyzing twenty six proteins with buried active sites from all six enzyme classes.

Read more

 

CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures

Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J., Damborsky, J., 2012, PLOS Computational Biology 8: e1002708.

CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. A new version of CAVER was developed enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

Read more

 

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Prokop, Z., Sato, Y., Brezovsky, J., Mozga, T., Chaloupkova, R., Koudelakova, T., Jerabek, P., Stepankova, V., Natsume, R., Leeuwen, J. G. E., Janssen, D. B., Florian, J., Nagata, Y., Senda, T., Damborsky, J., 2010, Angewandte Chemie International Edition 49: 6111-6115.

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Engineering of the surface loop in haloalkane dehalogenases affects their enantiodiscrimination behavior. The temperature dependence of the enantioselectivity (lnE versus 1/T) of β-bromoalkanes by haloalkane dehalogenases is reversed (red data points) by deletion of the surface loop; the selectivity switches back when an additional single-point mutation is made. This behavior is not observed for α-bromoesters.

Read more

 

Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate

Pavlova, M., Klvana, M., Chaloupkova, R., Banas, P., Otyepka, M., Wade, R., Nagata, Y., Damborsky, J., 2009, Nature Chemical Biology 5: 727-733.

Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate

Engineering enzymes to degrade anthropogenic compounds efficiently is challenging. We obtained Rhodococcus rhodochrous haloalkane dehalogenase mutants with up to 32-fold higher activity than wild type toward the toxic, recalcitrant anthropogenic compound 1,2,3-trichloropropane (TCP) using a new strategy. Key residues in access tunnels connecting the buried active site with bulk solvent by rational design were identified and randomized by directed evolution. The most active mutant has large aromatic residues at two out of three randomized positions and two positions modified by site-directed mutagenesis. These changes apparently enhance activity with TCP by decreasing accessibility of the active site for water molecules, thereby promoting activated complex formation.

Read more

 

HotSpot Wizard: a Web Server for Identification of Hot Spots in Protein Engineering

Pavelka, A., Chovancova, E., Damborsky, J., 2009, Nucleic Acids Research 37: W376-W383.

HotSpot Wizard: a Web Server for Identification of Hot Spots in Protein Engineering

HotSpot Wizard is a web server for automatic identification of ‘hot spots’ for engineering of substrate specificity, activity or enantioselectivity of enzymes and for annotation of protein structures. The web server implements the protein engineering protocol, which targets evolutionarily variable amino acid positions located in the active site or lining the access tunnels. The ‘hot spots’ for mutagenesis are selected through the integration of structural, functional and evolutionary information obtained from: (i) the databases RCSB PDB, UniProt, PDBSWS, Catalytic Site Atlas and nr NCBI and (ii) the tools CASTp, CAVER, BLAST, CD-HIT, MUSCLE and Rate4Site. The HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard/.

Read more

 

Article in Nature Chemical Biology
Sarka Bidmanova awarded Microbiological Society Prize
Article in Green Chemistry
New position: Laboratory technician
Registration Open for Summer School on Protein Engineering
US Patent Awarded
Article in Current Opinion in Chemical Biology
Sergio Marques awarded SoMoPro grant
Article in PLOS Computational Biology
Veronika Stepankova awarded Minister’s Prize