We have been invited to guest-edit the special issue on Novel Computational and Data-Driven Approaches for Protein Design and Their Application in Biomolecules journal. With CiteScore 2017 (Scopus) of 5.72, the journal ranks in Q1 in Biochemistry and Molecular Biology categories. Looking forward to the experience.
We have an open position for a Ph.D. candidate interested in molecular simulations of proteins and/or the development of computational tools in the domain of structural bioinformatics. The deadline for the application is August 10, 2018.
Jurcik A, Bednar D, Byska J, Marques SM, Furmanova K, Daniel L, Kokkonen P, Brezovsky J, Strnad O, Stourac J, Pavelka A, Manak M, Damborsky J, Kozlikova B, 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics (just accepted): doi:10.1093/bioinformatics/bty386. full text
Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications.
CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations.
CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz.
Kaushik S, Marques SM, Khirsariya P, Paruch K, Libichova L, Brezovsky J, Prokop Z, Chaloupkova R, Damborsky J, 2018: Impact of the Access Tunnel Engineering on Catalysis is Strictly Ligand-Specific. FEBS Journal (just accepted): doi: 10.1111/febs.14418. full text
The traditional way of rationally engineering enzymes to change their biocatalytic properties utilizes the modifications of their active sites. Another emerging approach is the engineering of structural features involved in the exchange of ligands between buried active sites and the surrounding solvent. However, surprisingly little is known about the effects of mutations that alter the access tunnels on the enzymes’ catalytic properties, and how these tunnels should be redesigned to allow fast passage of cognate substrates and products. Thus, we have systematically studied the effects of single-point mutations in a tunnel-lining residue of a haloalkane dehalogenase on the binding kinetics and catalytic conversion of both linear and branched haloalkanes. The hotspot residue Y176 was identified using computer simulations and randomized through saturation mutagenesis, and the resulting variants were screened for shifts in binding rates. Strikingly, opposite effects of the substituted residues on the catalytic efficiency towards linear and branched substrates were observed, which was found to be due to substrate-specific requirements in the critical steps of the respective catalytic cycles. We conclude that not only the catalytic sites but also the access pathways must be tailored specifically for each individual ligand, which is a new paradigm in protein engineering and de novo protein design. A rational approach is proposed here to address more effectively the task of designing ligand-specific tunnels using computational tools.
Our SONATA BIS project ranked the third among the grants awarded by National Science Centre (NCN). In this five-year research project, we plan to push the understanding of unexplored molecular factors essential for biological function of numerous enzymes with buried active sites connected with migration of small cognate molecules through the protein moieties.