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About Laboratory Of Bioinformatics And Protein Engineering

Our group is involved in theoretical and experimental research on nucleic acids and proteins. The current focus is on RNA sequence-structure-function relationships (in particular 3D modeling), RNA-protein complexes, and enzymes acting on RNA.
We study the rules that govern the sequence-structure-function relationships in proteins and nucleic acids and use the acquired knowledge to predict structures and functions for uncharacterized gene products, to alter the known structures and functions of proteins and RNAs and to engineer molecules with new properties.
Our key strength is in the integration of various types of theoretical and experimental analyses. We develop and use computer programs for modeling of protein three-dimensional structures based on heterogenous, low-resolution, noisy and ambivalent experimental data. We are also involved in genome-scale phylogenetic analyses, with the focus on identification of proteins that belong to particular families. Subsequently, we characterize experimentally the function of the most interesting new genes/proteins identified by bioinformatics. We also use theoretical predictions to guide protein engineering, using rational and random approaches. Our ultimate goal is to identify complete sets of enzymes involved in particular metabolic pathways (e.g. RNA modification, DNA repair) and to design proteins with new properties, in particular enzymes with new useful functions, which have not been observed in the nature.
We are well-equipped with respect to both theoretical and experimental analyses. Our lab offers excellent environment for training of young researchers in both bioinformatics and molecular biology/biochemistry of protein-nucleic acid interactions.

More Good Science

Model of EcEndoV-DNA complex.
Endonuclease V (EndoV) is a metal-dependent DNA repair enzyme involved in removal of deaminated bases, with pairing specificities different from the original bases. EndoV has been combined with DNA ligase to develop an enzymatic method for mutation scanning and has been engineered to obtain variants with different substrate specificities that serve as improved tools in mutation recognition and cancer mutation scanning. However, at the date of our analysis, little was known about the structure and mechanism of substrate DNA binding by EndoV. Thus, by combining fold-recognition, comparative modeling, de novo modeling and docking methods, we constructed a structural model of EndoV from Escherichia coli in complex with dsDNA and cofactor metal ions. The model has allowed us to provide a structural context for sequence conservation within EndoV proteins family, and to highlight the previously obtained mutations that have been shown to change its specificity. Shortly after the acceptance of the final version of our manuscript [1], the crystal structure of Thermotoga maritima EndoV was published [2] giving a possibility for direct comparison of our model with the native structure of the close homolog. Our modeling can be considered successful, as it correctly predicts EndoV topology as well as the position of all catalytic residues and several residues taking part in protein-DNA interaction. Although our model contains two cofactor Mg2+ ions and the crystal structure of TmEndoV contains only one, authors agree, that in organisms like E.coli, where Asp is the last catalytic residue of EndoV (TmEndoV contains His), the two-metal binding site would be preferred, with the second Mg2+ cation functioning as a bridge to diminish the phosphate-carboxylate electrostatic repulsion.

1. Majorek KA, Bujnicki JM. “Modeling of Escherichia coli Endonuclease V structure in complex with DNA.” (2009) J Mol Model. 15(2):173-82. 
2. Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjoras M. “Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair.” (2009) Nat Struct Mol Biol. 16(2):138-43.

Download structures:
EcEndoV-DNA model
Native structure of TmEndoV-DNA complex

Read our manuscript:
Download PDF 


Comparison of structures of our model and the native structure (PDB code: 2w35).Structures are colored according to the sequence index (N-terminus – blue, C-terminus – red). All the secondary structure elements and the region of catalytic core are modeled correctly. 

Correctly predicted functionally important residues of EcEndoV.We correctly predicted the position of catalytic/Mg2+ coordinating residues (red sticks) and several DNA contacting residues (yellow sticks).