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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

R.MvaI is a Type II restriction enzyme (REase), which specifically recognizes the pentanucleotide DNA sequence 5'-CC(A or T)GG-3'. It belongs to a family of enzymes, which recognize related sequences. Characterization of sequence-structure-function relationships in this family would facilitate understanding of evolution of sequence specificity among REases and could aid in engineering of enzymes with new specificities. However, at the date of our analysis, no structural information was available for any enzyme of this family. Thus we constructed a structural model of R.MvaI in complex with DNA and used it to identify amino acid residues involved in specific DNA recognition – in particular those, which may be responsible for different specificity of R.MvaI homologs that recognize different sequences. Shortly after the acceptance of the final version of our manuscript [1], the crystal structure of R.MvaI was published [2] giving a possibility for direct comparison of our model with the native structure. Our modeling appeared to be fairly successful. Our model correctly predicts all the key features of MvaI: its monomeric structure, the PD-(D/E)XK fold, relationship to MutH, all catalytic residues and several DNA contacting residues.

References: 
1. Kosinski, J., Kubareva, E. and Bujnicki, J.M. “A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.” (2007) Proteins 68(1):324-36 
2. Kaus-Drobek M, Czapinska H, Sokolowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M. "Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically." (2007) Nucleic Acids Res. 35(6):2035-46


Download structures:
R.MvaI-DNA model
Native structure of R.MvaI-DNA complex

Read our manuscript:
Download PDF 

Gallery:

 

Comparison of structures of our model and the native structure (PDB code: 2oaa).Structures are colored according to the sequence index (N-terminus – blue, C-terminus – red). We correctly predicted that R.MvaI exhibits the PD-(D/E)XK fold and that it binds and cleaves DNA as a monomer. The model is of good quality in regions responsible for catalysis and main DNA contacts. A part of the model (greenish region) was not modeled correctly. 

 

 

 

 

Correctly predicted functionally important residues of R.MvaI-DNA recognition.We predicted all catalytic residues (red sticks) and several DNA contacting residues (yellow sticks) including D207, R230 and R209 and that R209 residue is involved in the recognition of the central base pair.