@article {Sen2008, title = {Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA}, journal = {Biophysical journal}, volume = {94}, number = {7}, year = {2008}, month = {apr}, pages = {2482{\textendash}91}, publisher = {Elsevier}, abstract = {Escherichia coli requires an efficient transport and signaling system to successfully sequester iron from its environment. FecA, a TonB-dependent protein, serves a critical role in this process: first, it binds and transports iron in the form of ferric citrate, and second, it initiates a signaling cascade that results in the transcription of several iron transporter genes in interaction with inner membrane proteins. The structure of the plug and barrel domains and the periplasmic N-terminal domain (NTD) are separately available. However, the linker connecting the plug and barrel and the NTD domains is highly mobile, which may prevent the determination of the FecA structure as a whole assembly. Here, we reduce the conformation space of this linker into most probable structural models using the modeling tool CABS, then apply normal-mode analysis to investigate the motions of the whole structure of FecA by using elastic network models. We relate the FecA domain motions to the outer-inner membrane communication, which initiates transcription. We observe that the global motions of FecA assign flexibility to the TonB box and the NTD, and control the exposure of the TonB box for binding to the TonB inner membrane protein, suggesting how these motions relate to FecA function. Our simulations suggest the presence of a communication between the loops on both ends of the protein, a signaling mechanism by which a signal could be transmitted by conformational transitions in response to the binding of ferric citrate.}, keywords = {Cell Membrane, Cell Membrane: chemistry, Cell Surface, Cell Surface: chemistry, Cell Surface: ultrastructure, Chemical, Computer Simulation, Escherichia coli Proteins, Escherichia coli Proteins: chemistry, Escherichia coli Proteins: ultrastructure, Models, Molecular, Motion, Protein Conformation, Receptors}, isbn = {5152944294}, issn = {1542-0086}, doi = {10.1529/biophysj.107.116046}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2267147\&tool=pmcentrez\&rendertype=abstract}, author = {Taner Z. Sen and Margaret Kloster and Robert L. Jernigan and Andrzej Koli{\'n}ski and Janusz M. Bujnicki and Andrzej Kloczkowski} } @inbook {250, title = {Template-free predictions of three-dimensional protein structures: From first principles to knowledge-based potentials}, booktitle = {Prediction of Protein Structures, Functions, and Interactions}, year = {2008}, pages = {117-142}, publisher = {John Wiley \& Sons}, organization = {John Wiley \& Sons}, address = {Chichester, UK}, author = {Dominik Gront and Dorota Latek and Mateusz Kurcinski and Andrzej Koli{\'n}ski and Janusz M. Bujnicki} } @article {Ibryashkina2007, title = {Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily}, journal = {BMC Structural Biology}, volume = {7}, year = {2007}, month = {jan}, pages = {48}, abstract = {BACKGROUND: The majority of experimentally determined crystal structures of Type II restriction endonucleases (REases) exhibit a common PD-(D/E)XK fold. Crystal structures have been also determined for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI), and bioinformatics analyses supported by mutagenesis suggested that some REases belong to the HNH fold. Our previous bioinformatic analysis suggested that REase R.Eco29kI shares sequence similarities with one more unrelated nuclease superfamily, GIY-YIG, however so far no experimental data were available to support this prediction. The determination of a crystal structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling of R.Eco29kI and prompted us to validate the model experimentally. RESULTS: Using protein fold-recognition methods we generated a new alignment between R.Eco29kI and I-TevI, which suggested a reassignment of one of the putative catalytic residues. A theoretical model of R.Eco29kI was constructed to illustrate its predicted three-dimensional fold and organization of the active site, comprising amino acid residues Y49, Y76, R104, H108, E142, and N154. A series of mutants was constructed to generate amino acid substitutions of selected residues (Y49A, R104A, H108F, E142A and N154L) and the mutant proteins were examined for their ability to bind the DNA containing the Eco29kI site 5{\textquoteright}-CCGCGG-3{\textquoteright} and to catalyze the cleavage reaction. Experimental data reveal that residues Y49, R104, E142, H108, and N154 are important for the nuclease activity of R.Eco29kI, while H108 and N154 are also important for specific DNA binding by this enzyme. CONCLUSION: Substitutions of residues Y49, R104, H108, E142 and N154 predicted by the model to be a part of the active site lead to mutant proteins with strong defects in the REase activity. These results are in very good agreement with the structural model presented in this work and with our prediction that R.Eco29kI belongs to the GIY-YIG superfamily of nucleases. Our study provides the first experimental evidence for a Type IIP REase that does not belong to the PD-(D/E)XK or HNH superfamilies of nucleases, and is instead a member of the unrelated GIY-YIG superfamily.}, keywords = {Amino Acid Sequence, Binding Sites, Computational Biology, Computational Biology: methods, Deoxyribonucleases, DNA, DNA Cleavage, DNA: metabolism, Electrophoretic Mobility Shift Assay, Models, Molecular, Molecular Sequence Data, Mutation, Protein, Protein Conformation, Sequence Alignment, Structural Homology, Type II Site-Specific, Type II Site-Specific: chemist, Type II Site-Specific: metabol}, isbn = {1472680774}, issn = {1472-6807}, doi = {10.1186/1472-6807-7-48}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1952068\&tool=pmcentrez\&rendertype=abstract}, author = {Elena M. Ibryashkina and Marina V. Zakharova and Vladimir B. Baskunov and Ekaterina S. Bogdanova and Maxim O. Nagornykh and Marat M Den{\textquoteright}mukhamedov and Bogdan S. Melnik and Andrzej Koli{\'n}ski and Dominik Gront and Marcin Feder and Alexander S. Solonin and Janusz M. Bujnicki} } @article {Kolinski2005, title = {Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models}, journal = {Proteins}, volume = {61 Suppl. 7}, number = {April}, year = {2005}, month = {jan}, pages = {84{\textendash}90}, abstract = {To predict the tertiary structure of full-length sequences of all targets in CASP6, regardless of their potential category (from easy comparative modeling to fold recognition to apparent new folds) we used a novel combination of two very different approaches developed independently in our laboratories, which ranked quite well in different categories in CASP5. First, the GeneSilico metaserver was used to identify domains, predict secondary structure, and generate fold recognition (FR) alignments, which were converted to full-atom models using the "FRankenstein{\textquoteright}s Monster" approach for comparative modeling (CM) by recombination of protein fragments. Additional models generated "de novo" by fully automated servers were obtained from the CASP website. All these models were evaluated by VERIFY3D, and residues with scores better than 0.2 were used as a source of spatial restraints. Second, a new implementation of the lattice-based protein modeling tool CABS was used to carry out folding guided by the above-mentioned restraints with the Replica Exchange Monte Carlo sampling technique. Decoys generated in the course of simulation were subject to the average linkage hierarchical clustering. For a representative decoy from each cluster, a full-atom model was rebuilt. Finally, five models were selected for submission based on combination of various criteria, including the size, density, and average energy of the corresponding cluster, and the visual evaluation of the full-atom structures and their relationship to the original templates. The combination of FRankenstein and CABS was one of the best-performing algorithms over all categories in CASP6 (it is important to note that our human intervention was very limited, and all steps in our method can be easily automated). We were able to generate a number of very good models, especially in the Comparative Modeling and New Folds categories. Frequently, the best models were closer to the native structure than any of the templates used. The main problem we encountered was in the ranking of the final models (the only step of significant human intervention), due to the insufficient computational power, which precluded the possibility of full-atom refinement and energy-based evaluation.}, keywords = {Algorithms, Computational Biology, Computational Biology: methods, Computer Simulation, Computers, Data Interpretation, Databases, Dimerization, Models, Molecular, Monte Carlo Method, Protein, Protein Conformation, Protein Folding, Protein Structure, Proteomics, Proteomics: methods, Reproducibility of Results, Secondary, Sequence Alignment, Software, Statistical, Tertiary}, issn = {1097-0134}, doi = {10.1002/prot.20723}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16187348}, author = {Andrzej Koli{\'n}ski and Janusz M. Bujnicki} } @article {Bujnicki2001, title = {Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics}, journal = {Protein Engineering}, volume = {14}, number = {10}, year = {2001}, month = {oct}, pages = {717{\textendash}721}, abstract = {Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain (CD) of the I-TevI homing endonuclease, a representative of the GIY-YIG superfamily of homing endonucleases. The secondary structure of the I-TevI CD has been determined using NMR spectroscopy, but computational sequence analysis failed to detect any protein of known tertiary structure related to the GIY-YIG nucleases (Kowalski et al., Nucleic Acids Res., 1999, 27, 2115-2125). To provide further insight into the structure-function relationships of all GIY-YIG superfamily members, including the recently described subfamily of type II restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9-11), we incorporated the experimentally determined and predicted secondary and tertiary restraints in a reduced (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available experimental data to be put into a structural context and suggests that the GIY-YIG domain may dimerize in order to bring together the conserved residues of the active site.}, keywords = {Algorithms, Binding Sites, Biomolecular, Endodeoxyribonucleases, Endodeoxyribonucleases: chemistry, Models, Molecular, Monte Carlo Method, Nuclear Magnetic Resonance, Protein Structure, Sequence Alignment, Tertiary}, issn = {0269-2139}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11739889}, author = {Janusz M. Bujnicki and Piotr Rotkiewicz and Andrzej Koli{\'n}ski and Leszek Rychlewski} }