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Applying In Silico approaches for designing a chimeric InaV/N-DFPase protein and evaluating its binding with diisopropyl-fluorophosphate

100%
Allahyari H., Karami A., Tebyanian H., Nouri H. R., Khodi S., Farnoosh G., Arab S. S., Latifi A. M.
International Letters of Natural Sciences
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2019
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tom 75
The N-terminal domain of the ice-nucleation protein InaV (InaV-N) of Pseudomonas syringae was applied to display the DFPase on the cell surface. In silico techniques were used to generate a model in order to examine the possibility of DFPase exhibition on the cell surface. The secondary and tertiary structures of a chimeric protein were determined and then, the predicted model was subjected to several repeated cycles of stereochemical evaluation and energy minimization. The homology-modeled structure of the InaV/N-DFPase protein was docked to DFP. The optimized inaV/N-dfpase gene was translated to 519 amino acids. The minimum free energy of the best-predicted secondary structures was formed by RNA molecules (-215.45 kcal/mol). SOPMA analysis results showed that the main helix peak corresponded to the anchor fragment. Validation of the 3D model indicated that 86.1% of amino acid residues were incorporated into the favored regions. The moldock score was 360.22 for DFP. Results of this study indicated that according to in silico analysis, all of these findings were effective in targeting DFPase.
2
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In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana

86%
Sahu M., Dehury B., Sarmah R., Sahoo S., Sahu J., Sarma K., Sen P., Modi M. K., Barooah M.
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
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2013
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tom 94
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nr 4
Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana . This protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance of this protein, very little information is available regarding its structure and function in plants. In this study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID: 1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand interaction study.
3

TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling

86%
Trojanowski S., Rutkowska A., Kolinski A.
Acta Biochimica Polonica
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2010
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tom 57
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nr 1
125-133
A new approach to comparative modeling of proteins, TRACER, is described and benchmarked against classical modeling procedures. The new method unifies true three-dimensional threading with coarse-grained sampling of query protein conformational space. The initial sequence alignment of a query protein with a template is not required, although a template needs to be somehow identified. The template is used as a multi-featured fuzzy three-dimensional scaffold. The conformational search for the query protein is guided by intrinsic force field of the coarse-grained modeling engine CABS and by compatibility with the template scaffold. During Replica Exchange Monte Carlo simulations the model chain representing the query protein finds the best possible structural alignment with the template chain, that also optimizes the intra-protein interactions as approximated by the knowledge based force field of CABS. The benchmark done for a representative set of query/template pairs of various degrees of sequence similarity showed that the new method allows meaningful comparative modeling also for the region of marginal, or non-existing, sequence similarity. Thus, the new approach significantly extends the applicability of comparative modeling.
4

Protein modelling and structure prediction with a reduced representation

86%
Kolinski A.
Acta Biochimica Polonica
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2004
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tom 51
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nr 2
Protein modeling could be done on various levels of structural details, from simpli­fied lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular me­chanics. Here I describe a new high resolution reduced model, its force field and ap­plications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sam­pling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic pro­tein-like conformational biases, statistical potentials for the short-range confor- mational propensities, a model of the main chain hydrogen bonds and context-de­pendent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.
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