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Predicted 3D Structures

 

 

Three different servers for protein structure and function prediction were used to predict the 3D structure of eEF2K; Phyre, Raptor and Tasser. 

The predicted 3D models of eEF2K as well as the domain structures were then rendered using Pymol (1).

 

Phyre predicted 3D model of eEF2K

Phyre was used to predict the tertiary structure of eEF2K (2). 64% of the residues were modelled a >90% confidence. The alpha kinase domain had the highest reliability as it was modelled with 100% confidence using the templates 3pdtA (43% identity) and 3lmhB (41% identity), both of which are the alpha kinase domain of Dicytostelium MHCK A. 

Raptor predicted 3D model of eEF2K

Raptor X was also used to predict the structure of eEF2K (3). Raptor X is a server which uses an input sequence and detects similar proteins in the PDB and predicts secondary and tertiary structure, disordered regions and binding sites. Raptor X detected 3 domains and predicted structure composition being 35% helices, 12% beta strands and 51% coiled structures. 21% (157 amino acid residues) were predicted as disordered. The TM score measures structural similarity between two structures and a value >0.5 indicates that the model’s topology is correct and the first model scored 0.39  0.13.

Tasser predicted 3D model of eEF2K

We have also used Iterative Threading ASSEmbly Refinement (I-TASSER) to determine the protein’s structure and predicted biological function (4, 5, 6). An amino acid sequence is submitted and the programme detects known proteins in the PDB that have similar folds to the protein (but without using close homologous proteins) in question to create a ‘best fit’. It then aligns the target sequence with the proteins from the database and then the folds are assembled to create the most probable three dimensional protein model. Finally, the sequence is annotated the structural domains and their functions. I-TASSER predicted 5 final models whose C-score (on a scale between -5 to 2) ranged between -3.18 to 2.85 which is relatively low, which indicates the quality of the predicted models. We have only included the first model out of the five generated. The eEF2K protein was predicted to consist of 34.6% helical, 9.5% beta strands and 55.9% coiled structures.

References:

 

1. The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.

 

2. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protocols. 2015;10(6):845-58. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25950237

 

3. Kallberg M, Wang H, Wang S, Peng J, Wang Z, Lu H, et al. Template-based protein structuremodeling using the RaptorX web server. Nat Protoc. 2012;7(8):1511-22. Available from:http://www.ncbi.nlm.nih.gov/pubmed/22814390

 

4. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12(1):7-8. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25549265

 

5. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010;5(4):725-38. Available from: http://www.ncbi.nlm.nih.gov/pubmed/20360767/

 

6. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008;9:40. Available from: http://www.ncbi.nlm.nih.gov/pubmed/18215316

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