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Filtering protein models by fuzzy restraints

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Example: discrimination of native-like complexes from low-resolutions docking decoys of pseudouridine synthase TruA from Thermus thermophilus

The example file set of low-resolution docking decoys was obtained by a docking with GRAMM {Vakser 1995} of a TruA enzyme structure (PDB code 1VS3, apo form) to its tRNA substrate (PDB code 2V0G, a complex with an unrelated protein). As a reference we used the native structure of this complex (PDB code 2NR0; Figure 1). We produced 30000 decoys with the grid step = 3.5 , and repulsion parameter = 20. The grid-step radius was used as a projection of an atom. The systematic search through the rotational coordinates was performed every 10 degree.
While original published file set contained 30k decoys and had to be splitted into three parts due to system limitations, we encourage you to try a shorter example of 100 decoys.

For discrimination of native-like complexes with FILTREST3D we used six distance restraints. First, we chose protein residues R50 and N52 known to be involved in catalysis of isomerization of U39 in tRNA and introduced two specific amino acid-nucleotide restraints. Second, we identified additional putative RNA-binding residues (R23, H119, R162.) that were both predicted as RNA-binding by the PPRINT webserver (Figure 2A) and were located in regions of positive electrostatic potential (Figure 2B), as calculated with the APBS tool with the PyMol program {DeLano 2002} for performing electrostatic calculations. For these four residues we defined a general restraint for interactions with any nucleotide of the whole tRNA molecule.

We filled Filtrest3D’s server form and ran a filtering process. After one minute the result for 100 testing decoys appeared.

As visible in the output 2 decoys satisfy restraints completely. They the RMSD to the native structure of 22.36 Å and 26.56 Å. They are similar to each other and can be considered native-like (Figure 3).

Figure 1: Native structure of this complex (PDB code 2NR0.)

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Figure 2: The analysis of the protein surface of TruA. A – Regions, which according to PPRINT server could interact with RNA are colored yellow. B – Electrostatic map of the protein surface. The positive charged regions are blue, while negative charged regions are red.

Picture A

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Picture B

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Figure 3: A,B – Each of two best scored decoys, which were found by Filtrest3D superimposed on the reference structure of complex. Only proteins are superimposed. Reference structure is colored in blue tones, while decoys are colored in red tones. All atoms, which were used to make restraints have VDW representation. Cα of marked amino acids are colored white, while O3’ atoms of nucleic acids are yellow. C – Two best scored decoys. Proteins are superimposed.

Picture A

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Picture B

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Picture C

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