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Screening method of non-ribosomal protein-RNA composite near-nature structure

A screening method and protein technology, which can be applied in the fields of instrumentation, computing, electrical digital data processing, etc., can solve problems such as inappropriate screening of protein-RNA complexes

Inactive Publication Date: 2014-01-08
BEIJING UNIV OF TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, this model is not suitable for the screening of near-native structures of protein-RNA complexes

Method used

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  • Screening method of non-ribosomal protein-RNA composite near-nature structure
  • Screening method of non-ribosomal protein-RNA composite near-nature structure
  • Screening method of non-ribosomal protein-RNA composite near-nature structure

Examples

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Embodiment 1

[0057] The following takes the near-native structure screening of the protein-RNA complex 1F7U as an example to introduce the implementation process of this method. The goal is, given the protein monomer structure and the RNA monomer structure of 1F7U, to obtain a near-native structure of its complex by implementing the method.

[0058] step 1:

[0059] The protein and RNA monomer structure files of the protein-RNA complex are respectively recorded as 1F7U-protein.parsed and 1F7U-rna.parsed, and the conformational search is performed by FTDock software, and the specific commands are as follows:

[0060] ftdock-static1F7U-protein.parsed-mobile1F7U-rna.parsed-noelec-out1F7U.dat noelec indicates that electrostatic effects are not considered in the conformational search. Other conformational search parameters, such as molecular surface thickness and angular sampling step size, were set by default (Ref. [2]). A total of 10000 binding patterns were generated and stored in the fil...

Embodiment 2

[0070] The method of the present invention is used to screen the near-native structures of another 16 protein-RNA systems mentioned in reference [11] (a total of 17 systems, Example 1 is one of them). In the near-native conformation screening, for proteins and RNA molecules in these complex structures, if there is a corresponding monomer structure in the PDB (Protein Data Bank) database, we will use the monomer structure; if there is no experimentally obtained monomer structure in the database For bulk structures, the corresponding bound protein and RNA molecules in the complex are used. The results of the near-native structure screening are shown in Table 3 (all 17 systems are listed).

[0071] Among the 17 systems, there are 10 systems (58.8%) whose near-natural structure ranks in the top 5; there are 14 systems (accounting for 82.4%) whose near-natural structure ranks in the top 50. From the overall analysis of all systems, 75.4% of the binding modes in the top 2000 ranked...

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Abstract

The invention provides a screening method of a non-ribosomal protein-RNA composite near-nature structure, and belongs to the field of protein-RNA molecular docking composite structure prediction. Firstly, various possible combination modes of protein-RNA are obtained through conformation searching; then rationality of the combination modes is assessed, static and van and der waals interaction energy among the protein-RNA molecules and amino acid nucleotide pairing preference on composite interfaces are comprehensively taken into consideration, and the weight of each item is obtained in the mode that a linear regression method is adopted and accordingly fitting of a ligand root-mean-square deviation and weighted combination values of energy items of a docking structure is carried out; finally, according to the order that the values are sequenced from smaller ones to larger ones, a near-nature structure is judged. The screening method has a good effect on screening of the non-ribosomal protein-RNA molecular docking near-nature structure, the successful rate is high, and the method can be used for the field of protein-RNA composite structure prediction and provides an important basis for molecule improvement and design.

Description

technical field [0001] The invention belongs to the field of protein-RNA molecular docking complex structure prediction, and relates to a method for screening non-ribosomal protein-RNA pairs close to natural structures. Background technique [0002] Many functions of intracellular RNA, such as mRNA splicing, tRNA transport, and protein translation regulation, must form specific interactions with certain proteins to achieve [1]. At present, with the development of experimental technology, it is relatively easy to obtain the structure of protein monomers or RNA monomers by experimental means such as X-ray diffraction and nuclear magnetic resonance, but it is very difficult to obtain the structure of protein-RNA complexes. Therefore, it is particularly important to obtain the near-native structure of protein-RNA through the structure prediction method of protein-RNA complex—molecular docking. This method can not only be used in the field of complex structure prediction, but al...

Claims

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Application Information

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IPC IPC(8): G06F19/22
Inventor 李春华张弘古村刘斌谢小露张蕾谭建军张小轶王存新
Owner BEIJING UNIV OF TECH
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