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Structure prediction method of voltage-gating sodium ion channel

A technology of sodium ion channel and prediction method, which is applied in the field of structure prediction of voltage-gated sodium ion channel, can solve the problem of not fully considering the information of transmembrane region, and achieves the effect of reliable method, wide applicability and high reliability

Active Publication Date: 2017-10-13
YELLOW SEA FISHERIES RES INST CHINESE ACAD OF FISHERIES SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

These methods have achieved certain results in the structural modeling of membrane proteins, but these methods did not fully consider the information of the transmembrane region at the beginning of the model construction

Method used

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  • Structure prediction method of voltage-gating sodium ion channel
  • Structure prediction method of voltage-gating sodium ion channel
  • Structure prediction method of voltage-gating sodium ion channel

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Experimental program
Comparison scheme
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Embodiment 1

[0022] Embodiment 1: The structure prediction method for voltage-gated sodium ion channel of the present invention

[0023] Include the following steps:

[0024] 1) Through the Na in NCBI v 1.5 Definition and division of each structural domain, determine Na v The amino acid sequence composition of 1.5_PD is as follows:

[0025] DI:

[0026] DVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTALNGTNGSVEADGLVWESLDLYLSDPENYLLKNGTSDVLLCGNSSDAGTCPEGYRCLKAGENPDHGYTSFDSFAWAFLALFRLMTQDCWERLYQQTLRSAGKIYMIFFMLVIFLGSFYLVNLILAVVAMA

[0027] DII:

[0028] ALGNLTVLAIIVFIFAVVGMQLFGKNYSELRDSDSGLLPRWHMMDFFHAFLIIFRILCGEWIETMWDCMEVSGQSLCLLVFLLVMVIGNLVVLNLFLALLL

[0029] DIII:

[0030] AIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFGRCINQTEGDLPLNYTIVNNKSQCESLNLTGELYWTKVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRGYEEQPQWEYNLYMYIYFVIFIIFGSFFTLNLFIGVII

[0031] DIV:

[0032]ALFNIGLLLFLVMFIYSIFGMANFAYVKWEAGIDDMFNFQTFANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPTLPNSNGSRGDCGSPAVGILFFTTYIIISFLIVVNMYIAIIL

[0033] (2) Using the HHpred method, the N...

Embodiment 2

[0050] Example 2 Na v 1.5 The interaction sites with open local anesthetic drugs are consistent with the experimental results

[0051] (1)Na v 1.5 Complexes with open local anesthetics (Na v 1.5_LA) can be constructed and selected for Na v 1.5 Four local anesthetic drug molecules (LA) acting in the open state: Flecainide, Pilsicainide, Cocaine, Ranolazine as inhibitor molecules. The molecular docking method used is: use REDUCE, Autodock Tools and Autodoc4 to complete. First pass the REDUCE procedure to Na v 1.5 Add hydrogen, and then use Autodock Tools script to Na respectively v 1.5 and LA molecules add Gaussian charges. Select the grid center to The space area within the scope of is the docking grid area, and AutoGrid is used to delineate the grid. Using LA and Na v 1.5 A fully flexible docking method for the binding site region, using Autodock4 for docking. during the docking process. Scoring adopts the method of combining Autodock4's own scoring and Xscore scor...

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Abstract

The invention discloses a structure prediction method of a voltage-gating sodium ion channel, and particularly relates to a structure modeling method of constructing the eukaryotic voltage-gating sodium ion channel Nav1.5 pore structural domain open state based on a template. The method includes the steps that a rosetta membrane protein homology modeling method is used for obtaining a germ sodium ion channel template of a crystal tripolar structure, and four subunit structures of the Nav1.5 pore structural domain are constructed and composed preliminarily; sorting is carried out according to the grading condition of all construction models, the structure with the maximum score is selected as the initial structure of all the structural domains; the four constructed subunit structures are compared to four 4CBC subunits, and the assembled overall structure is optimized; based on structure data and test data of existing local anesthetics drugs, molecular docking is carried out on the optimized structures, screening and evaluating strategies are set according to the existing experiment data to determine the reliability of model construction.

Description

technical field [0001] The present invention relates to the structure prediction method of voltage-gated sodium ion channel, especially relates to the voltage-gated sodium ion channel Na v 1.5 Pore Domain (Na v 1.5_PD) Structural modeling method with open state as the target. Background technique [0002] Voltage-gated sodium ions (Na v ) channels are widely distributed in excitatory cells, mainly selectively allowing Na+ to pass through the membrane, and its main function is to maintain cell excitability and its conduction. Na v 1.5α subunit is Na v The core subunit that l.5 plays a role in is encoded by the SCN5A gene in humans. When its structure and function are abnormal, it will change the electrophysiological properties of sodium ion channels, resulting in "sodium channel diseases", such as congenital and acquired long QT syndromes (LQTs), Brugada syndrome (BrS) and so on. To treat such diseases, channel drugs such as antiarrhythmics and antiepileptics have been ...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F19/16G06F19/22
CPCG16B15/00G16B30/00G16C20/50
Inventor 纪晓峰盛军郑媛王致鹏
Owner YELLOW SEA FISHERIES RES INST CHINESE ACAD OF FISHERIES SCI
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