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Method for estimating protein conformation morphological characteristics based on nanopore via current

Active Publication Date: 2021-11-23
INST OF MECHANICS - CHINESE ACAD OF SCI
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] The purpose of the present invention is to provide a method for estimating protein conformation and morphology characteristics based on nanopore through-hole current, so as to solve the problem that the through-hole current is difficult to reflect protein conformation and morphology characteristics in the prior art

Method used

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  • Method for estimating protein conformation morphological characteristics based on nanopore via current
  • Method for estimating protein conformation morphological characteristics based on nanopore via current
  • Method for estimating protein conformation morphological characteristics based on nanopore via current

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0063] This example is to estimate the shape characteristics of butyrylcholinesterase based on nanopore sensing technology, the principle is as follows figure 1 shown.

[0064] Obtain the two directions with the largest and smallest projected area of ​​butyrylcholinesterase as two special orientations. Place the three-dimensional space structure of butyrylcholinesterase crystal (PDBID: 1P0I) in the three-dimensional space coordinate system, coincide the centroid of the protein with the dot on the coordinate axis, and step along the Z, Y, and X coordinate axes at an angle of 1°. Rotate sequentially along the three coordinate axes, and finally obtain the two special orientations of the protein crystal on the X-Y plane, the orientation of the largest projected area (ID: 73-133-110) and the orientation of the smallest projected area (ID: 0-16-37) .

[0065] Five arbitrary orientations of the three-dimensional structure of butyrylcholinesterase crystals were obtained. Arbitraril...

Embodiment 2

[0078] This example is to estimate the morphology characteristics of acetylcholinesterase based on nanopore sensing technology.

[0079] The two directions with the largest and smallest projected area of ​​acetylcholinesterase were obtained as the two special orientations. The three-dimensional space structure of acetylcholinesterase crystal (PDBID: 3LII) was placed in the three-dimensional space coordinate system, and the centroid of the protein was coincident with the dot on the coordinate axis, and arbitrarily rotated along the Z, Y, and X coordinate axes to obtain 1000 orientations. Among the 1000 random orientations, find out the two special orientations of the protein crystal on the X-Y plane, the orientation of the largest projected area (ID: 65-214-290) and the orientation of the smallest projected area (ID: 134-144-185).

[0080] Obtain 998 arbitrary orientations of the three-dimensional structure of acetylcholinesterase crystals. In the above steps, the orientations...

Embodiment 3

[0100] This example is to estimate the morphology characteristics of high-affinity integrins based on nanopore sensing technology.

[0101] The two directions with the largest and smallest projected areas of high-affinity integrins were obtained as two special orientations. The integrin protein (PDBID: 3k6s) was processed by stretching molecular dynamics to obtain its high-affinity conformation. Place the three-dimensional space structure of the conformation of the high-affinity state in the three-dimensional space coordinate system, the centroid of the protein coincides with the dot of the coordinate axis, and step along the three coordinate axes at an angle of 1° along the Z, Y, and X coordinate axes Rotate sequentially respectively, and finally obtain two special orientations of the protein crystal on the X-Y plane, the orientation of the largest projected area and the orientation of the smallest projected area.

[0102] Obtain 5 random orientations of the three-dimensiona...

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Abstract

The invention discloses a method for estimating protein conformation morphological characteristics based on nanopore via hole current, which comprises the following steps of: morphological estimation is performed on protein conformation through one or more spheroids based on nanopore characteristic current; for the spheroidic protein, a spheroidic body is adopted for estimating the morphological characteristics, and the axial length of the spheroidic body is obtained by analyzing the relation between the relative blocking current and the orientation angle; and for non-spheroidic proteins, the morphology of the non-spheroidic proteins is estimated by adopting a conjoined body of a plurality of spheroidic bodies, and the axial length of each spheroidic body is obtained by analyzing the relation between the relative blocking current and the orientation angle and the relation between the angles of various spheroidic bodies. The method solves the problem that in the prior art, through hole current is difficult to reflect protein conformation morphological characteristics.

Description

technical field [0001] The invention relates to the technical field of nanopore biomolecular sensing, in particular to a method for estimating protein conformation and morphology characteristics based on nanopore through-hole current. Background technique [0002] The conformation of a protein is the basis for its biological function. Exploring the conformation of proteins and the allosteric pathways between different conformational states is the key to elucidating their structure-function relationships. With the development of nanotechnology, nanopore sensing technology has important application prospects in the field of biomacromolecule detection. Nanopore sensing technology has the advantages of single-molecule, label-free, and high-throughput, and has been successfully used in protein research. When the protein passes through the nanopore under the action of electrophoresis, the conductance in the nanopore will be changed due to the occupation effect, forming a charact...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01B7/28
CPCG01B7/28
Inventor 张明焜龙勉吕守芹
Owner INST OF MECHANICS - CHINESE ACAD OF SCI
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