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Method for calculating force between protein and DNA by computer simulation

A technology of analog computing and protein, applied in computing, special data processing applications, instruments, etc., to achieve the effects of easy preparation, high equipment utilization, and low equipment requirements

Inactive Publication Date: 2008-02-13
SHANDONG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, using NAMD_2.6 calculation software and VMD-1.8.6 analysis software to perform molecular dynamics simulations on proteins and DNA to calculate the magnitude of the interaction force between them has not been reported at home and abroad.

Method used

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  • Method for calculating force between protein and DNA by computer simulation
  • Method for calculating force between protein and DNA by computer simulation

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0035] (1) Obtain the complex data file coded 1o4x from the PDB database (http: / / www.rcsb.org / pdb / home / home.do), and name it 1o4x.pdb;

[0036] (2) Use VMD-1.8.6 software to extract the target protein and DNA fragments to be studied, and dissolve them into a cuboid water tank (84 Ȧ*70 Ȧ*61 Ȧ) filled with 0.9% NaCl solution to obtain protein-DNA- Salt solution system (see Figure 1); the structure containing non-hydrogen atom spatial position data in the system is named 1o4x_ionized.pdb, and the structure containing hydrogen atoms and hydrogen bond parameters is named 1o4x_ionized.psf;

[0037](3) Utilize NAMD_2.6 software, adopt Charmm27 force field, use Steepest Descent method, under periodic boundary conditions (Periodic Boundary Conditions PBC), the total time length of the above-mentioned protein-DNA-salt solution system is 100 picoseconds (ps) ) energy minimization (Minimize) process, in which every 1 femtosecond (fs) calculates the van der Waals force of other atoms in th...

Embodiment 2

[0046] (1) Obtain the complex data file coded 1wtq from the PDB database (http: / / www.rcsb.org / pdb / home / home.do), named 1wtq.pdb;

[0047] (2) Utilize the VMD-1.8.6 software to extract the target protein and DNA fragments to be studied, and dissolve them in a cuboid water tank filled with 0.9% NaCl solution to obtain a protein-DNA-salt solution system; the system contains non- The structure of the hydrogen atom spatial position data is named 1wtq_ionized.pdb, and the structure containing hydrogen atoms and hydrogen bond parameters is named 1wtq_ionized.psf;

[0048] (3) Utilize NAMD_2.6 software, adopt Charmm27 force field, use Steepest Descent method, under periodic boundary conditions (Periodic Boundary Conditions PBC), the total time length of the above-mentioned protein-DNA-salt solution system is 100 picoseconds (ps) ) energy minimization (Minimize) process, in which every 1 femtosecond (fs) calculates the van der Waals force of other atoms in the spherical space with each...

Embodiment 3

[0057] (1) Obtain the complex data file coded 1hry from the PDB database (http: / / www.rcsb.org / pdb / home / home.do), named 1hry.pdb;

[0058] (2) Utilize the VMD-1.8.6 software to extract the target protein and DNA fragments to be studied, and dissolve them in a cuboid water tank filled with 0.9% NaCl solution to obtain a protein-DNA-salt solution system; the system contains non- The structure of the hydrogen atom spatial position data is named 1wtq_ionized.pdb, and the structure containing hydrogen atoms and hydrogen bond parameters is named 1wtq_ionized.psf;

[0059] (3) Utilize NAMD_2.6 software, adopt Charmm27 force field, use Steepest Descent method, under periodic boundary conditions (Periodic Boundary Conditions PBC), the total time length of the above-mentioned protein-DNA-salt solution system is 100 picoseconds (ps) ) energy minimization (Minimize) process, in this process, every 1 femtosecond (fs) calculates the van der Waals force of other atoms in the spherical space w...

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Abstract

The invention discloses a method of computing the interactive force between proteins and DNA through computer simulating. In the method, the NAMD_2.6 computing software and the VMD-1.8.6 analysis software are used for molecule dynamics simulation: firstly the protein structure in the PDB database is made into an appropriate research system, then the system is treated for energy minimization, and when the system is heated to the preset temperature, the system is treated for multi-stage balancing; then molecule dynamics simulation is carried out for the system, the target research objects in the system are marked, SMD simulation is carried out for the system, and finally data are processed and analyzed to acquire change of the interactive force between proteins and DNA, and to calculate the maximum interactive force. The method is characterized by wide range of test objects, easy preparation of experimental material, low requirements to devices, high utilization rate, easy and widely application in the fields of life science, physical chemistry and medicine related to molecule identification and gene representing behaviors.

Description

technical field [0001] The invention relates to a method for calculating the interaction force between protein and DNA by computer simulation, in particular to a method for quantitatively studying the interaction force between protein and DNA by using NAMD_2.6 and VMD-1.8.6 software. Background technique [0002] The interaction between protein and DNA is a key step in the process of life activities, such as the recognition of specific sites on DNA by transcription factors, the activation or shutdown of the transcription of a specific gene, and the regulation of DNA replication. Conventional experimental methods use the determination of reaction equilibrium constants to detect the binding strength between proteins and DNA. Atomic force microscopy can also be used to operate on single molecules to separate proteins and DNA to provide information for the dissociation process. However, due to the difficulty in preparing experimental materials, neither the determination of the r...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F19/18
Inventor 时永香连鹏步宇翔
Owner SHANDONG UNIV
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