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Method for screening phosphoglycerate kinase and substrate binding mode

A combination technology of phosphoglycerate kinase and substrate, which is applied in the fields of bioinformatics, informatics, instruments, etc., to achieve the effect of accurate prediction, screening and improvement of accuracy

Pending Publication Date: 2021-04-16
DALIAN INST OF CHEM PHYSICS CHINESE ACAD OF SCI
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] Aiming at the deficiency of predicting the binding mode of PGK1 and substrate by single molecular simulation research means, the present invention proposes a new method of binding dynamics simulation, which can realize more accurate enzyme-substrate binding mode screening

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  • Method for screening phosphoglycerate kinase and substrate binding mode
  • Method for screening phosphoglycerate kinase and substrate binding mode
  • Method for screening phosphoglycerate kinase and substrate binding mode

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0034] Example 1 (screening and determination of PGK1 and CE binding mode):

[0035] 1. Prepare the structural information of the predicted substrate CE

[0036] The structural information of the predicted substrate CE comes from the open source database (https: / / pubchem.ncbi.nlm.nih.gov), query ID: 176079, and its two-dimensional structure is attached figure 2 shown. The atomic types contained in the structure and their corresponding coordinate information were imported into the quantum chemical calculation software gauss 09D01 (M.J.Frisch, et al., Gaussian 09, revision D.1.2010: Gaussian, Inc., Wallingford, CT.), and the density general The B3LYP method is used to optimize the calculation of quantum chemistry under the basis set conditions of 6-31+g* (the basis set parameters come from https: / / www.basissetexchange.org / , query keywords: 6-31+G*), optimize Obtain the calculation result of energy convergence, which contains the new coordinate information of each atom after t...

Embodiment 2

[0266] Example 2 (verification of the binding mode of PGK1 and CE):

[0267] 1. Long-range dynamics simulation of the confirmed binding mode system

[0268]Calculated in Step 7 of Example 1, the No. 7 system determined in Step 9 is calculated through 2ns dynamics simulation, and the new prod_Alt_CE_M7.rst file containing system atom type information and topology information and the original system containing atom type information and atomic coordinates The Alt_CE_M7.top file of information and atomic charge information, the Apo blank control system calculated in step 7, after 2ns dynamics simulation calculation, the new prod_receptor.rst file containing the system atom type information and topology information and the system atom obtained in step 2 The receptor.top file of type information, atomic coordinate information and atomic charge information is used as the input file, and the general dynamics simulation process of constant temperature and constant pressure under the co...

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Abstract

The invention discloses a method for screening a phosphoglycerate kinase and substrate binding mode, and relates to a method for calculating and screening the phosphoglycerate kinase and substrate binding mode. The invention provides a method for exploring the interaction mode of phosphoglycerate kinase and a substrate. By combining quantum chemistry calculation, molecular simulation, molecular dynamics conformation collection and conformation-based combination free energy calculation, the combination mode of phosphoglycerate kinase and a substrate is accurately screened, and a good effect is achieved on prediction of the combination mode of phosphoglycerate kinase 1 (PGK1) and a potential calendula officinalis glycoside substrate (CE).

Description

technical field [0001] The invention provides a screening method for the binding mode of phosphoglycerate kinase and substrate. By combining quantum chemical calculations, molecular simulations, molecular dynamics conformation collection, and conformation-based binding free energy calculations, the binding mode of phosphoglycerate kinase and substrates can be accurately screened. Based on this binding mode, the regulatory effect of substrate binding on phosphoglycerate kinase is consistent with experimental expectations, and good results have been achieved in predicting the binding mode of phosphoglycerate kinase 1 (PGK1) and potential calenduladin substrate (CE). Effect. Background technique [0002] Phosphoglycerate kinase 1 (PGK1) (2.7.2.3) is the first enzyme that produces ATP during glycolysis, which catalyzes the substrate adenosine diphosphate (ADP) to obtain a phosphate group from 1,3-bisphosphoglyceride to thereby Generate adenosinetriphosphate (ATP) and 3-phospho...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B25/00
Inventor 韩克利王家悦
Owner DALIAN INST OF CHEM PHYSICS CHINESE ACAD OF SCI
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