CN110317263B - Bovine serum albumin modification method for efficiently detecting PAEs (platelet-activating proteins) based on homologous modeling - Google Patents
Bovine serum albumin modification method for efficiently detecting PAEs (platelet-activating proteins) based on homologous modeling Download PDFInfo
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Abstract
The invention provides a bovine serum albumin modification method for efficiently detecting PAEs (platelet activating proteins) based on homologous modeling, belonging to the technical field of spectrum detection. Removing water molecules in a bovine serum albumin structure, adding hydrogen and charges, fusing target PAEs molecules into a receptor binding cavity, and replacing hydrophilic amino acids at an active site of the bovine serum albumin with hydrophobic amino acids; constructing the structure of the bovine serum albumin after amino acid substitution by using a homologous modeling method; and (3) screening the bovine serum albumin structure by using a PROCHECK server, wherein the map shows that all amino acid residues are positioned in an allowable area, and the percentage of the amino acid residues falling in the optimal area, the allowable area and the maximum allowable area meets more than 95%, so that the bovine serum albumin for efficiently detecting PAEs is obtained. The method is simple and convenient to operate, rapid in calculation and easy to realize, realizes the novel bovine serum albumin which is improved in binding affinity with the target PAEs and enhanced in fluorescence spectrum intensity, and provides direct theoretical guidance for realizing high-sensitivity fluorescence spectrum detection of the PAEs.
Description
Technical Field
The invention relates to the technical field of bovine serum albumin, in particular to a bovine serum albumin modification method for efficiently detecting PAEs (platelet activating proteins) based on homologous modeling.
Background
Phthalate esters (PAEs) are mainly used in the plastic industry, and are also widely used in products such as cosmetics, food packaging materials and the like. With the use of a large number of plastic packaging products, the pollution caused by the residual and migration processes of phthalate compounds in the environment is increasingly serious, and the air, water, soil, food and the like are polluted by PAEs (polycyclic aromatic acids), which are typical environmental estrogens, have wide distribution and are difficult to degrade.
The fluorescence spectrometry has the advantages of high sensitivity, simple and convenient method and the like, and because PAEs molecules cannot emit fluorescence per se, the detection cannot be directly carried out by using a fluorescence method, and the traditional PAEs fluorescence detection method mainly carries out indirect fluorescence detection by means of the interaction with Bovine Serum Albumin (BSA) with fluorescence spectrum characteristics. Bovine serum albumin has the advantages of small molecular weight, good stability, good affinity with ligands and the like, and a fluorescence spectrum detection method of PAEs-BSA system interaction is established in the prior research. The homologous modeling provides a new means for predicting the protein structure, can quickly and effectively obtain the protein structure, provides a theoretical basis for further understanding and modifying the function of the protein based on data provided by the structure, and can provide a guide for efficiently detecting the protein modification of the PAEs.
Disclosure of Invention
The invention aims to provide a bovine serum albumin modification method for efficiently detecting PAEs (platelet activating proteins) based on homologous modeling, so as to solve the technical problems in the background technology.
In order to achieve the purpose, the invention adopts the following technical scheme:
the bovine serum albumin modification method for efficiently detecting PAEs based on homologous modeling comprises the following process steps:
step S110: removing water molecules in a bovine serum albumin structure, and performing hydrogenation and charging treatment to determine a receptor binding cavity of the bovine serum albumin;
step S120: fusing target PAEs molecules into a receptor binding cavity, and carrying out semi-flexible butt joint with bovine serum albumin to obtain amino acid residues contained around the target PAEs molecules;
step S130: replacing hydrophilic amino acid at the active site of bovine serum albumin with hydrophobic amino acid;
step S140: constructing the structure of the bovine serum albumin after amino acid substitution by using a homologous modeling method;
step S150: screening the bovine serum albumin structure obtained in the step S140 by using a PROCHECK server to obtain a bovine serum albumin structure meeting a certain condition, namely the bovine serum albumin for efficiently detecting PAEs; wherein the satisfying of the certain condition includes that when the map shows that all the amino acid residues are located in the allowable region, and the percentage of the amino acid residues falling within the optimum region + the allowable region + the maximum allowable region satisfies more than 95%.
Preferably, the method further comprises the following steps:
and (4) carrying out molecular docking on the bovine serum albumin obtained in the step (S150) and the target PAEs, and evaluating the binding affinity and the fluorescence spectrum intensity.
Preferably, the bovine serum albumin structure is obtained from a PDB protein database.
Preferably, the hydrophilic amino acids at the active site are Arg198 and Arg 256.
Preferably, the hydrophobic amino acid is a combination of one or more of Ile, Phe, Val, or Leu.
The invention has the beneficial effects that: the method is simple and convenient to operate, rapid in calculation and easy to implement, can theoretically verify the feasibility of a bovine serum albumin modification scheme, can further explore novel bovine serum albumin which is improved in binding affinity with target PAEs and enhanced in fluorescence spectrum intensity, and provides direct theoretical guidance for high-sensitivity fluorescence spectrum detection of the PAEs.
Moreover, the bovine serum albumin modification mode for efficiently detecting PAEs has short research and development period and low cost, can save a large amount of manpower, material resources and financial resources, and provides a new idea for the fluorescence spectrum detection of the PAEs with high sensitivity. Compared with the fluorescence intensity of PAEs molecules combined with original bovine serum albumin, the fluorescence intensity of DMP, DBP and DNOP molecules combined with novel bovine serum albumin is increased to some extent, and the increase range can reach 1.80 times, 103.50 times and 61.43 times, which shows that the improvement effect of novel bovine serum albumin is obvious in the detection and enhancement effect of PAEs. .
Additional aspects and advantages of the invention will be set forth in part in the description which follows, and in part will be obvious from the description, or may be learned by practice of the invention.
Drawings
In order to more clearly illustrate the technical solutions of the embodiments of the present invention, the drawings needed to be used in the description of the embodiments are briefly introduced below, and it is obvious that the drawings in the following description are only some embodiments of the present invention, and it is obvious for those skilled in the art to obtain other drawings based on these drawings without creative efforts.
Fig. 1 is a flowchart of a bovine serum albumin modification method for efficiently detecting PAEs based on homology modeling in embodiment 1 of the present invention.
Fig. 2 is a flowchart of a bovine serum albumin modification method for efficiently detecting PAEs based on homology modeling in embodiment 2 of the present invention.
Fig. 3 is a structural diagram of bovine serum albumin transformed by the bovine serum albumin transformation method for efficiently detecting PAEs based on homology modeling in embodiment 2 of the present invention.
Detailed Description
The embodiments described below with reference to the accompanying drawings are illustrative only for the purpose of explaining the present invention, and are not to be construed as limiting the present invention.
As used herein, the singular forms "a", "an", "the" and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms "comprises" and/or "comprising," when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and/or modules, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, modules, and/or groups thereof.
It will be understood by those skilled in the art that, unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the prior art and will not be interpreted in an idealized or overly formal sense unless expressly so defined herein.
For the convenience of understanding of the embodiments of the present invention, the following description will be further explained by taking specific embodiments as examples with reference to the drawings, and the embodiments are not to be construed as limiting the embodiments of the present invention.
It will be understood by those of ordinary skill in the art that the figures are merely schematic representations of one embodiment and that the elements or devices in the figures are not necessarily required to practice the present invention.
Example 1
As shown in fig. 1, embodiment 1 of the present invention provides a bovine serum albumin modification method for efficiently detecting PAEs based on homologous modeling, which includes the following steps:
step S110: removing water molecules in a bovine serum albumin structure, and performing hydrogenation and charging treatment to determine a receptor binding cavity of the bovine serum albumin;
step S120: fusing target PAEs molecules into a receptor binding cavity, and carrying out semi-flexible butt joint with bovine serum albumin to obtain amino acid residues contained around the target PAEs molecules;
step S130: replacing hydrophilic amino acid at the active site of bovine serum albumin with hydrophobic amino acid;
step S140: constructing the structure of the bovine serum albumin after amino acid substitution by using a homologous modeling method;
step S150: screening the bovine serum albumin structure obtained in the step S140 by using a PROCHECK server to obtain a bovine serum albumin structure meeting a certain condition, namely the bovine serum albumin for efficiently detecting PAEs; wherein the satisfying of the certain condition includes that when the map shows that all the amino acid residues are located in the allowable region, and the percentage of the amino acid residues falling within the optimum region + the allowable region + the maximum allowable region satisfies more than 95%.
Also comprises the following steps:
and (4) carrying out molecular docking on the bovine serum albumin obtained in the step (S150) and the target PAEs, and evaluating the binding affinity and the fluorescence spectrum intensity.
In the present embodiment 1, in step S110, the bovine serum albumin structure is obtained from the PDB protein database.
In example 1 of the present invention, the hydrophilic amino acids at the active site were Arg198 and Arg 256.
In example 1 of the present invention, the hydrophobic amino acid is a combination of one or more of Ile, Phe, Val, or Leu.
Example 2
As shown in fig. 2, embodiment 2 of the present invention provides a method for modifying bovine serum albumin for efficiently detecting PAEs based on homologous modeling, which is used to obtain novel bovine serum albumin.
And step A, acquiring the structure of bovine serum albumin by means of a PDB protein database, and then entering step B.
In practical application, the Protein structure of Bovine Serum Albumin (BSA) is derived from Protein Data Bank (http:// www.rcsb.org/PDB), and the PDB ID is 3V 03.
And step B, introducing the protein in the step A by using Discovery Studio 4.0 software, removing water molecules from the protein, performing hydrogenation and charging treatment to determine a receptor binding cavity of the bovine serum albumin, and then entering the step C.
And step D, fusing target PAEs molecules into a formed protein binding cavity by means of a Dock-ligands (Libdock) module in the Discovery Studio 4.0 software package, carrying out semi-flexible butt joint on the target PAEs molecules and bovine serum albumin, and then entering the step D.
And D, according to the molecular docking of the target PAEs and the bovine serum albumin, obtaining amino acid residues contained around the target PAEs molecules, and then entering the step E.
And E, according to the amino acid hydrophilicity and hydrophobicity, replacing hydrophilic amino acids Arg198 and Arg256 at the active site of the bovine serum albumin with hydrophobic amino acids such as Ile, Phe, Val, Leu and the like one by one, formulating a fixed-point modification scheme of the bovine serum albumin, and then entering the step F.
And step F, submitting the modified bovine serum albumin amino acid sequence in the step E to a SWISS-MODEL server, constructing a novel bovine serum albumin structure by using a homologous modeling method, evaluating the novel bovine serum albumin structure by using a PROCHECK server for further verifying the structural rationality of the constructed MODEL, and determining that the reliability of the MODEL is met when a map shows that all amino acid residues of the protein are located in an allowable area and the percentage of the amino acid residues falling in the optimal area, the allowable area and the maximum allowable area is more than 95%.
In the step F, a novel bovine serum albumin structure is constructed by a homologous modeling method, and SWISS-MODEL (http:// www.swissmodel.expasy.org) provided by Glaxo Smith Kline center in Geneva, Switzerland is adopted.
In the step F, an online evaluation server PROCHECK (http:// services. mbi. ula. edu/SAVES /) is used for evaluating the structural rationality of the established model.
And G, carrying out molecular docking on the novel bovine serum albumin obtained in the step F and the target PAEs, evaluating the binding affinity and the fluorescence spectrum intensity of the novel bovine serum albumin and the target PAEs, and exploring the change of the binding affinity between the bovine serum albumin and the target PAEs before and after modification and the influence of the modified novel bovine serum albumin on the molecular fluorescence spectrum detection of the target PAEs.
In practical application, the implementation of the steps A to G is carried out to obtain the novel bovine serum albumin, namely the novel bovine serum albumin for obtaining the PAEs.
The bovine serum albumin modification method for efficiently detecting PAEs through homologous modeling, which is designed by the technical scheme, has the advantages of simple and convenient operation, quick calculation and easy realization, can theoretically verify the feasibility of the bovine serum albumin modification scheme, can further explore novel bovine serum albumin which is improved in binding affinity with target PAEs and enhanced in fluorescence spectrum intensity, and provides direct theoretical guidance for realizing high-sensitivity fluorescence spectrum detection of PAEs; moreover, the bovine serum albumin modification mode for efficiently detecting PAEs has short research and development period and low cost, can save a large amount of manpower, material resources and financial resources, and provides a completely new thought for the fluorescence spectrum detection of the PAEs with high sensitivity.
Comparative experimental data:
by comparing the fluorescence spectrum intensity values of the novel bovine serum albumin designed by the invention and the original bovine serum albumin combined with the target PAEs, it can be seen from Table 1 that compared with the fluorescence intensity of the target PAEs molecule combined with the original bovine serum albumin, the fluorescence spectrum intensity of the target PAEs molecule combined with the novel BSA protein is enhanced, wherein the fluorescence spectrum intensity of DMP molecules is enhanced by 1.80 times at most, the fluorescence spectrum intensity of DBP molecules is enhanced by 103.50 times at most, and the fluorescence spectrum intensity of DNOP molecules is enhanced by 61.43 times at most.
TABLE 1
In conclusion, the method provided by the embodiment of the invention is simple and convenient to operate, rapid in calculation and easy to implement, can theoretically verify the feasibility of a bovine serum albumin modification scheme, can further explore a novel bovine serum albumin which is improved in binding affinity with target PAEs and enhanced in fluorescence spectrum intensity, and provides direct theoretical guidance for realizing high-sensitivity fluorescence spectrum detection of the PAEs.
Moreover, the bovine serum albumin modification mode for efficiently detecting PAEs has short research and development period and low cost, can save a large amount of manpower, material resources and financial resources, and provides a new idea for the fluorescence spectrum detection of the PAEs with high sensitivity. Compared with the fluorescence intensity of PAEs molecules combined with original bovine serum albumin, the fluorescence intensity of DMP, DBP and DNOP molecules combined with novel bovine serum albumin is increased to some extent, and the increase range can reach 1.80 times, 103.50 times and 61.43 times, which shows that the improvement effect of novel bovine serum albumin is obvious in the detection and enhancement effect of PAEs.
The above description is only for the preferred embodiment of the present invention, but the scope of the present invention is not limited thereto, and any changes or substitutions that can be easily conceived by those skilled in the art within the technical scope of the present invention are included in the scope of the present invention. Therefore, the protection scope of the present invention shall be subject to the protection scope of the claims.
Claims (1)
1. A bovine serum albumin modification method for efficiently detecting PAEs based on homologous modeling is characterized by comprising the following flow steps:
step S110: removing water molecules in a bovine serum albumin structure, and performing hydrogenation and charging treatment to determine a receptor binding cavity of the bovine serum albumin;
step S120: fusing target PAEs molecules into a receptor binding cavity, and carrying out semi-flexible butt joint with bovine serum albumin to obtain amino acid residues contained around the target PAEs molecules;
step S130: replacing hydrophilic amino acid at the active site of bovine serum albumin with hydrophobic amino acid;
step S140: constructing the structure of the bovine serum albumin after amino acid substitution by using a homologous modeling method;
step S150: screening the bovine serum albumin structure obtained in the step S140 by using a PROCHECK server to obtain a bovine serum albumin structure meeting a certain condition, namely the bovine serum albumin for efficiently detecting PAEs; wherein, the satisfying of the certain condition includes that, when the map shows that all amino acid residues are located in the allowable region, and the percentage of amino acid residues falling within the optimum region + the allowable region + the maximum allowable region satisfies more than 95%;
performing molecular docking on the bovine serum albumin obtained in the step S150 and target PAEs, and evaluating the binding affinity and the fluorescence spectrum intensity; obtaining the bovine serum albumin structure through a PDB protein database; the hydrophilic amino acids at the active site are Arg198 and Arg 256; the hydrophobic amino acid is one or the combination of Ile, Phe, Val or Leu.
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