CN112521476B

CN112521476B - Screening method and application of molecular analogue saxitoxin specific polypeptide

Info

Publication number: CN112521476B
Application number: CN202011494201.3A
Authority: CN
Inventors: 刘冰; 朱艳杰; 王硕
Original assignee: Tianjin University of Science and Technology
Current assignee: Tianjin University of Science and Technology
Priority date: 2020-12-17
Filing date: 2020-12-17
Publication date: 2022-10-18
Anticipated expiration: 2040-12-17
Also published as: CN112521476A

Abstract

The invention provides a screening method and application of a molecular saxitoxin-mimetic specific polypeptide, which comprises the following steps: intercepting parent peptide segments through molecular docking to obtain parent polypeptides, constructing a polypeptide library specifically combined with saxitoxin through virtual amino acid mutation, primarily screening the polypeptides by using molecular dynamics, finally screening the specific polypeptides by using an electrochemical method, and constructing a sensor method. The screening method of saxitoxin specific polypeptide provided by the invention utilizes computer software to perform virtual combination and optimization of compound molecules, realizes high-throughput design, has important significance for screening out polypeptide chains specifically combined with saxitoxin, and provides a new thought and method for actually, rapidly, trace and accurately detecting saxitoxin.

Description

Screening method and application of molecular analogue saxitoxin specific polypeptide

Technical Field

The invention belongs to the field of food safety, and particularly relates to a screening method and application of molecular simulated saxitoxin specific polypeptide.

Background

Saxitoxin (STX) belongs to the guanamine neurotoxin and is the main subject of paralytic shellfish poison. STX was originally derived from certain toxic marine algae, primarily the genus dinoflagellate, and recently it has been discovered that certain bacteria and red algae also produce such toxins. STX is mainly from secondary metabolites of some harmful plankton in seawater or fresh water, and is accumulated in aquatic products such as various shellfish, crabs, some fishes and the like mainly for filter feeding through a food chain, and then is transmitted to higher predators, the toxin has no toxic effect on the animals, and when human beings or animals eat water products polluted by the toxin and drink water sources containing toxic algae, paralytic poisoning symptoms can be caused. The symptoms of poisoning vary according to the intake, but nausea, vomiting and diarrhea occur slightly, neuromuscular paralysis and arrhythmia occur in the middle, and death occurs within minutes if the symptoms are severe. At present, no specific medicine is available for timely and accurate treatment, and certain risks are caused to the health condition of people.

The STX content in 100g shellfish meat is considered by food and drug administration to be unsafe when it exceeds 80 μ g. The world health organization stipulates that the PSP limit for the edible portion of shellfish is 100g to be 80 μ g. China considers any sample with the content value of paralytic shellfish poison more than 800 mug/kg as harmful to human consumption. Therefore, it is very important to establish a rapid, sensitive and accurate detection method.

With the accumulation of bioinformatics results, research on aspects such as virtual combination, screening and interaction simulation display of each component by adopting molecular simulation is increasing. The computer simulation technology is used for simulating molecular docking between receptor and ligand, the interaction between amino acid residues in a CDR region of the protein is explained by virtual amino acid mutation, the biological characteristics of the structure after the virtual amino acid mutation are changed, the overall affinity and stability can be improved, meanwhile, the molecular dynamics can simulate a real experimental environment, and the conformation can be further optimized.

A biosensor refers to an analytical device that can convert a biological response into a measurable and processable signal, and is composed of two parts, a receptor (various bioactive substances for molecular recognition) and a signal converter (mainly including both optical and electrochemical converters). The electrochemical detection technology is widely applied to biosensors with instant detection and no mark, and has the characteristics of high response speed, low maintenance cost, portability and the like.

The nanogold (AuNPs) is one of the most commonly used nanomaterials, has uniform particle size, good dispersibility and stability, large specific surface area, unique optical effect, good conductivity and biocompatibility. The reduced graphene oxide (rGO) has high specific surface area and can provide a good carrier for subsequent modification. Compared with a single nano material, the nano composite material has the advantages of enhancing the conductivity, improving the sensitivity, increasing the loading capacity and the like, overcomes the disadvantages of easy agglomeration, single function, unobvious synergism and the like of the single material, can fully exert the respective performances, improves the dispersibility and amplifies the response signal by synergistic interaction.

At present, rapid detection methods such as an enzyme linked immunosorbent assay kit method and an immunochromatography technology are adopted. In the immunosensor technology, one of the key steps is the preparation of highly specific antibodies. However, the preparation steps of antibodies are complicated, and there is a certain failure rate in animal immunization, and in recent years, the inclusion of antibody-specific recognition elements (aptamers, small antibodies, molecularly imprinted polymers, etc.) has been a research focus. The polypeptide is a substance between amino acid and protein, has the advantages of small molecular weight, high activity, strong specificity, no immunogenicity, easy synthesis and the like, and simultaneously has structural diversity, specificity and binding affinity to a target analyte, so the polypeptide can be used as a specific recognition element to be applied to the establishment of an actual detection method. However, the electrochemical polypeptide sensor for STX detection, which is designed, optimized and screened by computer molecular simulation technology, is rarely reported.

Disclosure of Invention

In view of this, the present invention provides a screening method and application of a molecular saxitoxin-mimetic specific polypeptide, aiming at overcoming the defects in the prior art.

In order to achieve the purpose, the technical scheme of the invention is realized as follows:

a method for screening molecular simulated saxitoxin specific polypeptide comprises the following steps: intercepting parent polypeptide through molecular docking, constructing a polypeptide library specifically combined with saxitoxin through virtual amino acid mutation, primarily screening the polypeptide by using molecular dynamics, and finally screening the specific polypeptide by using an electrochemical method.

Further, the virtual amino acid mutation step specifically comprises:

(1) Firstly, determining key amino acids by adopting stability-based virtual amino acid site-directed mutagenesis, then performing saturation mutagenesis on the key amino acids to determine the optimal mutation type, then performing random permutation and combination to obtain a result sequence, respectively inserting the head ends of the result sequence into cysteine, respectively inserting the tail ends of the result sequence into cysteine, respectively mutating the head ends of the parent polypeptides into cysteine, respectively mutating the tail ends of the parent polypeptides into cysteine, and simultaneously and respectively mutating the head ends and the tail ends of the parent polypeptides into cysteine, wherein the result sequence, the head end cysteine insertion result sequence, the tail end cysteine insertion result sequence, the head end mutating parent polypeptides, the tail end mutating parent polypeptides and the head end and tail end simultaneously mutating parent polypeptides form the polypeptide library;

(2) Then selecting polypeptide chains with lowest and highest energy scores from the result sequences, selecting polypeptide chains with lowest and highest energy scores from the result sequences with cysteine inserted at the head ends, selecting polypeptide chains with lowest and highest energy scores from the result sequences with cysteine inserted at the tail ends, combining the selected polypeptide chains with parent polypeptides, parent polypeptides with mutated head ends and parent polypeptides with mutated tail ends to form polypeptide sequences, carrying out site-directed mutagenesis on each polypeptide chain in the polypeptide sequences to obtain cysteine, and then carrying out primary screening on the obtained mutated sequences by using molecular dynamics.

Further, the peptide fragment in the step of intercepting is bound by the ligand in a range of

The conditions of the primary screening are as follows: the temperature is 298.15K, and the amino acid sequence of the polypeptide screened in the preliminary screening step is shown as SEQ ID NO.2-SEQ ID NO. 7;

the final screening step specifically comprises: modifying the polypeptide as an identification element on the surface of a gold electrode, and screening out specific polypeptide with strong specific binding capacity with saxitoxin by comparing the resistance value change before and after dropping; the resistance values before and after the dripping are measured by an electrochemical alternating-current impedance method.

A saxitoxin-specific parent polypeptide, the amino acid sequence of which is shown in SEQ ID NO.1, is obtained by molecular docking and interception by using a molecular simulation technology.

A saxitoxin specific polypeptide screened by the method, the amino acid sequence of the polypeptide is shown in SEQ ID NO. 5; the polypeptide is obtained by constructing and screening electrochemical methods through molecular simulation software.

A method for screening specific polypeptide combined with electrochemical sensor, modifying polypeptide on the surface of gold electrode as recognition element, screening out specific polypeptide with strong specific binding ability with target object by comparing resistance value change before and after dripping; the resistance values before and after the dripping are measured by an electrochemical alternating-current impedance method.

A method for detecting saxitoxin-specific polypeptide comprises the following steps:

(1) The glassy carbon electrode surface modification composite material comprises the following steps: placing the pretreated electrode in a mixed solution of a nano material containing chloroauric acid for electropolymerization, and increasing the surface load of the electrode on the basis of increasing the surface area;

(2) Self-assembly of polypeptides: dropwise coating a certain concentration of polypeptide solution on the surface of the electrode modified in the step (1), and covalently bonding the gold nanoparticles and the polypeptide through Au-S bonds;

(3) Blocking of mercaptohexanol: dripping MCH blocking liquid on the basis of the step (2) to block the non-self-assembled binding sites of the residual polypeptide solution;

(4) Detecting a peak current value: and (3) combining saxitoxin with specific polypeptide, determining peak current value, and analyzing the relation between the current change condition and the concentration of saxitoxin.

Further, the surface modification composite material of the glassy carbon electrode in the step (1) comprises the following specific steps: adding HAuCl ₄ Adding the mixture into a mixed solution of GO and a nano material, inserting an electrode into the mixed solution, performing Cyclic Voltammetry (CV) scanning in a voltage range of-1.5 to +0.5V, setting the number of scanning circles to be 5 to 25 circles to obtain rGO-AuNPs/GCE, and performing differential pulse voltammetry scanning in a range of +0.6 to-0.2V; the specific steps of the self-assembly of the polypeptide in the step (2) are as follows: dripping the polypeptide solution with the concentration of 0.1-5 mug/mL on the surface of a glassy carbon electrode, incubating for 30-150 min in a dark place to obtain Peptide/rGO-AuNPs/GCE, and scanning by a differential pulse voltammetry within the range of + 0.6-minus 0.2V; the specific steps of the step (3) of blocking mercaptohexanol are as follows: dripping MCH solution on the surface of an electrode, standing and incubating for 10-70 min in a dark place to obtain MCH/Peptide/rGO-AuNPs/GCE, and scanning by differential pulse voltammetry within the range of + 0.6-minus 0.2V; the specific steps of detecting the peak current value in the step (4) are as follows: dripping STX solution on the prepared electrochemical polypeptide sensor, and keeping out of the sunStanding and incubating for 30-150 min to obtain STX/MCH/Peptide/rGO-AuNPs/GCE, and then scanning by differential pulse voltammetry within the range of + 0.6-minus 0.2V; the nano material is a carbon nano material; the carbon nano material is at least one of carbon black, mesoporous carbon or carbon nano tubes.

The application of the screening method of the molecular simulation saxitoxin specific polypeptide, the application of the method in the food field; the method is applied to the preparation of detection and identification elements of pesticides, veterinary drugs or toxins; the method is applied to the preparation of a kit or a test strip.

The application of the method for detecting the saxitoxin-specific polypeptide, and the application of the method in the food field; the method is applied to the preparation of detection and identification elements of pesticides, veterinary drugs or toxins; the method is applied to the preparation of a kit or a test strip.

Compared with the prior art, the invention has the following advantages:

the screening method of saxitoxin specific polypeptide provided by the invention utilizes computer software to perform virtual combination and optimization of compound molecules, realizes high-throughput design, has important significance for screening out polypeptide chains specifically combined with saxitoxin, and provides a new thought and method for actually, rapidly, trace and accurately detecting saxitoxin.

The molecular simulation technology adopted by the screening method of saxitoxin specific polypeptide of the invention can greatly shorten the experimental time, save the experimental cost and avoid the interference of human error, environment and other uncontrollable factors.

Drawings

FIG. 1 is a diagram illustrating the steps of a method for screening polypeptides specific to a molecular mimetic saxitoxin according to an embodiment of the present invention;

FIG. 2 is an impedance profile before and after modification according to an embodiment of the present invention;

FIG. 3 is a standard graph illustrating an embodiment of the present invention.

Detailed Description

Unless defined otherwise, technical terms used in the following examples have the same meanings as commonly understood by one of ordinary skill in the art to which the present invention belongs. The test reagents used in the following examples, unless otherwise specified, are all conventional biochemical reagents; the experimental methods are conventional methods unless otherwise specified.

The present invention will be described in detail with reference to examples.

Example 1 interception of parent peptide fragments by molecular docking to obtain parent polypeptides

(1) Molecular docking

Using Discovery Studio2016 molecular simulation software to download and preprocess a ligand-receiving structure, setting an input receptor to be 6O0F, setting an input ligand to be STX: all, setting a conformation cluster radius to be 0.5, setting other parameters to be default, and carrying out CDOCKER semi-flexible molecular docking by clicking operation.

(2) Analysis of docking results

After the operation is successful, opening a molecular docking result report, checking a 2D graphic representation of the interaction of the ligand, analyzing the docking result, determining the amino acid peptide segment which takes the main effect, and determining the optimal peptide segment length according to the principle of the specific binding of similar antigen and antibody. And screening out a final parent chain peptide segment according to a molecular docking result, and naming the finally determined parent polypeptide segment as S0.

Example 2 construction of a library of polypeptides that bind specifically to saxitoxin by virtual amino acid mutagenesis

Selection of ligand binding in S0 chain

The amino acid residues in the range are ILE782, PHE784, ASP785, GLN787, ASP794, TYR795, respectively, as the main amino acids. And (2) carrying out stability-based virtual amino acid site-directed mutation on main amino acids to determine key amino acids which are respectively positioned at 782, 785, 787, 794 and 795, and carrying out saturation mutation on the key amino acids to determine the optimal mutation types of the key amino acids so as to obtain TRP782, GLN785, TRP787, ASN794 and PHE795. And verifying the consistency of the results with the stability mutation by affinity-based virtual amino acid mutation, and finally, mutational targetingThe results were randomly arranged and combined. Because later electrochemical verification is involved, polypeptide chains are modified on the surface of the gold electrode, and therefore, the amino acid is artificially added or mutated into cysteine at the head and tail ends under the condition of random permutation and combination.

The specific method comprises the following steps: and randomly arranging and combining the optimal mutation types to obtain a result sequence, respectively inserting the head ends of the result sequence into cysteine, respectively inserting the tail ends of the result sequence into the cysteine, respectively mutating the head ends of the parent polypeptides into the cysteine, respectively mutating the tail ends of the parent polypeptides into the cysteine, respectively mutating the head ends of the parent polypeptides into the cysteine, and simultaneously mutating the head ends and the tail ends of the parent polypeptides into the cysteine, wherein the result sequence, the head end cysteine-inserted result sequence, the tail end-inserted cysteine result sequence, the head end-mutated parent polypeptide, the tail end-mutated parent polypeptide and the head end-and tail end-simultaneously mutated parent polypeptide form the polypeptide library.

Then selecting polypeptide chains with lowest and highest energy scores from the obtained result sequences, selecting polypeptide chains with lowest and highest energy scores from the result sequences with cysteine inserted at the head end, selecting polypeptide chains with lowest and highest energy scores (total 6) from the result sequences with cysteine inserted at the tail end, combining the selected polypeptide chains, the parent polypeptides with mutated head end and the parent polypeptides with mutated tail end to form polypeptide sequences (total 9), carrying out site-directed mutagenesis on each polypeptide chain in the polypeptide sequences, and then carrying out primary screening on the obtained mutated sequences by using molecular dynamics.

Example 3 preliminary screening of polypeptides using molecular dynamics

And (3) performing molecular dynamics simulation on the screened 9 polypeptide chains under the normal-temperature setting condition, performing further structure optimization on the specific polypeptide chains, displaying the actual state to the maximum extent, and setting a temperature parameter (298.15K). After the molecular dynamics are operated, the last frame of image is selected as a receptor structure and then is subjected to molecular docking with a ligand, and six polypeptide chains S1-S6 which are finally used for actual verification are selected according to the component values. Specific amino acid sequences and interaction energies are shown in table 1.

TABLE 1 peptide chain sequence and molecular docking energy score

Example 4 Final screening of specific polypeptides by electrochemical methods

The electrode is modified layer by layer, and under the condition that the redox probe exists, the electron transfer capability is inhibited, the peak current is reduced, and the resistance is gradually increased. The electrochemical alternating-current impedance method is adopted, the frequency parameter is set to be 100mHz-100kHz, and the difference of the combination capacity of the six polypeptide chains and the STX is compared from the angle of resistance value change. The method comprises the following specific steps:

(1) The method for self-assembling the polypeptide on the surface of the gold electrode comprises the following steps: accurately apply 10. Mu.L of 1 × 10 ^-6 And (3) dropwise coating the g/mL polypeptide solution on the surface of the gold electrode, and incubating for 2h in a dark place to perform electrochemical alternating current impedance detection.

(2) The method for blocking mercaptohexanol comprises the following steps: accurately dripping 10 mu L of MCH solution with the concentration of 1mmol/L on the surface of the electrode, standing in the dark for incubation for 1h, and then carrying out electrochemical alternating current impedance detection.

(3) The specific method for detecting the STX comprises the following steps: and respectively and accurately dripping 10 mu L of STX solution with the same concentration on the six prepared electrochemical biosensors taking the polypeptide as the identification element, standing and incubating for 2 hours in a dark place, and then carrying out electrochemical alternating current impedance detection.

(4) The electrochemical sensing technology is used for evaluating and screening specific polypeptides, the sequence of specific binding capacity of the polypeptide chains and STX is S4> S6> S5> S3> S2> S1, wherein the impedance spectrum before and after S4 modification is shown in figure 2, and therefore S4 can be selected as a specific recognition element for further research.

Example 5 detection method establishment of electrochemical sensor based on S4

Differential pulse voltammetry scanning is carried out in a potential range of +0.6 to-0.2V by adopting a differential pulse method. The method comprises the following specific steps:

(1) The surface modification composite material of the glassy carbon electrode comprises the following specific steps:

adding 25mmol/L HAuCl ₄ The solution was added to 1mg/mL GO solution and HAuCl was added ₄ The final concentration was 1mmol/L. Ultrasonically mixing for 30min, blowing nitrogen for 3min to remove oxygen, inserting an electrode into the mixed solution, and performing Cyclic Voltammetry (CV) scanning at a scanning rate of 50mV/s within a voltage range of-1.5 to +0.5V, wherein the number of scanning circles is set to be 10 circles, so as to obtain the rGO-AuNPs/GCE.

(2) The self-assembly of the polypeptide comprises the following specific steps:

and (3) accurately dripping 10 mu L of 0.5 mu g/mL polypeptide solution on the surface of a glassy carbon electrode, and incubating for 90min in a dark place to obtain Peptide/rGO-AuNPs/GCE.

(3) The method for blocking mercaptohexanol comprises the following steps:

and (3) accurately dripping 10 mu L of 1mmol/L MCH solution on the surface of the electrode, and standing and incubating for 50min in a dark place to obtain MCH/Peptide/rGO-AuNPs/GCE.

(4) The method for detecting the peak current value comprises the following specific steps:

accurately dripping 10 mu L of STX solution on the prepared electrochemical polypeptide sensor, standing in a dark place and incubating for 90min to obtain STX/MCH/Peptide/rGO-AuNPs/GCE.

(5) The method comprises the following steps of:

a) And (3) dripping STX standard solutions with different concentrations on the surface of the prepared electrode, exploring electric signal response under different STX concentration gradient conditions by adopting a differential pulse voltammetry method, and finally analyzing the relation between the electric signal response and the STX concentration according to the current change condition. The response value of the differential pulse is in a linear relation with the concentration of the STX within the range of 10-1000 ng/L. The standard curve is established as shown in fig. 3.

b) Detection of STX in real samples: detecting the STX in three different practical samples of seawater, artificial seawater and oyster powder by using the prepared sensor; the method comprises the following specific steps:

the electrochemical polypeptide sensor is utilized to carry out the standard adding recovery experiment on actual samples (seawater, artificial seawater and oyster powder). The differential pulse method in a Parstart 2273 electrochemical workstation system of America Ametek company is selected for detection, wherein the voltage range is set to be +0.6 to-0.2V. The recovery rate of the constructed sensor to the STX in the actual sample is in the range of 87.3-116.2%, which shows that the detection method established by the invention has certain practical feasibility.

The above description is only for the purpose of illustrating the preferred embodiments of the present invention and should not be taken as limiting the scope of the present invention, which is intended to cover any modifications, equivalents, improvements, etc. within the spirit and scope of the present invention.

Sequence listing

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Claims

1. A saxitoxin-specific polypeptide, characterized by: the amino acid sequence of the polypeptide is shown as SEQ ID NO. 5; the polypeptide is obtained by constructing and screening electrochemical methods through molecular simulation software.

2. Use of a saxitoxin-specific polypeptide according to claim 1, characterized in that: the polypeptide is applied to the preparation of an electrochemical polypeptide sensor for detecting saxitoxin.