A molecular dynamics simulation method based on fibronectin adsorption

Abstract

The present invention discloses a molecular dynamics simulation method based on fibronectin adsorption. The method expands the piezoelectric polymer unit model into a piezoelectric polymer monolayer film without gaps and juxtapositions; constructs a piezoelectric inorganic filler-doped piezoelectric polymer composite film model with a piezoelectric polymer monolayer film and a piezoelectric inorganic filler; the constructed piezoelectric polymer composite film model and the fibronectin model are respectively energy minimized, a computational model of a composite film-protein binary system is constructed, and molecular dynamics simulation is performed to obtain the interaction energy between the protein and the composite film, the center of mass distance of RGD-PHSRN, and then the biocompatibility of the piezoelectric inorganic filler and the piezoelectric polymer is evaluated. The method of the present invention is low in cost and high in efficiency. After analyzing the simulation results, the biocompatibility of the composite film can be predicted, and the prediction results can be used to guide the preparation of inorganic-organic composite piezoelectric flexible biocompatible implant materials.

Description

Technical Field

[0001] The present invention relates to the technical field of molecular simulation, in particular to a molecular dynamics simulation method based on fibronectin adsorption, and specifically to a molecular dynamics simulation method based on fibronectin adsorption on the surface of a piezoelectric high molecular polymer composite film doped with a piezoelectric inorganic filler. Background Art

[0002] The adsorption of proteins on the surface of materials is a common biological phenomenon in nature. It is an important part of biointerface science and also one of the important research contents of biomaterials science. When biomedical materials enter the biological environment, biological proteins and some inorganic molecules will be rapidly adsorbed on their surface and reach saturation in a short time, followed by cell recognition, adhesion, proliferation, differentiation and migration. Fibronectin, as an important functional protein in the extracellular matrix, plays a role in recognizing extracellular integrins during cell adhesion. Therefore, its adsorption on the surface of implant materials has a decisive influence on the biocompatibility of the materials. Polyvinylidene fluoride-trifluoroethylene / barium titanate composite membrane, as a flexible implant material with outstanding performance, has attracted widespread research interest in recent years. Related studies have shown that the morphology and distribution of barium titanate fillers in composite materials will affect the adsorption quantity, intensity, orientation, conformation, etc. of fibronectin. However, experimental studies cannot obtain information on the molecular scale during protein adsorption and are expensive, which makes it urgent to develop a new method for studying the adsorption mechanism of fibronectin and its simulation and regulation of adsorption behavior on the surface of polyvinylidene fluoride-trifluoroethylene / barium titanate composite membrane.

[0003] With the rapid development and widespread application of computer technology, the research and application of computational chemistry has made great strides since the 1990s. As a link between theoretical analysis and scientific experiments, computational chemistry plays a key role in explaining experimental phenomena and predicting theoretical results. The combination of theoretical, computational and experimental work has effectively improved research efficiency. As one of the branches of computational chemistry, molecular simulation is widely used in the research of proteins, nucleic acids, phospholipids and polymer material systems due to its moderate computational cost and computational scale. It can be predicted that with the improvement of theoretical models and algorithms, as well as the improvement of computing power, molecular simulation will play an increasingly important role in scientific research and industrial development.

[0004] Chinese invention patent 2019102426942 discloses a simulation regulation method for the adsorption behavior of proteins on the surface of titanium dioxide. The method constructs a material surface model; establishes a protein-surface-solution system model, and simulates the adsorption process of proteins on the surface through molecular dynamics software; calculates the root mean square deviation, gyration radius, secondary structure content, and adsorption energy changes over time to describe the adsorption behavior of proteins; changes the pore size of the surface to achieve the regulation of the adsorption behavior of proteins on the surface, and guides the preparation of medical titanium dioxide implant materials. However, this method only focuses on the effect of titanium dioxide surfaces with different topological structures on protein adsorption, and is not suitable for molecular dynamics simulation to study the protein adsorption behavior on the surface of piezoelectric high-molecular polymer composite membrane materials doped with piezoelectric inorganic fillers. In addition, this method does not consider the conformation of the protein after adsorption. This key factor has an important influence on whether the protein can exert its biological activity, so it cannot be used to judge the biological activity of the organism. In reality, for the adsorption results of proteins at the interface, both high firmness and better conformation are expected, and materials that meet both of these requirements can have the best biocompatibility. Summary of the invention

[0005] The purpose of the present invention is to provide a molecular dynamics simulation method based on fibronectin adsorption that is suitable for predicting the biocompatibility of piezoelectric inorganic filler-piezoelectric polymer composite film materials, which significantly saves time and cost. The prediction results of the simulation method can be used to guide the preparation of inorganic-organic composite piezoelectric flexible biocompatible implant materials.

[0006] The purpose of the present invention is achieved through the following technical solutions:

[0007] A molecular dynamics simulation method based on fibronectin adsorption comprises the following steps:

[0008] 1) Using Materials Studio to construct a piezoelectric polymer molecular chain, assign lattice parameters to the molecular chain, and obtain a piezoelectric polymer unit model; and expand the piezoelectric polymer unit model into a piezoelectric polymer monolayer film without gaps;

[0009] Import the crystal structure data of the piezoelectric inorganic filler into Materials Studio software to construct a unit model of the piezoelectric inorganic filler; expand the unit model of the piezoelectric inorganic filler into a piezoelectric inorganic filler in the shape of particles or fibers without gaps;

[0010] A piezoelectric polymer monolayer film is placed in the first layer, a piezoelectric inorganic filler is evenly spread in the second layer, and m layers of piezoelectric polymer monolayer films are placed under the second layer of piezoelectric inorganic filler to obtain a piezoelectric polymer composite film model doped with piezoelectric inorganic fillers with a multi-layer structure; wherein 1≤m≤20;

[0011] 2) The constructed piezoelectric inorganic filler-doped piezoelectric polymer composite film model and fibronectin model are respectively energy minimized, and the energy-minimized fibronectin is centered at 1.25 to 2.0 nm above the upper surface of the energy-minimized piezoelectric polymer composite film, and the two are combined to obtain a computational model of the composite membrane-protein binary system; the fibronectin model is downloaded from the RCSB structure database, has a complete structural domain and contains key active residues RGD and PHSRN sequences;

[0012] 3) Molecular dynamics simulation of the computational model of the composite membrane-protein binary system was performed with the help of Gromacs software, and the interaction energy between the protein and the composite membrane and the center-of-mass distance of RGD-PHSRN were obtained; if the absolute value of the interaction energy between fibronectin and the composite membrane is greater than or equal to 100 kJ / mol, it is defined as high firmness of protein adsorption; if the center-of-mass distance of RGD-PHSRN is It is defined as a dominant conformation; it simultaneously satisfies both high firmness of protein adsorption and a dominant conformation, and is determined to have excellent biocompatibility between the piezoelectric inorganic filler and the piezoelectric high molecular polymer.

[0013] To further achieve the purpose of the present invention, preferably, the piezoelectric inorganic filler is barium titanate or potassium sodium niobate, and the crystal structure data of the piezoelectric inorganic filler is downloaded from the Inorganic Crystal Structure Database (ICSD).

[0014] Preferably, the piezoelectric polymer is one of polyvinylidene fluoride, polytrifluoroethylene, hexafluoropropylene, or a copolymer of two or more thereof.

[0015] Preferably, the mass fraction of the piezoelectric inorganic filler in the piezoelectric high-molecular polymer composite film model doped with the piezoelectric inorganic filler is 0.5% to 30%.

[0016] Preferably, the piezoelectric inorganic filler is in the form of particles or fibers with an aspect ratio of n, where n is greater than or equal to 2.

[0017] Preferably, the energy minimization of the piezoelectric polymer composite film model doped with piezoelectric inorganic fillers is first performed at a step size of 1 fs until the energy converges to a maximum interatomic force of ≤100 kJ / (mol·nm). In this process, the piezoelectric polymer chains can move freely and the piezoelectric inorganic fillers are frozen; in all subsequent processes, the piezoelectric polymer chains are fixed.

[0018] Preferably, the interaction energy between the protein and the composite membrane is obtained by the sum of the van der Waals interaction energy and the electrostatic interaction energy.

[0019] Preferably, the van der Waals interaction energy and the electrostatic interaction energy are obtained by the following steps:

[0020] a. Using the steepest descent method to minimize energy to achieve energy convergence of the entire system, and obtain an energy converged structure; the judgment standard of the energy convergence is that the maximum force between atoms is ≤100 kJ / (mol·nm);

[0021] b. Perform NVT ensemble relaxation of t1 on the structure after energy convergence, and use V-rescale heat bath to control the temperature at T to obtain the relaxed structure; t1 is 0.5ns~1000ns, and T is 273.15K~323.15K;

[0022] c The structure after NVT relaxation was simulated by molecular dynamics simulation of t2. The simulation process used CHARMM27 force field, particle-mesh Ewald (PME) algorithm to calculate electrostatic interaction energy, and cut-off method to calculate van der Waals interaction energy; the t2 value was 0.5ns~1000ns.

[0023] Preferably, the centroid distance of RGD-PHSRN is calculated by the distance module of Gromacs software. First, the two key residue sequences RGD and PHSRN are set as two groups with different numbers, and finally the distance between the centroids of the two groups is calculated by the distance module.

[0024] The composite film in the present invention refers to a piezoelectric high molecular polymer composite film doped with piezoelectric inorganic fillers.

[0025] In the present invention, the crystal form of the piezoelectric inorganic filler is any one of its naturally existing crystal forms; the piezoelectric polymer is one of polyvinylidene fluoride, polytrifluoroethylene, tetrafluoroethylene, or a copolymer formed by two or more thereof. Its crystal form is any one of its naturally existing crystal forms; if a certain crystal form is selected, the lattice parameters of the corresponding crystal form are selected when establishing the unit model in step (1). The inorganic piezoelectric filler in the piezoelectric polymer composite film model doped with piezoelectric inorganic filler has a single morphology, that is, it contains only particles or only fibers.

[0026] In the present invention, the fibronectin model is downloaded from the RCSB structural database, which is a fragment of human or animal origin or derived from homologous modeling, has a complete structural domain and contains key active residues RGD and PHSRN sequences.

[0027] In the present invention, the criterion for judging the firmness is whether the absolute value of the interaction energy between fibronectin and the composite membrane is greater than or equal to 100 kJ / mol. If the interaction energy is negative and its absolute value is greater than 100 kJ / mol, it indicates that the firmness of protein adsorption is high, otherwise, it indicates that the firmness is low. The calculated center of mass distance of protein RGD-PHSRN is 35 ± is the dominant conformation, otherwise, it is not the dominant conformation;

[0028] The present invention comprehensively analyzes the adsorption results of proteins on the composite membrane surface of piezoelectric inorganic fillers of different forms from the two aspects of protein adsorption firmness and conformation, specifically including the following situations:

[0029] If the adsorption results satisfy both high firmness and a dominant conformation, the composite membrane has excellent biocompatibility;

[0030] If the adsorption result satisfies high firmness but does not satisfy the dominant conformation, the composite membrane does not have excellent biocompatibility;

[0031] If the adsorption result does not satisfy high firmness but satisfies the dominant conformation, the composite membrane does not have excellent biocompatibility;

[0032] If the adsorption result does not satisfy the high firmness and the dominant conformation, the composite membrane does not have excellent biocompatibility;

[0033] The invention summarizes the rule that protein adsorption behavior is affected by the mass fraction and morphology of piezoelectric inorganic fillers, and screens out a composite membrane with good biocompatibility.

[0034] Compared with the prior art, the present invention has the following advantages and beneficial effects:

[0035] (1) The present invention provides a method for constructing a piezoelectric high-molecular polymer composite film model doped with piezoelectric high-inorganic fillers of different fillers. The model has a high degree of restoration to the actual situation and can obtain detailed atomic-scale action details.

[0036] (2) The present invention uses the advanced open source molecular dynamics software Gromacs to accurately obtain the dynamic process of fibronectin adsorption on the surface of piezoelectric polymer / piezoelectric inorganic filler composite films with different piezoelectric inorganic fillers, which is highly consistent with the experimental results.

[0037] (3) The present invention establishes a time-saving and cost-saving method based on computer simulation to simulate the adsorption behavior of fibronectin on the surface of piezoelectric polymer / piezoelectric inorganic filler composite membranes, and provides a method for predicting the biocompatibility of piezoelectric polymer composite membranes doped with piezoelectric inorganic fillers based on multi-dimensional data.

[0038] (4) The present invention has low computational cost and high efficiency, and provides a powerful tool for developing high-performance organic-inorganic composite piezoelectric flexible implant materials.

[0039] (5) The analytical simulation results of the molecular dynamics simulation method based on fibronectin adsorption of the present invention can predict the biocompatibility of the composite membrane, and the prediction results can be used as a guide to significantly save testing time and cost. BRIEF DESCRIPTION OF THE DRAWINGS

[0040] Figure 1 This is a three-dimensional schematic diagram of the barium titanate unit model in Example 1.

[0041] Figure 2 It is a three-dimensional schematic diagram of the poly(ethylene trifluoroethylene) fluoride unit model in Example 1.

[0042] Figure 3 This is a three-dimensional schematic diagram of the gapless juxtaposition process in Example 1.

[0043] Figure 4 This is a three-dimensional schematic diagram of the composite film model of the particle-shaped barium titanate filler in Example 1.

[0044] Figure 5 This is a bar graph of the interaction energy on the surface of the composite membrane of fibronectin and fiber filler in Example 1.

[0045] Figure 6 This is a three-dimensional schematic diagram of the molecular dynamics simulation results of fibronectin adsorption in the composite membrane system of barium titanate filler in particle form in Example 1. DETAILED DESCRIPTION

[0046] In order to better understand the present invention, the present invention is further described below with reference to the accompanying drawings and examples, but the embodiments of the present invention are not limited thereto.

[0047] In the embodiments, MD simulation is the abbreviation of Molecular Dynamics Simulation.

[0048] Example 1

[0049] In this embodiment, a polyvinylidene fluoride-trifluoroethylene composite film doped with barium titanate particle filler is constructed, wherein the crystal phases of barium titanate and polyvinylidene fluoride-trifluoroethylene are tetragonal phase and β phase, respectively, and the mass fractions are 30% and 70%, respectively. The fibronectin in the MD simulation adopts the fibronectin model downloaded from the RCSB structure database (PDB ID: 1FNF).

[0050] A molecular dynamics simulation method based on fibronectin adsorption comprises the following steps:

[0051] (1) Using Materials Studio software, a poly(difluoroethylene trifluoro) molecular chain was constructed, and the molecular chain was given a β-phase lattice parameter to obtain a poly(difluoroethylene trifluoro) molecular chain unit model; the poly(difluoroethylene trifluoro) molecular chain unit model was seamlessly expanded into a poly(difluoroethylene trifluoro) molecular chain monolayer film; the structure data of tetragonal barium titanate crystal (BTO) was downloaded from the Inorganic Crystal Structure Database (ICSB) and then imported into Materials Studio software to construct a barium titanate unit model. Figure 1 The constructed barium titanate unit model includes a complete barium titanate BaTiO3 structure and its lattice parameters; Figure 2 It is a unit model of poly(difluoroethylene trifluoroethylene). Similarly, this unit model contains a complete poly(difluoroethylene trifluoroethylene) molecular structure and its lattice parameters.

[0052] Then the barium titanate unit model is expanded into particle packing without gaps and the polyvinylidene fluoride-trifluoroethylene unit model is expanded into a single layer film. Figure 3 This is a schematic diagram of the expansion of gapless juxtaposition; gapless means that there is no gap between adjacent unit models, and juxtaposition means that all unit models are arranged in parallel and have the same orientation, where the left and right sides of the figure are the models before and after expansion respectively. Place a poly(difluoroethylene trifluoroethylene) molecular chain monolayer membrane on the first layer, evenly spread barium titanate fillers on the second layer, and place 3 layers of poly(difluoroethylene trifluoroethylene) monolayer membranes under the second layer of barium titanate fillers to obtain a poly(difluoroethylene trifluoroethylene) composite membrane model doped with barium titanate particle fillers. Figure 4 As shown, the composite film is a 5-layer "sandwich" structure, wherein the second layer is a uniformly distributed barium titanate particle filler with a mass fraction of 30%;

[0053] (2) The energy of the constructed barium titanate particle filler-doped poly(difluoroethylene-trifluoroethylene) composite membrane model was minimized separately. The specific steps were as follows: first, the energy was minimized at a step size of 1 fs until the energy converged to 100 kJ / (mol·nm). During this process, the poly(difluoroethylene-trifluoroethylene) molecular chains could move freely, while the barium titanate filler was frozen; then, the entire composite membrane was frozen and applied to the next molecular dynamics simulation process; then, the fibronectin model downloaded from the RCSB structure database (PDB ID: 1FNF) was minimized separately until the energy converged to 100 kJ / (mol·nm). Then, the energy-minimized fibronectin was centered 1.25 nm above the upper surface of the energy-minimized composite membrane, and the two were merged to obtain the computational model of the composite membrane-protein binary system;

[0054] (3) MD simulation was performed on the computational model of the composite membrane-protein binary system. The specific steps are as follows: First, the steepest descent method was used to minimize the energy to achieve the energy convergence of the entire system to 100 kJ / (mol·nm); the structure after energy convergence was used for the next 1 ns NVT ensemble relaxation, and the temperature was controlled at 310.15 K using a V-rescale heat bath; after NVT, a 20 ns MD simulation was performed. The simulation process used the CHARMM27 force field, the PME algorithm was used to calculate the electrostatic interaction energy, and the cut-off method was used to calculate the van der Waals interaction energy. The cutoff values ​​of the electrostatic interaction and van der Waals interaction were set to 1.0 nm. After the simulation, the results of the MD simulation were extracted with the help of the Gromacs built-in module, including the interaction energy between the protein and the complex (obtained by superimposing the van der Waals interaction energy and the electrostatic interaction energy), the calculation of the distance between the center of mass of key residues, the change of the minimum distance between the protein and the composite membrane over time, the root mean square deviation of fibronectin, the rotation radius of fibronectin, etc.

[0055] (4) Based on the results of MD simulation in (3), the electrostatic interaction energy and the van der Waals interaction energy are added to obtain the interaction energy between the protein and the composite film of poly(ethylene difluoride-trifluoroethylene) / barium titanate particle filler. Specifically, the electrostatic interaction energy is calculated by the PME algorithm, and the van der Waals interaction energy is obtained by the cut-off method. Figure 5 As shown in the figure, the electrostatic interaction energy and van der Waals interaction energy between the barium titanate particle filler composite film and the protein are -83.51 and -24.41 KJ / mol, respectively. The sum of the two gives an interaction energy of -107.92 KJ / mol between the protein and the composite film. This result shows that the fibronectin adsorbed on the surface of the composite film doped with particle barium titanate fiber filler is relatively firm. The distance module of the distance software of Gromacs was used to calculate the center of mass distance of the key synergistic activity sequence of the protein. The specific steps are to first set the two key residue sequences RGD and PHSRN as two groups with different numbers, and then use the distance module to calculate the distance between the centers of mass of the two groups, that is, to obtain the center of mass distance of RGD-PHSRN, as shown in the figure. Figure 6 As shown in Figure 2, the center-of-mass distance of the key residues RGD-PHSRN in the barium titanate particle filler composite film-protein system was calculated to be It can be seen that the result is The difference is quite large and it is not the dominant conformation.

[0056] (5) The adsorption results of proteins on the composite membrane surface of the two forms of barium titanate fillers were comprehensively analyzed from the two aspects of protein adsorption firmness and conformation. Because the adsorption results of the composite membrane of the barium titanate filler in the particle form have high firmness, but do not meet the dominant conformation, the composite membrane does not have excellent biocompatibility. In addition, barium titanate fillers with different morphologies are selected to repeat the above steps until a composite membrane of barium titanate fillers with excellent biocompatibility is obtained.

[0057] Example 2

[0058] In this embodiment, a polyvinylidene fluoride-trifluoroethylene composite membrane doped with barium titanate fiber filler with an aspect ratio of 8 was constructed, wherein the crystal forms of barium titanate and polyvinylidene fluoride-trifluoroethylene were tetragonal and β crystal forms, respectively, and the mass fractions were 30% and 70%, respectively. The fibronectin model downloaded from the RCSB structure database (PDB ID: 1TTF) was used for the MD simulation.

[0059] A molecular dynamics simulation method based on fibronectin adsorption comprises the following steps:

[0060] (1) Using Materials Studio to construct a poly(difluoroethylene-trifluoroethylene) molecular chain, assigning the molecular chain a β-phase lattice parameter, and obtaining a poly(difluoroethylene-trifluoroethylene) molecular chain unit model, and then expanding the poly(difluoroethylene-trifluoroethylene) molecular chain unit model into a poly(difluoroethylene-trifluoroethylene) molecular chain monolayer film without gaps; downloading the tetragonal barium titanate crystal (BTO) structure data from the Inorganic Crystal Structure Database (ICSB), and then importing it into Materials Studio software to construct a barium titanate unit model, and then expanding the barium titanate unit model into a fiber filler with an aspect ratio of 8 without gaps. A poly(difluoroethylene-trifluoroethylene) molecular chain monolayer film is placed on the first layer, and barium titanate fillers are evenly dispersed on the second layer. Three layers of poly(difluoroethylene-trifluoroethylene) monolayer film are placed under the second layer of barium titanate fillers, and a five-layer "sandwich" structure poly(difluoroethylene-trifluoroethylene) composite film model doped with fiber fillers with an aspect ratio of 8 is obtained, wherein the mass fraction of barium titanate fillers in the composite film is 30%;

[0061] (2) Energy minimization was performed on the constructed composite membrane model separately. The specific steps were as follows: first, energy minimization was performed at a step size of 1 fs until the energy converged to 100 kJ / (mol·nm). During this process, the polyvinylidene fluoride-trifluoroethylene molecular chains could move freely, while the barium titanate filler was frozen; then, the entire composite membrane was frozen and applied to the next molecular dynamics simulation process; then, energy minimization was performed on the fibronectin model downloaded from the RCSB structure database (PDB ID: 1TTF) until the energy converged to 100 kJ / (mol·nm). Then, the energy-minimized fibronectin was centered 1.25 nm above the upper surface of the energy-minimized composite membrane, and the two were merged to obtain the computational model of the composite membrane-protein binary system;

[0062] (3) MD simulation was performed on the computational model of the composite membrane-protein binary system. The specific steps are as follows: First, the steepest descent method was used to minimize the energy to achieve the energy convergence of the entire system to 100 kJ / (mol·nm), and the energy-converged structure was obtained; the energy-converged structure was used for the next 1 ns NVT ensemble relaxation, and the temperature was controlled at 310.15 K using a V-rescale heat bath; the structure after the NVT ensemble relaxation was used for the next 20 ns MD simulation, and the simulation process used the CHARMM27 force field, the PME algorithm was used to calculate the electrostatic interaction, and the cut-off method was used to calculate the van der Waals interaction. The cutoff values ​​of the electrostatic interaction and the van der Waals interaction were set to 1.0 nm. After the simulation, the results of the MD simulation were extracted with the help of the Gromacs built-in module, including the interaction energy between the protein and the complex (obtained by superimposing the van der Waals interaction energy and the electrostatic interaction energy), the calculation of the distance between the center of mass of key residues, the change of the minimum distance between the protein and the composite membrane over time, the root mean square deviation of fibronectin, the rotation radius of fibronectin, etc.;

[0063] (4) According to the results of MD simulation in (3), the electrostatic interaction energy and the van der Waals interaction energy are added to obtain the interaction energy between the protein and the composite film of poly(ethylene difluoride-trifluoroethylene) / barium titanate particle filler. Specifically, the electrostatic interaction energy is calculated by the PME algorithm, and the van der Waals interaction energy is obtained by the cut-off method. The electrostatic interaction energy and the van der Waals interaction energy between the composite film of barium titanate fiber filler with an aspect ratio of 8 and the protein are -118.50 and -32.34 KJ / mol, respectively. The addition of the two gives an interaction energy of -150.84 KJ / mol between the protein and the composite film. This result shows that the fibronectin adsorbed on the surface of the composite film doped with barium titanate fiber filler with an aspect ratio of 8 is relatively firm; the distance module of the distance module of the Gromacs software was used to calculate the center of mass distance of the key synergistic activity sequence of the protein. The specific steps are to first set the two key residue sequences RGD and PHSRN as two groups with different numbers, and then use the distance module to calculate the distance between the centers of mass of the two groups, that is, the center of mass distance of RGD-PHSRN is obtained. It can be seen that the result is Proximity is the dominant conformation.

[0064] (5) The adsorption results of proteins on the composite membrane surface of the barium titanate fiber filler with an aspect ratio of 8 were comprehensively analyzed from the two points of firmness and conformation of protein adsorption. Since the adsorption results of the composite membrane of the barium titanate fiber filler with an aspect ratio of 8 have high firmness and advantageous conformation, the composite membrane has excellent biocompatibility. The barium titanate fiber filler is a recommended filler.

[0065] Example 3

[0066] In this embodiment, a poly(difluoroethylene-tetrafluoroethylene) composite membrane doped with potassium sodium niobate fiber filler having an aspect ratio of 10 is constructed, wherein the crystal forms of barium titanate and poly(difluoroethylene-tetrafluoroethylene) are cubic and α crystal forms, respectively, and the mass fractions are 15% and 85%, respectively. The fibronectin model in the MD simulation adopts the fibronectin model obtained by homology modeling.

[0067] A molecular dynamics simulation method based on fibronectin adsorption comprises the following steps:

[0068] (1) Using Materials Studio to construct a poly(difluorotetrafluoroethylene) molecular chain, assigning the molecular chain an α-phase lattice parameter to obtain a poly(difluorotetrafluoroethylene) molecular chain unit model, and then seamlessly extending the poly(difluorotetrafluoroethylene) molecular chain unit model into a poly(difluorotetrafluoroethylene) molecular chain monolayer membrane; downloading cubic potassium sodium niobate crystal structure data from the Inorganic Crystal Structure Database (ICSB), importing it into Materials Studio software to construct a potassium sodium niobate unit model, and then seamlessly extending the potassium sodium niobate unit model into a fiber filler with an aspect ratio of 10. A poly(difluoro-tetrafluoroethylene) molecular chain monolayer membrane is placed on the first layer, potassium sodium niobate fillers are evenly spread on the second layer, and 6 layers of poly(difluoro-tetrafluoroethylene) monolayer membranes are placed under the second layer of potassium sodium niobate fillers, thereby obtaining an 8-layer "sandwich" structure poly(difluoro-tetrafluoroethylene) composite membrane model doped with potassium sodium niobate fiber fillers with an aspect ratio of 10, wherein the mass fraction of potassium sodium niobate fillers in the two composite membranes is the same and is 15%;

[0069] (2) The energy of the constructed composite membrane model is minimized separately. The specific steps are as follows: first, the energy is minimized at a step size of 1 fs until the energy converges to 100 kJ / (mol·nm). In this process, the poly(difluorotetrafluoroethylene) molecular chain can move freely, while the potassium sodium niobate filler is frozen; then, the entire composite membrane is frozen and applied to the next molecular dynamics simulation process; then, the fibronectin model containing the key residues RGD and PHSRN obtained by homology modeling is minimized separately until the energy converges to 100 kJ / (mol·nm). Then, the energy-minimized fibronectin is centered 2.0 nm above the upper surface of the energy-minimized composite membrane, and the two are merged to obtain the computational model of the composite membrane-protein binary system;

[0070] (3) MD simulation was performed on the computational model of the composite membrane-protein binary system. The specific simulation process is as follows: First, the steepest descent method was used to minimize the energy to achieve the energy convergence of the entire system to 100 kJ / (mol·nm), and the structure after energy convergence was obtained; the structure after energy convergence was used for the next 5 ns NVT ensemble relaxation, and the temperature was controlled at 315.15 K using a V-rescale heat bath; the structure after NVT ensemble relaxation was used for the next 100 ns MD simulation, and the simulation process used the CHARMM27 force field, the PME algorithm was used to calculate the electrostatic interaction, and the cut-off method was used to calculate the van der Waals interaction. The cutoff values ​​of the electrostatic interaction and the van der Waals interaction were set to 1.0 nm. After the simulation, the results of the MD simulation were extracted with the help of the Gromacs built-in module, including the interaction energy between the protein and the complex (obtained by superimposing the van der Waals interaction energy and the electrostatic interaction energy), the calculation of the distance between the center of mass of key residues, the change of the minimum distance between the protein and the composite membrane over time, the root mean square deviation of fibronectin, the rotation radius of fibronectin, etc.;

[0071] (4) According to the results of MD simulation in (3), the electrostatic interaction energy and the van der Waals interaction energy were added to obtain the interaction energy between the protein and the poly(difluoroethylene-tetrafluoroethylene) composite membrane doped with potassium sodium niobate fiber filler with an aspect ratio of 10. Specifically, the electrostatic interaction energy was calculated by the PME algorithm, and the van der Waals interaction energy was obtained by the cut-off method. The electrostatic interaction energy and van der Waals interaction energy between the composite membrane of potassium sodium niobate filler with an aspect ratio of 10 and the protein were -110.50 and -52.33 KJ / mol, respectively. The sum of the two obtained the interaction energy between the protein and the composite membrane was -162.83 KJ / mol. This result shows that the fibronectin adsorbed on the surface of the composite membrane doped with potassium sodium niobate fiber filler with an aspect ratio of 10 is very firm; the distance module of the distance of the center of mass of the key synergistic activity sequence of the protein was calculated by the distance module of the Gromacs software. The specific steps are to first set the two key residue sequences RGD and PHSRN as two groups with different numbers, and then use the distance module to calculate the distance between the centers of mass of the two groups, that is, the distance between the centers of mass of RGD-PHSRN is obtained. It can be seen that the result is The difference is quite large and it is not the dominant conformation.

[0072] (5) The adsorption results of proteins on the composite membrane surface of potassium sodium niobate fiber filler with an aspect ratio of 10 were comprehensively analyzed from the two aspects of protein adsorption firmness and conformation. Since the adsorption results of the composite membrane of barium titanate fiber filler with an aspect ratio of 10 have high firmness but do not meet the dominant conformation, the composite membrane does not have excellent biocompatibility. In addition, barium titanate fillers with different morphologies are selected to repeat the above steps until a composite membrane of barium titanate filler with excellent biocompatibility is obtained.

[0073] It can be seen from the above embodiments that the present invention is a molecular dynamics simulation method for the adsorption of fibronectin on the surface of a piezoelectric high molecular polymer composite film (composite film) doped with a piezoelectric inorganic filler. In the prediction of the biocompatibility of a piezoelectric inorganic filler-piezoelectric high molecular polymer composite film material, the method of the present invention provides a method for establishing a composite film model, simulation steps and data extraction methods, and provides a criterion for judging the quality of biocompatibility. The present invention uses the advanced open source molecular dynamics software Gromacs to accurately obtain the dynamic process of fibronectin adsorption on the surface of a piezoelectric high molecular polymer / piezoelectric inorganic filler composite film with different piezoelectric inorganic fillers, which is highly consistent with the experimental results; the present invention has low computational cost and high efficiency, and provides a powerful tool for the development of high-performance organic-inorganic composite piezoelectric flexible implant materials.

[0074] The above embodiments are only for illustrating the technical concept and features of the present invention, and their purpose is to enable people familiar with the technology to understand the content of the present invention and implement it accordingly, and they cannot be used to limit the protection scope of the present invention. Any equivalent changes or modifications made according to the spirit of the present invention should be included in the protection scope of the present invention.

Claims

1. A molecular dynamics simulation method based on fibronectin adsorption, characterized in that The steps include: 1) Using Materials Studio, construct a piezoelectric polymer molecular chain, assign lattice parameters to the molecular chain, and obtain a piezoelectric polymer unit model; expand the piezoelectric polymer unit model into a piezoelectric polymer monolayer film without gaps; Import the crystal structure data of the piezoelectric inorganic filler into Materials Studio software to construct a unit model of the piezoelectric inorganic filler; expand the unit model of the piezoelectric inorganic filler into a piezoelectric inorganic filler in the shape of particles or fibers without gaps; A piezoelectric polymer monolayer film is placed in the first layer, a piezoelectric inorganic filler is evenly spread in the second layer, and m layers of piezoelectric polymer monolayer films are placed under the second layer of piezoelectric inorganic filler to obtain a piezoelectric polymer composite film model doped with piezoelectric inorganic fillers with a multi-layer structure; wherein 1≤m≤20; 2) The constructed piezoelectric inorganic filler-doped piezoelectric polymer composite film model and fibronectin model were energy minimized respectively, and the energy-minimized fibronectin was centered at 1.25 to 2.0 nm above the upper surface of the energy-minimized piezoelectric polymer composite film, and then merged to obtain a computational model of the composite membrane-protein binary system; the fibronectin model was downloaded from the RCSB structure database, had a complete structural domain and contained key active residues RGD and PHSRN sequences; 3) Molecular dynamics simulation of the computational model of the composite membrane-protein binary system was carried out with the help of Gromacs software, and the interaction energy between the protein and the composite membrane and the center of mass distance of RGD-PHSRN were obtained; the interaction energy between the protein and the composite membrane was obtained by the sum of the van der Waals interaction energy and the electrostatic interaction energy; if the absolute value of the interaction energy between fibronectin and the composite membrane is greater than or equal to 100 kJ / mol, it is defined as a high firmness of protein adsorption; if the center of mass distance of RGD-PHSRN is 35±10Å, it is defined as a dominant conformation; if both the high firmness of protein adsorption and the dominant conformation are satisfied at the same time, it is determined that the piezoelectric inorganic filler and the piezoelectric polymer have excellent biocompatibility.

2. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The piezoelectric inorganic filler is barium titanate or potassium sodium niobate, and the crystal structure data of the piezoelectric inorganic filler is downloaded from an inorganic crystal structure database.

3. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The piezoelectric polymer is one of polyvinylidene fluoride, polytrifluoroethylene and hexafluoropropylene, or a copolymer formed by two or more thereof.

4. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The mass fraction of the piezoelectric inorganic filler in the piezoelectric high molecular polymer composite film model doped with the piezoelectric inorganic filler is 0.5% to 30%.

5. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The piezoelectric inorganic filler is in the form of particles or fibers with an aspect ratio of n, where n is greater than or equal to 2.

6. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The energy minimization of the piezoelectric polymer composite film model doped with piezoelectric inorganic fillers is first performed at a step size of 1 fs until the energy converges to a maximum interatomic force of ≤100 kJ / (mol•nm). In this process, the piezoelectric polymer chains can move freely and the piezoelectric inorganic fillers are frozen; in all subsequent processes, the piezoelectric polymer chains are fixed.

7. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The van der Waals interaction energy and electrostatic interaction energy are obtained by the following steps: a. Using the steepest descent method to minimize energy to achieve energy convergence of the entire system and obtain an energy-convergent structure; the energy convergence judgment standard is that the maximum force between atoms is ≤100 kJ / (mol•nm); b. Perform NVT ensemble relaxation of t1 on the structure after energy convergence, and use V-rescale heat bath to control the temperature at T to obtain the relaxed structure; t1 is 0.5ns~1000ns, and T is 273.15K~323.15K; c The structure after NVT relaxation was subjected to molecular dynamics simulation of t2. The simulation process used the CHARMM27 force field, the particle-mesh Ewald algorithm to calculate the electrostatic interaction energy, and the truncation algorithm to calculate the van der Waals interaction energy; the t2 value was 0.5ns~1000ns.

8. The molecular dynamics simulation method based on fibronectin adsorption according to claim 1, characterized in that: The centroid distance of RGD-PHSRN is calculated by the distance module of Gromacs software. First, the two key residue sequences RGD and PHSRN are set as two groups with different numbers, and finally the distance module is used to calculate the distance between the centroids of the two groups.

Images