蛋白質(zhì)在材料表面吸附的分子動(dòng)力學(xué)模擬
發(fā)布時(shí)間：2018-09-02 08:40
【摘要】：蛋白質(zhì)與材料間相互作用并會(huì)自發(fā)吸附到材料表面是自然界中廣泛存在的一種現(xiàn)象。在許多情況下,蛋白質(zhì)吸附是有利的,但在更多時(shí)候,蛋白質(zhì)吸附到材料表面會(huì)帶來(lái)不希望的結(jié)果。特別是在海洋環(huán)境中發(fā)生的生物污損,因海洋生物附著引起的污損會(huì)加速在海中作業(yè)的金屬設(shè)備腐蝕,影響設(shè)施的正常使用,增加船舶的航行阻力并會(huì)使海中儀表或轉(zhuǎn)動(dòng)機(jī)失靈等。而海洋生物污染的初期主要是海洋生物分泌的蛋白質(zhì)粘液在表面的吸附,因此研究蛋白質(zhì)與材料間相互作用過(guò)程中蛋白質(zhì)的構(gòu)型變化、作用機(jī)理及不同材料對(duì)吸附的影響等,有助于我們理解材料吸附蛋白質(zhì)作用機(jī)理,以求找到具有更好防污效果的防污材料。本論文主要運(yùn)用分子動(dòng)力學(xué)模擬方法研究了蛋白質(zhì)與不同固體材料表面間的相互作用。分子動(dòng)力學(xué)模擬可以大大降低實(shí)驗(yàn)的盲目性和重復(fù)實(shí)驗(yàn)的耗材與耗時(shí)性,同時(shí)還可以直觀地從分子水平上觀察到體系中蛋白質(zhì)三維結(jié)構(gòu)的變化,加深對(duì)蛋白質(zhì)在不同材料表面吸附機(jī)理的認(rèn)識(shí),以求找到更好的防污材料。具體研究?jī)?nèi)容包括以下幾個(gè)方面：(1)采用分子動(dòng)力學(xué)模擬方法研究了溶菌酶蛋白在兩種典型聚合物防污材料聚乙二醇(PEG)和聚二甲基硅氧烷(PDMS)表面的吸附行為,在微觀上探討了聚合物膜表面性質(zhì)對(duì)溶菌酶蛋白吸附的影響。對(duì)蛋白質(zhì)在聚合物膜表面的吸附現(xiàn)象,能量變化和表面水化層分子的動(dòng)力學(xué)行為進(jìn)行分析,發(fā)現(xiàn)：相比PEG膜,蛋白質(zhì)與PDMS膜表面的結(jié)合能量較高,使其結(jié)合更加緊密穩(wěn)定；蛋白質(zhì)要吸附到材料表面需克服表面水化層分子引起的能障,PEG表面與水分子之間結(jié)合緊密,造成蛋白質(zhì)在其表面吸附需要克服更高的能量,不利于蛋白質(zhì)的吸附,合理地解釋了PEG防污膜相對(duì)于PDMS膜具有更佳防污效果的原因。(2)運(yùn)用分子動(dòng)力學(xué)手段分析了蛋白質(zhì)與不同末端官能團(tuán)終止的自組裝單分子層膜(SAMs)間的相互作用。SAMs表面結(jié)構(gòu)和化學(xué)性質(zhì)可以通過(guò)改變表面組成和末端官能團(tuán)來(lái)調(diào)節(jié),能在分子尺度上進(jìn)行很好的表征,是研究蛋白質(zhì)界面行為的理想平臺(tái)。通過(guò)分析溶菌酶蛋白與疏水性的CH3-SAM及兩種親水性的CH2OH-SAM和COOH-SAM間的相互作用,對(duì)比蛋白質(zhì)在膜表面的參數(shù)變化和膜表面水分子的動(dòng)力學(xué)行為,得到結(jié)論：溶菌酶蛋白與疏水性的CH3-SAMs膜間的相互作用能最大,在其上發(fā)生的形變較大,利于蛋白質(zhì)吸附并在吸附后難以自行脫附；親水性SAMs膜表面與水化層分子的結(jié)合更加緊密,蛋白質(zhì)要吸附到膜表面需要克服更高的能量,吸附更加困難,對(duì)比COOH-SAMs, CH2OH-SAMs阻抗蛋白質(zhì)吸附的能力較強(qiáng),防污效果最好。(3)采用分子動(dòng)力學(xué)模擬方法研究疏水蛋白在二氧化硅表面的動(dòng)力學(xué)行為。疏水蛋白是目前已知的具有最強(qiáng)表面活性的蛋白質(zhì),其在材料表面能夠降低材料表面水的表面張力,率先吸附到材料表面形成一層真菌保護(hù)膜并產(chǎn)生孢子,對(duì)于海洋生物污染初期形成的生物條件膜有重要貢獻(xiàn)作用。為揭示海洋環(huán)境中巖石表面蛋白質(zhì)吸附現(xiàn)象機(jī)理,我們研究了疏水蛋白從4個(gè)不同方向(每個(gè)方向旋轉(zhuǎn)90°)放置在二氧化硅表面的吸附狀況及蛋白質(zhì)的構(gòu)型變化,結(jié)果表明：蛋白質(zhì)不同方向的放置會(huì)影響其與基底間的相互作用,甚至發(fā)生不吸附的現(xiàn)象,并且蛋白質(zhì)在整個(gè)動(dòng)力學(xué)過(guò)程中的翻轉(zhuǎn)變化和最終吸附構(gòu)型是不同的,統(tǒng)計(jì)吸附的氨基酸類型,發(fā)現(xiàn)疏水性氨基酸所占比例較大；分析4個(gè)體系的蛋白質(zhì)構(gòu)型參數(shù)變化,回轉(zhuǎn)半徑和均方根偏差相差不大,蛋白質(zhì)不同方向的放置對(duì)構(gòu)型變化的影響不大,且在模擬時(shí)間內(nèi)沒有發(fā)生變性行為；對(duì)比4個(gè)體系的能量變化,發(fā)現(xiàn)能量大小與蛋白質(zhì)吸附在表面的氨基酸類型有關(guān),且吸附越緊密的體系能量越高。
[Abstract]:It is a widespread phenomenon in nature that proteins interact with materials and spontaneously adsorb onto their surfaces. In many cases, protein adsorption is beneficial, but in more cases, protein adsorption on the surface of materials can lead to undesirable results. Especially in marine environments, biofouling occurs because of marine organisms. The fouling caused by attachment will accelerate the corrosion of metal equipment in marine operation, affect the normal use of facilities, increase the navigation resistance of ships and cause the failure of instruments or rotating machines in the sea. The structural changes of proteins, the mechanism of action and the effect of different materials on adsorption are helpful for us to understand the mechanism of protein adsorption and find better antifouling materials. Interaction. Molecular dynamics simulation can greatly reduce the blindness of the experiment and the consumptivity and time-consuming of repeated experiments. At the same time, the changes of three-dimensional structure of proteins in the system can be observed intuitively at the molecular level. The understanding of the adsorption mechanism of proteins on different materials can be deepened to find better antifouling materials. The research contents include the following aspects: (1) The adsorption behavior of lysozyme on the surface of two typical polymer antifouling materials, polyethylene glycol (PEG) and polydimethylsiloxane (PDMS), was studied by molecular dynamics simulation. The effect of the surface properties of polymer membrane on the adsorption of lysozyme was discussed microscopically. Adsorption phenomena, energy changes and kinetic behavior of surface hydration layer molecules were analyzed. It was found that the binding energy between protein and PDMS membrane was higher than that of PEG membrane, and the binding energy between protein and PDMS membrane was tighter and more stable. The tight binding between the molecules makes it necessary to overcome higher energy for protein adsorption on its surface, which is not conducive to protein adsorption. The reason why PEG antifouling membrane has better antifouling effect than PDMS membrane is reasonably explained. (2) The self-assembled monolayer membrane (SA) terminated by different end functional groups was analyzed by molecular dynamics. The surface structure and chemical properties of SAMs can be well characterized at the molecular scale by changing the surface composition and terminal functional groups. It is an ideal platform for studying the interfacial behavior of proteins. The interaction between Lysozyme protein and hydrophobic CH3-SAMs membrane was studied. The results showed that the interaction energy between Lysozyme protein and hydrophobic CH3-SAMs membrane was the greatest, and the deformation on it was larger, which was beneficial to protein adsorption and difficult to desorb after adsorption. Compared with COOH-SAMs, CH2OH-SAMs have stronger ability of impedance protein adsorption and the best antifouling effect. (3) The kinetic behavior of hydrophobic protein on the surface of silica was studied by molecular dynamics simulation. Proteins with the strongest surface activity are known to reduce the surface tension of water on the surface of materials. They take the lead in adsorbing to the surface of materials to form a protective film of fungi and produce spores. The adsorption of hydrophobic proteins on silica surface from four different directions (rotating 90 degrees in each direction) and the structural changes of the proteins were studied. The results showed that the different orientations of the proteins would affect the interaction between the proteins and the substrate, and even lead to non-adsorption. The inversion and final adsorption configurations were different in the whole kinetic process, and the hydrophobic amino acids accounted for a large proportion according to the type of adsorption amino acids. Compared with the energy changes of the four systems, it was found that the energy was related to the type of amino acids adsorbed on the surface of the protein, and the energy of the system with the tighter adsorption was higher.
【學(xué)位授予單位】：山東大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2015
【分類號(hào)】：O647.31;X55
本文編號(hào)：2218836
[Abstract]:It is a widespread phenomenon in nature that proteins interact with materials and spontaneously adsorb onto their surfaces. In many cases, protein adsorption is beneficial, but in more cases, protein adsorption on the surface of materials can lead to undesirable results. Especially in marine environments, biofouling occurs because of marine organisms. The fouling caused by attachment will accelerate the corrosion of metal equipment in marine operation, affect the normal use of facilities, increase the navigation resistance of ships and cause the failure of instruments or rotating machines in the sea. The structural changes of proteins, the mechanism of action and the effect of different materials on adsorption are helpful for us to understand the mechanism of protein adsorption and find better antifouling materials. Interaction. Molecular dynamics simulation can greatly reduce the blindness of the experiment and the consumptivity and time-consuming of repeated experiments. At the same time, the changes of three-dimensional structure of proteins in the system can be observed intuitively at the molecular level. The understanding of the adsorption mechanism of proteins on different materials can be deepened to find better antifouling materials. The research contents include the following aspects: (1) The adsorption behavior of lysozyme on the surface of two typical polymer antifouling materials, polyethylene glycol (PEG) and polydimethylsiloxane (PDMS), was studied by molecular dynamics simulation. The effect of the surface properties of polymer membrane on the adsorption of lysozyme was discussed microscopically. Adsorption phenomena, energy changes and kinetic behavior of surface hydration layer molecules were analyzed. It was found that the binding energy between protein and PDMS membrane was higher than that of PEG membrane, and the binding energy between protein and PDMS membrane was tighter and more stable. The tight binding between the molecules makes it necessary to overcome higher energy for protein adsorption on its surface, which is not conducive to protein adsorption. The reason why PEG antifouling membrane has better antifouling effect than PDMS membrane is reasonably explained. (2) The self-assembled monolayer membrane (SA) terminated by different end functional groups was analyzed by molecular dynamics. The surface structure and chemical properties of SAMs can be well characterized at the molecular scale by changing the surface composition and terminal functional groups. It is an ideal platform for studying the interfacial behavior of proteins. The interaction between Lysozyme protein and hydrophobic CH3-SAMs membrane was studied. The results showed that the interaction energy between Lysozyme protein and hydrophobic CH3-SAMs membrane was the greatest, and the deformation on it was larger, which was beneficial to protein adsorption and difficult to desorb after adsorption. Compared with COOH-SAMs, CH2OH-SAMs have stronger ability of impedance protein adsorption and the best antifouling effect. (3) The kinetic behavior of hydrophobic protein on the surface of silica was studied by molecular dynamics simulation. Proteins with the strongest surface activity are known to reduce the surface tension of water on the surface of materials. They take the lead in adsorbing to the surface of materials to form a protective film of fungi and produce spores. The adsorption of hydrophobic proteins on silica surface from four different directions (rotating 90 degrees in each direction) and the structural changes of the proteins were studied. The results showed that the different orientations of the proteins would affect the interaction between the proteins and the substrate, and even lead to non-adsorption. The inversion and final adsorption configurations were different in the whole kinetic process, and the hydrophobic amino acids accounted for a large proportion according to the type of adsorption amino acids. Compared with the energy changes of the four systems, it was found that the energy was related to the type of amino acids adsorbed on the surface of the protein, and the energy of the system with the tighter adsorption was higher.
【學(xué)位授予單位】：山東大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2015
【分類號(hào)】：O647.31;X55
【參考文獻(xiàn)】
相關(guān)期刊論文 前1條
1 趙曉燕;海洋天然產(chǎn)物防污研究進(jìn)展[J];材料開發(fā)與應(yīng)用;2001年04期
，本文編號(hào)：2218836
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