基于机器人机构学的F_0F_1ATP合成酶马达能量储存研究
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摘要
生物纳米机器人是科学研究的前沿领域,分子马达作为动力装置在生物纳米机器人中具有重要的作用。F0F1ATP合成酶马达是天然存在的分子马达,当把ADP和Pi合成ATP分子时,电势能将首先转化为机械能,然后又转化为化学能储存在ATP分子中；当ATP分子被分解为ADP和Pj时,能量又能按照相反的方向进行转化。因其具有在能量转化和传递效率上接近100%的特性,引起了学者的关注,成为生物纳米机器人研究中的一个热点。
基于F0F1ATP合成酶是一种特殊的蛋白质,是由氨基酸通过肽键连接而成的多肽链,多肽链在结构上类似于若干构件通过转动副连接而成的超冗余度机器人的事实,本学位论文首次运用机器人机构学原理从氢键的能量变化来研究F0F1ATP合成酶马达能量储存这一重要问题。论文的主要工作如下：
首先,使用机器人机构学原理,基于蛋白质多肽链的性质和各原子的位置关系首次建立了考虑肽键扭转的蛋白质多肽链的机器人机构学模型。
其次,利用考虑肽键扭转的蛋白质多肽链的机器人机构学模型对蛋白质二级结构中最常见的α螺旋、β折叠和β回折等进行了仿真计算。结果表明此模型能够准确的表达蛋白质二级结构的空间构象,由此证明了所建立模型的正确性。
再次,基于多肽链的机器人机构学模型,提出了一种简单、快捷的的氢键静电能的计算方法。
最后,应用多肽链的机器人机构学模型,深入到原子水平,研究了F0F1ATP合成酶马达的能量储存机制。从氢键静电能变化的角度分析Neukirch提出的γ和b子组串联储能模型和K.Kinosita小组提出的γ单子组储能模型。分析结果表明Neukirch模型较合理,K.Kinosita小组模型不合理。
借助于MATLAB软件完成了本论文的建模、仿真和计算工作。
Bio-nano-robot is one of the scientific research frontiers nowadays. The molecular motor as power section plays an important role in bio-nano-robot. The F0F1ATP synthase motor as one of molecular motor widely and naturally exists inside the living creatures. When ADP and Pi synthesize into ATP molecules, the F0F1ATP synthase firstly transforms electric potential energy into mechanical energy, then transforms mechanical energy into chemical energy and storages it into the ATP molecules; and when ATP molecules discompose into ADP and Pi, the energy will be transformed in the opposite way. F0F1ATP synthase motor has drawn more and more attention of researchers and become a hot spot in bio-nano-robot research because its energy transformation efficiency can approximately reach to 100%.
F0F1ATP synthase is a special kind of protein which is composed by polypeptide chains of amino acid connected by peptide bonds. Based on the fact that, the polypeptide chain is similar to a hyper-redundant robot whose linkages are connected with revolute pairs the key issue of the energy storage in F0F1ATP synthase moter has been studied from the energy change of hydrogen bond by applying the robotic mechanism theory for the first time in this thesis as follows.
Firstly, by applying the theory of robotic mechanisms, the robotic mechanism model of protein polypeptide chain considering peptide bond twist is established, based on the properties of the protein polypeptide chain and the atoms'positions.
Secondly, the a-helix、β-sheet and (3-turn, which are the most common in the protein secondary structure, are simulated by utilizing the above mentioned model of the protein polypeptide chain. And the simulation results show that, the space conformation of protein secondary structure can be accurately manifested by this model and then the validity of the model is proved.
Thirdly, a simple and quick method for calculating hydrogen bonding electrostatic is proposed based on the robotic mechanism model of the protein polypeptide chain.
Finally, the energy storage mechanism of F0F1ATP synthase motor is studied from the atomic level by using the model presented. Neukirch's y and b module in series and K.Kinosita group'only y module stored energy model are analysed from the standpoint of change of hydrogen bond electrostatic, and according to the result, the former is reasonable and the latter is unreasonable.
The above mentioned modeling, simulations and calculations are completed by means of MATLAB.
基于F0F1ATP合成酶是一种特殊的蛋白质,是由氨基酸通过肽键连接而成的多肽链,多肽链在结构上类似于若干构件通过转动副连接而成的超冗余度机器人的事实,本学位论文首次运用机器人机构学原理从氢键的能量变化来研究F0F1ATP合成酶马达能量储存这一重要问题。论文的主要工作如下：
首先,使用机器人机构学原理,基于蛋白质多肽链的性质和各原子的位置关系首次建立了考虑肽键扭转的蛋白质多肽链的机器人机构学模型。
其次,利用考虑肽键扭转的蛋白质多肽链的机器人机构学模型对蛋白质二级结构中最常见的α螺旋、β折叠和β回折等进行了仿真计算。结果表明此模型能够准确的表达蛋白质二级结构的空间构象,由此证明了所建立模型的正确性。
再次,基于多肽链的机器人机构学模型,提出了一种简单、快捷的的氢键静电能的计算方法。
最后,应用多肽链的机器人机构学模型,深入到原子水平,研究了F0F1ATP合成酶马达的能量储存机制。从氢键静电能变化的角度分析Neukirch提出的γ和b子组串联储能模型和K.Kinosita小组提出的γ单子组储能模型。分析结果表明Neukirch模型较合理,K.Kinosita小组模型不合理。
借助于MATLAB软件完成了本论文的建模、仿真和计算工作。
Bio-nano-robot is one of the scientific research frontiers nowadays. The molecular motor as power section plays an important role in bio-nano-robot. The F0F1ATP synthase motor as one of molecular motor widely and naturally exists inside the living creatures. When ADP and Pi synthesize into ATP molecules, the F0F1ATP synthase firstly transforms electric potential energy into mechanical energy, then transforms mechanical energy into chemical energy and storages it into the ATP molecules; and when ATP molecules discompose into ADP and Pi, the energy will be transformed in the opposite way. F0F1ATP synthase motor has drawn more and more attention of researchers and become a hot spot in bio-nano-robot research because its energy transformation efficiency can approximately reach to 100%.
F0F1ATP synthase is a special kind of protein which is composed by polypeptide chains of amino acid connected by peptide bonds. Based on the fact that, the polypeptide chain is similar to a hyper-redundant robot whose linkages are connected with revolute pairs the key issue of the energy storage in F0F1ATP synthase moter has been studied from the energy change of hydrogen bond by applying the robotic mechanism theory for the first time in this thesis as follows.
Firstly, by applying the theory of robotic mechanisms, the robotic mechanism model of protein polypeptide chain considering peptide bond twist is established, based on the properties of the protein polypeptide chain and the atoms'positions.
Secondly, the a-helix、β-sheet and (3-turn, which are the most common in the protein secondary structure, are simulated by utilizing the above mentioned model of the protein polypeptide chain. And the simulation results show that, the space conformation of protein secondary structure can be accurately manifested by this model and then the validity of the model is proved.
Thirdly, a simple and quick method for calculating hydrogen bonding electrostatic is proposed based on the robotic mechanism model of the protein polypeptide chain.
Finally, the energy storage mechanism of F0F1ATP synthase motor is studied from the atomic level by using the model presented. Neukirch's y and b module in series and K.Kinosita group'only y module stored energy model are analysed from the standpoint of change of hydrogen bond electrostatic, and according to the result, the former is reasonable and the latter is unreasonable.
The above mentioned modeling, simulations and calculations are completed by means of MATLAB.
引文
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