蛋白质分块量子化学计算方法的发展和振动斯塔克效应的研究
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摘要
蛋白质是生命活动的主要承载体,研究蛋白质的结构和功能有着非常重要的工业和医药价值。存在于蛋白质表面及其内部的静电场作为蛋白质内部主要相互作用的来源影响着蛋白质结构和功能的方方面面。对于蛋白质内部静电性质的研究吸引了大批实验和理论科学家的关注。振动斯塔克光谱在实验上被广泛的应用于探测蛋白质内部动力学行为的变化。通过向蛋白质内部插入含有某些特殊基团的探针的方法,通过线性斯塔克光谱可以在实验上比较精确的测量蛋白质内部静电场变化。理论上基于分子力场的动力学模拟方法为在微观尺度上揭示蛋白质的各种性质提供了非常有力的工具。基于分子力场的计算结果可以直接与实验上测得的数据进行比较,从而可以在分子层面上更加深入的分析和解释实验数据,甚至做出合理的预测。现在常用的分子力场模型比如AMBER,CHARMM,OPLS等在静电性质的计算上大多采用平均场近似的电荷模型的方法,缺少了由于蛋白质内部特殊的静电环境所带来的静电极化效应。虽然这种近似的电荷模型方法对于蛋白质动力学行为模拟的影响是有限的,但是越来越多的理论工作指出在蛋白质的某些性质的计算中已经达到了不可忽略的程度。在前人工作的基础上,我们把运用了量子化学计算方法从而考虑了蛋白质特殊的静电环境带来的极化效应的电荷polarized protein-specific charge (PPC)运用到人体醛糖还原酶(hALR2)线性斯塔克光谱的计算中,同时进行了基于传统的非极化AMBER力场的光谱计算。通过直接和实验值进行比较,我们发现基于极化电荷模型的力场比传统非极化的AMBER力场能给出更切合实验数据的计算结果,说明极化效应在蛋白斯塔克光谱的计算方面有着非常重要的作用,同时也揭示出现在常用的非极化的AMBER力场在与静电直接相关的性质的计算上需要进一步的提高。
通过对蛋白质内部电场和stark光谱的研究,我们发现经典的力场模型在借助于高等级的量子化学计算后,能够更好重复试验的结果,而在现存的理论计算方法中,基于量子力学的计算方法是最为精确和可靠的。对于小的体系,在采用了适当的方法后,我们通常可以完成化学精度甚至于光谱精度的计算。理论化学家总是希望能够将量子化学的计算方法应用到尽可能大的分子体系中去。虽然近些年来计算机的发展对于含有几百甚至上千原子的分子,已经基本可以实现量子力学级别的计算,但是现在许多科学研究中要研究的分子所包含的原子的数目通常要远超出这个数值。比如像蛋白质分子,要进行传统意义上的量子化学的计算仍然是一项比较巨大的挑战。为了解决这样的问题,我们课题组自主开发和编写了一套基于分块的线性标度的量子化学的计算方法：Molecular Fractionation with Conjugate Caps (MFCC,分子碎片共轭帽),这种方法已经被应用到蛋白质性质计算的很多方面。为了提高这种方法对于蛋白质总能量的计算精度一种新的Generalized Molecular Fractionation with Conjugate Caps/Molecular Mechanics (GMFCC/MM,推广的分子碎片共轭帽)方法被提出来。基于这种方法我们进一步发展了静电嵌入的推广的分子碎片共轭帽的方法：Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Cap(EE-GMFCC,静电嵌入的推广的分子碎片共轭帽)以便更精确地计算蛋白质总能量。在这种方法中蛋白质的总能量由各个碎片计算得到的能量的线性组合得来。在所有碎片分子的计算中,通过简单的静电嵌入的方式来引入除去碎片分子以外的环境效应。通过对18个真实蛋白质体系在HF/6-31G*水平上的计算我们发现与传统意义上的全体系的量子化学的计算结果相比较,静电嵌入的方案相对于原来的推广的分子碎片共轭帽的方法把平均误差缩减到2.39kcal/mol。我们通过采用不同的两体截断半径的方法测试了几个含有几百原子具有三维结构的蛋白质体系,结果表明两体的相互作用矫正对于计算精度也有较大的贡献。EE-GMFCC的方法在MP2和DFT水平上的计算相对于全体系的量子计算的结果误差也都只有几个kcal/mol。而相对于全体系量子化学的计算对于含有几百个原子的蛋白质我们这种方法的计算效率有非常明显的提高,从而可以把量子化学的计算方法推广到任意大小尺寸的蛋白质分子中。
蛋白质内部电场影响着蛋白质的结构和功能,而外电场对蛋白质空间结构的完整性同样有着重要的影响,有实验表明微波场能够在不引起热效应的前提下改变蛋白质的三维构象。外电场对蛋白质动力学的非热效应在实验上引起了广泛的关注。但是就现在的状况而言实验上的数据还不能对这些效应作出原子层面上的解释,借助于分子动力学的模拟我们能够在原子尺度上揭示其微观机理。应用分子动力学模拟的方法,我们在不同的外电场值下对牛胰岛素蛋白质进行了一系列长达1个微妙的动力学模拟,在模拟中我们发现0.15V/nm的外电场并没有对胰岛素蛋白的二级结构产生较大的影响,而0.25V/nm及以上强度的外电场可以破坏胰岛素的二级结构,当外加电场强度在0.15～0.60V/nm时,蛋白质二级结构开始出现破坏所需要的模拟时间与外加电场的大小没有十分明确的相关性。一系列的结果显示在这个外加电场的范围内(0.15～0.60V/nm)蛋白质长时间暴露在外电场中的时间累积效应是导致蛋白质二级结构破坏的主要因素。当外加电场的值大于0.60V/nm时,外电场的强度对蛋白质内部氢键的寿命有着非常重要的影响。蛋白质内部氢键在外加电场为1.0V/nnm时出现了快速演化显示出外加电场能够加速蛋白质的折叠或者破坏蛋白质的结构。
Protein plays a crucial role in the activities of lives. The studies of protein structures and functions have considerable medicinal and industrial applications. The electric fields produced by the charged and polar groups of protein have been considered as the main source of molecular interaction and influence nearly every aspect of protein structures and functions. Many theoretical and experimental works have been carried out to study the electrostatic of protein. Vibrational Stark effect (VSE) spectroscopy has been widely used to study the change of protein dynamic behaviors. Linear Stark effect gives the direct relationship between spectrum and electric field. Utilizing some specific-group-containing probes that can deliver a unique Stark vibration to the specific site of interest in the protein it is practical to experimentally reveal the change of electrostatic properties in the matrix of protein. With the help of molecular dynamics (MD) simulations based on force field, computer simulation has emerged as a powerful tool to study properties of protein. Despite much success in applications of standard force fields such as CHARMM, Amber, and OPLS, there is a fundamental limitation due to the lack of electronic polarization effects. The charge models in this force field are mean-field-like and do not include polarization effect due to the specific protein environment The contribution of the polarization effect could be neglected in some cases, while more and more theoretical works indicate its importance in the calculation of protein properties. Molecular dynamics simulations were carried out to compute linear Stark shift in human aldose reductase (hALR2) using a recently developed polarized protein-specific charge (PPC) model derived from quantum-chemistry calculations so as to include polarization effect due to the specific protein environment. The same calculations but based on conventional nonpolarizable Amber force field were also carried out. Our study demonstrates that the Stark shifts calculated based on the PPC model are in much better agreement with the experimental measured data than widely used nonpolarizable force fields, indicating that the electronic polarization effect is important for the accurate prediction of changes in the electric field inside proteins and traditional force field has still room for improvement for capturing the electrostatics of protein.
Our study of internal electric field and stark spectroscopy of protein indicates that the classical force field model after correction by high-level quantum chemistry calculation would give better agree with experimental results. It is well kown that in the existing theoretical methods, the calculations based on quantum mechanics (QM) could give very accurate and reliable results. For small systems one can achieve the desired calculation at either the chemical or even the spectroscopic accuracy level using appropriate methods. Theoretical chemists hope to perform quantum mechanics (QM) calculations on large molecular systems. Recent years, although the development of computer make it possible to perform quantum mechanics (QM) calculations on molecule that contain hundreds or even thousands of atoms, atoms contained in the molecule studied in many scientific researches are far more than this number. For example, it is still a grand challenge in computational chemistry to apply conventional quantum mechanical methods for large protein systems. For this problem, a linear-scaling quantum mechanical method called Molecular Fractionation with Conjugate Caps (MFCC) has been proposed and it has been used in many aspects of calculations of protein properties. In order to calculate the energy of proteins more accurately a generalized molecular fractionation with conjugate caps/MM (GMFCC/MM) method is developed. Based on which an Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Cap (EE-GMFCC) method was developed for further improving the computing accuracy. In the EE-GMFCC scheme, the total energy of protein is calculated by taking a linear combination of the QM energy of each fragment. All the fragment calculations are embedded in a field of point charges representing the remaining protein environment. Calculations of energy using the EE-GMFCC approach at the HF/6-31G*level are carried out on18real three-dimensional proteins. The overall mean unsigned error of EE-GMFCC for these18proteins is2.39kcal/mol with reference to the full system HF/6-31G*energies. The EE-GMFCC approach is also tested for proteins at the density functional theory (DFT) and second order many-body perturbation theory (MP2) level, also showing only a few kcal/mol deviation from the corresponding full system result. For protein that contains hundreds of atoms, our EE-GMFCC method shows a distinct advantage in the consumption of computing time when compared with conventional full system calculation and makes it possible to perform quantum mechanics (QM) calculations on protein molecule of any size.
Internal electric field inside a protein affects its structure, function and dynamics, while external electric field has a same significant effect on conformational integrity of protein. Some experimental works has confirmed that microwave radiation could alter protein conformation without bulk heating. Currently, the nonthermal effect of external electric fields acting on proteins has attracted a lot of theoretical and experimental research interest. While for traditional experimental approaches, it is still difficult to provide the details at the atomic level. By means of molecular simulation method computer simulation could give more detailed interpretation for dynamic behavior of peptides or proteins in external electric field. We perform a series of molecular dynamics (MD) simulations up to one μs for bovine insulin monomer in different external electric field. Our results indicated that the secondary structure of insulin is kept intact under the action of external electric field strength below0.15V/nm, but disruption of secondary structure would be observed at0.25V/nm or higher electric field. The corralation is not obvious between the starting time of secondary structure disruption of insulin and the strength of the external electric field ranging between0.15to0.60V/nm. Long time MD simulation up to one μs shows that the cumulative effect of exposure time under the electric field is a major cause for the damage of insulin's secondary structure. In addition, the strength of the external electric field has a significant impact on the lifetime of hydrogen bonds when it is higher than0.60V/nm. The fast evolution of some hydrogen bonds of bovine insulin in the presence of1.0V/nm electric field suggests that different microwaves could either speed up protein folding or destroy the secondary structure of globular proteins deponding on the intensity of the external electric field.
通过对蛋白质内部电场和stark光谱的研究,我们发现经典的力场模型在借助于高等级的量子化学计算后,能够更好重复试验的结果,而在现存的理论计算方法中,基于量子力学的计算方法是最为精确和可靠的。对于小的体系,在采用了适当的方法后,我们通常可以完成化学精度甚至于光谱精度的计算。理论化学家总是希望能够将量子化学的计算方法应用到尽可能大的分子体系中去。虽然近些年来计算机的发展对于含有几百甚至上千原子的分子,已经基本可以实现量子力学级别的计算,但是现在许多科学研究中要研究的分子所包含的原子的数目通常要远超出这个数值。比如像蛋白质分子,要进行传统意义上的量子化学的计算仍然是一项比较巨大的挑战。为了解决这样的问题,我们课题组自主开发和编写了一套基于分块的线性标度的量子化学的计算方法：Molecular Fractionation with Conjugate Caps (MFCC,分子碎片共轭帽),这种方法已经被应用到蛋白质性质计算的很多方面。为了提高这种方法对于蛋白质总能量的计算精度一种新的Generalized Molecular Fractionation with Conjugate Caps/Molecular Mechanics (GMFCC/MM,推广的分子碎片共轭帽)方法被提出来。基于这种方法我们进一步发展了静电嵌入的推广的分子碎片共轭帽的方法：Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Cap(EE-GMFCC,静电嵌入的推广的分子碎片共轭帽)以便更精确地计算蛋白质总能量。在这种方法中蛋白质的总能量由各个碎片计算得到的能量的线性组合得来。在所有碎片分子的计算中,通过简单的静电嵌入的方式来引入除去碎片分子以外的环境效应。通过对18个真实蛋白质体系在HF/6-31G*水平上的计算我们发现与传统意义上的全体系的量子化学的计算结果相比较,静电嵌入的方案相对于原来的推广的分子碎片共轭帽的方法把平均误差缩减到2.39kcal/mol。我们通过采用不同的两体截断半径的方法测试了几个含有几百原子具有三维结构的蛋白质体系,结果表明两体的相互作用矫正对于计算精度也有较大的贡献。EE-GMFCC的方法在MP2和DFT水平上的计算相对于全体系的量子计算的结果误差也都只有几个kcal/mol。而相对于全体系量子化学的计算对于含有几百个原子的蛋白质我们这种方法的计算效率有非常明显的提高,从而可以把量子化学的计算方法推广到任意大小尺寸的蛋白质分子中。
蛋白质内部电场影响着蛋白质的结构和功能,而外电场对蛋白质空间结构的完整性同样有着重要的影响,有实验表明微波场能够在不引起热效应的前提下改变蛋白质的三维构象。外电场对蛋白质动力学的非热效应在实验上引起了广泛的关注。但是就现在的状况而言实验上的数据还不能对这些效应作出原子层面上的解释,借助于分子动力学的模拟我们能够在原子尺度上揭示其微观机理。应用分子动力学模拟的方法,我们在不同的外电场值下对牛胰岛素蛋白质进行了一系列长达1个微妙的动力学模拟,在模拟中我们发现0.15V/nm的外电场并没有对胰岛素蛋白的二级结构产生较大的影响,而0.25V/nm及以上强度的外电场可以破坏胰岛素的二级结构,当外加电场强度在0.15～0.60V/nm时,蛋白质二级结构开始出现破坏所需要的模拟时间与外加电场的大小没有十分明确的相关性。一系列的结果显示在这个外加电场的范围内(0.15～0.60V/nm)蛋白质长时间暴露在外电场中的时间累积效应是导致蛋白质二级结构破坏的主要因素。当外加电场的值大于0.60V/nm时,外电场的强度对蛋白质内部氢键的寿命有着非常重要的影响。蛋白质内部氢键在外加电场为1.0V/nnm时出现了快速演化显示出外加电场能够加速蛋白质的折叠或者破坏蛋白质的结构。
Protein plays a crucial role in the activities of lives. The studies of protein structures and functions have considerable medicinal and industrial applications. The electric fields produced by the charged and polar groups of protein have been considered as the main source of molecular interaction and influence nearly every aspect of protein structures and functions. Many theoretical and experimental works have been carried out to study the electrostatic of protein. Vibrational Stark effect (VSE) spectroscopy has been widely used to study the change of protein dynamic behaviors. Linear Stark effect gives the direct relationship between spectrum and electric field. Utilizing some specific-group-containing probes that can deliver a unique Stark vibration to the specific site of interest in the protein it is practical to experimentally reveal the change of electrostatic properties in the matrix of protein. With the help of molecular dynamics (MD) simulations based on force field, computer simulation has emerged as a powerful tool to study properties of protein. Despite much success in applications of standard force fields such as CHARMM, Amber, and OPLS, there is a fundamental limitation due to the lack of electronic polarization effects. The charge models in this force field are mean-field-like and do not include polarization effect due to the specific protein environment The contribution of the polarization effect could be neglected in some cases, while more and more theoretical works indicate its importance in the calculation of protein properties. Molecular dynamics simulations were carried out to compute linear Stark shift in human aldose reductase (hALR2) using a recently developed polarized protein-specific charge (PPC) model derived from quantum-chemistry calculations so as to include polarization effect due to the specific protein environment. The same calculations but based on conventional nonpolarizable Amber force field were also carried out. Our study demonstrates that the Stark shifts calculated based on the PPC model are in much better agreement with the experimental measured data than widely used nonpolarizable force fields, indicating that the electronic polarization effect is important for the accurate prediction of changes in the electric field inside proteins and traditional force field has still room for improvement for capturing the electrostatics of protein.
Our study of internal electric field and stark spectroscopy of protein indicates that the classical force field model after correction by high-level quantum chemistry calculation would give better agree with experimental results. It is well kown that in the existing theoretical methods, the calculations based on quantum mechanics (QM) could give very accurate and reliable results. For small systems one can achieve the desired calculation at either the chemical or even the spectroscopic accuracy level using appropriate methods. Theoretical chemists hope to perform quantum mechanics (QM) calculations on large molecular systems. Recent years, although the development of computer make it possible to perform quantum mechanics (QM) calculations on molecule that contain hundreds or even thousands of atoms, atoms contained in the molecule studied in many scientific researches are far more than this number. For example, it is still a grand challenge in computational chemistry to apply conventional quantum mechanical methods for large protein systems. For this problem, a linear-scaling quantum mechanical method called Molecular Fractionation with Conjugate Caps (MFCC) has been proposed and it has been used in many aspects of calculations of protein properties. In order to calculate the energy of proteins more accurately a generalized molecular fractionation with conjugate caps/MM (GMFCC/MM) method is developed. Based on which an Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Cap (EE-GMFCC) method was developed for further improving the computing accuracy. In the EE-GMFCC scheme, the total energy of protein is calculated by taking a linear combination of the QM energy of each fragment. All the fragment calculations are embedded in a field of point charges representing the remaining protein environment. Calculations of energy using the EE-GMFCC approach at the HF/6-31G*level are carried out on18real three-dimensional proteins. The overall mean unsigned error of EE-GMFCC for these18proteins is2.39kcal/mol with reference to the full system HF/6-31G*energies. The EE-GMFCC approach is also tested for proteins at the density functional theory (DFT) and second order many-body perturbation theory (MP2) level, also showing only a few kcal/mol deviation from the corresponding full system result. For protein that contains hundreds of atoms, our EE-GMFCC method shows a distinct advantage in the consumption of computing time when compared with conventional full system calculation and makes it possible to perform quantum mechanics (QM) calculations on protein molecule of any size.
Internal electric field inside a protein affects its structure, function and dynamics, while external electric field has a same significant effect on conformational integrity of protein. Some experimental works has confirmed that microwave radiation could alter protein conformation without bulk heating. Currently, the nonthermal effect of external electric fields acting on proteins has attracted a lot of theoretical and experimental research interest. While for traditional experimental approaches, it is still difficult to provide the details at the atomic level. By means of molecular simulation method computer simulation could give more detailed interpretation for dynamic behavior of peptides or proteins in external electric field. We perform a series of molecular dynamics (MD) simulations up to one μs for bovine insulin monomer in different external electric field. Our results indicated that the secondary structure of insulin is kept intact under the action of external electric field strength below0.15V/nm, but disruption of secondary structure would be observed at0.25V/nm or higher electric field. The corralation is not obvious between the starting time of secondary structure disruption of insulin and the strength of the external electric field ranging between0.15to0.60V/nm. Long time MD simulation up to one μs shows that the cumulative effect of exposure time under the electric field is a major cause for the damage of insulin's secondary structure. In addition, the strength of the external electric field has a significant impact on the lifetime of hydrogen bonds when it is higher than0.60V/nm. The fast evolution of some hydrogen bonds of bovine insulin in the presence of1.0V/nm electric field suggests that different microwaves could either speed up protein folding or destroy the secondary structure of globular proteins deponding on the intensity of the external electric field.
引文
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