凝血酶适体DNA的动态NMR研究和Diagonal-Free COSY谱的应用
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摘要
在溶液中,结合金属离子形成四螺旋体结构的凝血酶适体DNA d(GGTTGGTGTGGTTGG)(TBA)能高亲和性地结合凝血酶从而抑制其活性,是非常有潜力的抗凝抗栓药物分子。本论文利用核磁共振(NMR)技术对凝血酶适体DNA进行了动力学研究,主要包括:一.运用NMR技术测量了凝血酶适体DNA分子中亚氨基质子交换速率,探讨了凝血酶适体DNA四螺旋体结构的解折叠机制;二.首次将凝聚态物理中的Vogel-Fulcher-Tammann(VFT)方程应用于生物分子领域并成功地解释了凝血酶适体DNA的动力学数据。此外,通过应用脉冲梯度场改进了一个脉冲序列,获得了只有交叉峰而没有对角峰的DF-COSY谱(Diagonal-Free COSY)。
在溶液中,凝血酶适体DNA能结合不同的金属离子形成椅式构象,但其结构不尽相同。利用NMR技术测量了在金属离子K+存在时凝血酶适体DNA四螺旋体结构中8个亚氨基质子的交换速率,这些动力学数据表明,与Sr2+-TBA复合物不同的是,K+-TBA复合物的TGT loop环的稳定性与两个TT loop环的稳定性相近,碱基T4、T13和T9在稳定TBA的四螺旋体结构中起着很大的作用。这些数据进一步支持了凝血酶适体DNA由椅式构象转变为自由单链的解折叠机制。然而,因结构的不同,K+-TBA复合物中四螺旋体结构解折叠的细节有其自身的特点。
凝聚态物理中的Vogel-Fulcher-Tammann(VFT)方程常常用来分析物质动态参数随温度的变化曲线偏离Arrhenius方程的现象。本研究首次运用VFT方程分析凝血酶适体DNA亚氨基质子的交换速率随温度的变化,这一过程的VFT方程可表示为:k ex= A exp[ ? ( E / R )/(T ? T0)],其中包含了一个温度常数T0。VFT方程能很好地拟合这些氢交换数据,而且VFT方程中的温度常数T0恰好是凝血酶适体DNA的变性温度。定量地讨论了VFT方程与Arrhenius方程的关系,并发现在合适的条件下VFT方程可以转化为Arrhenius方程。在成功分析凝血酶适体DNA氢交换数据的基础上,进一步把VFT方程应用到蛋白质分子中,在综合考虑生物分子氢交换机理后,将VFT方程和Arrhenius方程组合成新的拟合方程:l n ke x = C ? ( EV FT / R )/(T ? T0 ) ? ( Ea / R )/T,并用来拟合蛋白质的氢交换数据,结果表明新的拟合方程可以用来分析DNA、蛋白质等生物分子的氢交换。在某些特殊的条件下,新的拟合方程可以约化为VFT方程。
常规COSY谱是最有用的、使用也最广泛的2D谱之一,它能够提供有J耦合的核的拓扑结构信息。然而,靠近对角线的交叉峰常常掩埋在交叉峰色散信号的拖尾之中,因此丢失了交叉峰提供的信息。为此,引入脉冲梯度场来改进一个脉冲序列,获得了只有交叉峰而没有对角峰的DF-COSY谱(diagonal-free COSY,DF-COSY),保留了所有的交叉峰信息。DF-COSY谱可适用于生物大分子以及一些生物样品,如尿液、血液等等。
The thrombin binding aptamer d(GGTTGGTGTGGTTGG),with the short name TBA, is a 15-mer DNA, which specifically binds to the thrombin protein and inhibits thrombin-catalyzed fibrin during clot formation. Therefore, TBA could be used as a potential anticoagulant reagent for patients with thrombosis and embolism. TBA can form an intramolecular G-quadruplex in the presence of certain metal ions, with the ion fitted into the space in the quadruplex core. In this dissertation the dynamics of TBA in the presence of K+ have been studied. The exchange rates of the eight imino protons in the G-quadruplex structure are measured and the unfolding mechanism of TBA is discussed. At the same time, the Vogel-Fulcher-Tammann (VFT) equation can better fit the dynamic data of TBA, and this is the first time for VFT equation to be applied in biological kinetics. In addition, the diagonal-free COSY (DF-COSY) pulsed sequence is modified using pulse field gradient. When the DF-COSY pulse sequence was used, COSY-like spectrum without any diagonal peaks can be obtained.
TBA can form a chair-like conformation in the presence of various metal ions, however, their structures are different. The exchange rates of the eight imino protons of K+-TBA complex have been measured at different temperatures by NMR techniques. These dynamic data showed that the stability of the TGT loop is similar to the two TT loops in the K+-TBA complex, and that the bases T4, T13 and T9 play more important roles in keeping the hydrogen bond stable in the K+-TBA complex than in Sr2+-TBA complex. These data further support the unfolding mechanism of the transition of TBA from the G-quadruplex to random coil. However, the unfolding process of K+-TBA complex has its unique characteristics, because its structure is not exactly the same as others.
The Vogel-Fulcher-Tammann(VFT),which is widely applied in condensed mater physics for analysis of temperature-dependent dynamical data, is for the first time applied to fit the hydrogen exchange rates of TBA as a function of temperature. The VFT equation for the hydrogen exchange should read k ex= A exp[ ? ( E / R )/(T ? T0)], which contains a constant temperature T0. The VFT equation can better interpret these dynamic data, and the constant temperature T0 of the VFT equation happens to be the melting temperature of TBA. The relationship between the VFT equation and Arrhenius equation has been quantitatively discussed. Under suitable conditions the VFT equation can be reduced to the Arrhenius eqution. After successfully analyzing the data of TBA, the VFT equation was further applied in biological molecules. Considering the mechanism of the hydrogen exchange of the biological molecules, the VFT equation and the Arrhenius equation have combined to form a new equation, which can be written as: ln ke x = C ? ( EV FT / R) /(T ? T0 ) ? ( Ea / R) /T. The new equation can better interpret the data of the hydrogen exchange of the biological molecules, such as protein, DNA, RNA, etc. Under some condition, the Arrhenius term in the new equation could be left out and the new equation could be replaced by the VFT equation.
The general COSY spectrum is the most useful and widely applied in the studies of molecular structures, because the cross peaks of COSY spectrum can provide with the network information of the spin system which have J-coupling. However, many cross peaks, which are very close to diagonal, often overlap with the diagonal peaks which have dispersive line shape, and the information from cross peaks is lost. In order to avoid this, a pulse sequence was modified using pulse field gradint, and obtained diagonal-free COSY spectrum (DF-COSY), which is just COSY-like spectrum and has no diagonal peaks. Since the information of all cross peaks are retained. DF-COSY spectrum can be used as a quick tool for molecular studies, especially for large molecules and biological samples, such as protein, urea, blood serum, etc.
在溶液中,凝血酶适体DNA能结合不同的金属离子形成椅式构象,但其结构不尽相同。利用NMR技术测量了在金属离子K+存在时凝血酶适体DNA四螺旋体结构中8个亚氨基质子的交换速率,这些动力学数据表明,与Sr2+-TBA复合物不同的是,K+-TBA复合物的TGT loop环的稳定性与两个TT loop环的稳定性相近,碱基T4、T13和T9在稳定TBA的四螺旋体结构中起着很大的作用。这些数据进一步支持了凝血酶适体DNA由椅式构象转变为自由单链的解折叠机制。然而,因结构的不同,K+-TBA复合物中四螺旋体结构解折叠的细节有其自身的特点。
凝聚态物理中的Vogel-Fulcher-Tammann(VFT)方程常常用来分析物质动态参数随温度的变化曲线偏离Arrhenius方程的现象。本研究首次运用VFT方程分析凝血酶适体DNA亚氨基质子的交换速率随温度的变化,这一过程的VFT方程可表示为:k ex= A exp[ ? ( E / R )/(T ? T0)],其中包含了一个温度常数T0。VFT方程能很好地拟合这些氢交换数据,而且VFT方程中的温度常数T0恰好是凝血酶适体DNA的变性温度。定量地讨论了VFT方程与Arrhenius方程的关系,并发现在合适的条件下VFT方程可以转化为Arrhenius方程。在成功分析凝血酶适体DNA氢交换数据的基础上,进一步把VFT方程应用到蛋白质分子中,在综合考虑生物分子氢交换机理后,将VFT方程和Arrhenius方程组合成新的拟合方程:l n ke x = C ? ( EV FT / R )/(T ? T0 ) ? ( Ea / R )/T,并用来拟合蛋白质的氢交换数据,结果表明新的拟合方程可以用来分析DNA、蛋白质等生物分子的氢交换。在某些特殊的条件下,新的拟合方程可以约化为VFT方程。
常规COSY谱是最有用的、使用也最广泛的2D谱之一,它能够提供有J耦合的核的拓扑结构信息。然而,靠近对角线的交叉峰常常掩埋在交叉峰色散信号的拖尾之中,因此丢失了交叉峰提供的信息。为此,引入脉冲梯度场来改进一个脉冲序列,获得了只有交叉峰而没有对角峰的DF-COSY谱(diagonal-free COSY,DF-COSY),保留了所有的交叉峰信息。DF-COSY谱可适用于生物大分子以及一些生物样品,如尿液、血液等等。
The thrombin binding aptamer d(GGTTGGTGTGGTTGG),with the short name TBA, is a 15-mer DNA, which specifically binds to the thrombin protein and inhibits thrombin-catalyzed fibrin during clot formation. Therefore, TBA could be used as a potential anticoagulant reagent for patients with thrombosis and embolism. TBA can form an intramolecular G-quadruplex in the presence of certain metal ions, with the ion fitted into the space in the quadruplex core. In this dissertation the dynamics of TBA in the presence of K+ have been studied. The exchange rates of the eight imino protons in the G-quadruplex structure are measured and the unfolding mechanism of TBA is discussed. At the same time, the Vogel-Fulcher-Tammann (VFT) equation can better fit the dynamic data of TBA, and this is the first time for VFT equation to be applied in biological kinetics. In addition, the diagonal-free COSY (DF-COSY) pulsed sequence is modified using pulse field gradient. When the DF-COSY pulse sequence was used, COSY-like spectrum without any diagonal peaks can be obtained.
TBA can form a chair-like conformation in the presence of various metal ions, however, their structures are different. The exchange rates of the eight imino protons of K+-TBA complex have been measured at different temperatures by NMR techniques. These dynamic data showed that the stability of the TGT loop is similar to the two TT loops in the K+-TBA complex, and that the bases T4, T13 and T9 play more important roles in keeping the hydrogen bond stable in the K+-TBA complex than in Sr2+-TBA complex. These data further support the unfolding mechanism of the transition of TBA from the G-quadruplex to random coil. However, the unfolding process of K+-TBA complex has its unique characteristics, because its structure is not exactly the same as others.
The Vogel-Fulcher-Tammann(VFT),which is widely applied in condensed mater physics for analysis of temperature-dependent dynamical data, is for the first time applied to fit the hydrogen exchange rates of TBA as a function of temperature. The VFT equation for the hydrogen exchange should read k ex= A exp[ ? ( E / R )/(T ? T0)], which contains a constant temperature T0. The VFT equation can better interpret these dynamic data, and the constant temperature T0 of the VFT equation happens to be the melting temperature of TBA. The relationship between the VFT equation and Arrhenius equation has been quantitatively discussed. Under suitable conditions the VFT equation can be reduced to the Arrhenius eqution. After successfully analyzing the data of TBA, the VFT equation was further applied in biological molecules. Considering the mechanism of the hydrogen exchange of the biological molecules, the VFT equation and the Arrhenius equation have combined to form a new equation, which can be written as: ln ke x = C ? ( EV FT / R) /(T ? T0 ) ? ( Ea / R) /T. The new equation can better interpret the data of the hydrogen exchange of the biological molecules, such as protein, DNA, RNA, etc. Under some condition, the Arrhenius term in the new equation could be left out and the new equation could be replaced by the VFT equation.
The general COSY spectrum is the most useful and widely applied in the studies of molecular structures, because the cross peaks of COSY spectrum can provide with the network information of the spin system which have J-coupling. However, many cross peaks, which are very close to diagonal, often overlap with the diagonal peaks which have dispersive line shape, and the information from cross peaks is lost. In order to avoid this, a pulse sequence was modified using pulse field gradint, and obtained diagonal-free COSY spectrum (DF-COSY), which is just COSY-like spectrum and has no diagonal peaks. Since the information of all cross peaks are retained. DF-COSY spectrum can be used as a quick tool for molecular studies, especially for large molecules and biological samples, such as protein, urea, blood serum, etc.
引文
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