金属离子与DNA碱基对相互作用的理论研究
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摘要
核酸是最重要的生物大分子,是生物储存和传递信息的载体。金属离子不仅在核酸的生物合成、构象维持、功能发挥与调控等方面起着重要的作用,而且金属及其配合物与核酸相互作用还是开发抗癌药物、制造光谱探针及反应性探针、以及发展以DNA为基础的金属纳米器件技术的基础。因而,深入研究金属与核酸相互作用的化学本质成为了核酸研究的前沿课题之一。
本文以DNA为研究对象,采用高级别量子化学计算程序并结合化学理论基础知识,对金属离子与DNA碱基对相互作用中存在的某些实验现象及问题进行了理论研究,并讨论了这种相互作用在相关生命现象的意义,主要内容有:
1.从不同金属离子( Mg~(2+), Mn~(2+), Ni~(2+), Zn~(2+) )在GC Watson-Crick碱基对和GG r-Hoogsteen碱基对中鸟嘌呤碱基上金属离子最佳成键位点N7位成键的研究出发,采用密度泛函理论方法、高级电子相关方法以及AIM和NBO分析方法,较为深入探讨了这些金属离子存在下双螺旋DNA熔化温度Tm差异的根源。从金属离子作用前后碱基对结构、拓扑分析、电荷分布、相互作用能以及碱基对间氢键的差异、碱基对在不同金属离子作用前后形成碱基离子对能量的不同、不同金属离子在碱基骨架变化后配位数变化所需的能量补偿不同等方面的比较研究,结果表明决定不同金属离子存在下双螺旋DNA熔化温度Tm的差异主要是由于不同金属离子在碱基骨架变化后引起的配位数变化所需能量补偿不同所致。
2.采用密度泛函理论方法、高级电子相关方法以及AIM和NBO分析方法,比较了不同金属离子(Na+、Mg~(2+)和Zn~(2+))在DNA的AT Watson-Crick碱基对大沟金属最佳位点N7位和小沟金属最佳位点N3位上配位后碱基的几何结构、电荷分布以及碱基对间氢键能的差异,讨论了DNA螺旋结构碱基在大沟和小沟中不同金属位点作用后碱基间氢键作用的差异。结果显示与孤立AT碱基对中氢键比较,水合金属离子配位于A( N3 )位与配位于A( N7 )位时对AT碱基对氢键的影响明显不同。水合金属离子与AT碱基对的A( N3 )位作用能够有效地增加碱基对间氢键的强度,因而处于DNA小沟位置中碱基A的N3位也可能是一个有潜力的金属抗癌药物化学疗法成键位点。
3.采用密度泛函理论方法、高级电子相关方法以及AIM分析方法,从几何结构、相互作用能、临界点的电荷密度以及作用的净电荷等方面讨论了不同金属离子对G4聚合物结构稳定性的影响及G4聚合物对金属离子的选择性。通过在B3LYP/SDD以及MPWB95/6-31+G(d,p)和MP2/6-31G理论计算级别下,计算了金属离子在G4-MZ+-G4复合物(MZ+=Li~+、Na~+、K~+、Rb~+、Cs~+、Mg~(2+)、Ca~(2+)、Sr~(2+)、Ba~(2+))中分子间相互作用能的大小顺序,结果发现即使是采用水合能进行校正与否,都与实验结果相矛盾。对于G4-M~+-G4复合物,AIM分析表明在O-M~+相互作用临界点上电荷密度值ρb的大小顺序为K~+ > Na~+ > Li~+,也就意味着在G4-M~+-G4复合物中K~+比Na~+和Li~+要稳定,且与稳定性实验结果K~+ > Na~+ >> Li~+相一致,说明G4-MZ+-G4复合物对金属离子的选择性主要取决于“最佳适合尺寸”而不是相对水合自由能。
4.采用B3LYP/6-31++G(d,p)理论方法,就碱基对(GC Watson-Crick碱基对、GG r-Hoogsteen碱基对及AT Watson-Crick碱基对)在水合金属离子作用前后的静电势变化进行了计算。从碱基对的静电势可知,金属正离子与碱基对可在多个位点成键。金属离子在碱基对负电势位点成键后,基本观测不到碱基对的负电势区,而正电势区扩大且正电势值增加。由此可推测金属离子作用碱基对前后其静电势的变化必然会改变碱基周围的微环境,从而引起相应结构、动力学与相关性质的改变。5.采用B3LYP/6-31++G(d,p)理论方法以及AIM理论分析,探讨了谷氨酸离子在蛋白质酪氨酸(Yz)硝化中的作用。就谷氨酸离子的存在对Yz性质的影响、对Yz·的形成机理以及谷氨酸离子如何引导·NO_2至Yz·附近以形成NT后可能的质子迁移机理等方面进行了研究。结果表明,Yz残基附近Glu离子存在能通过它与Yz残基形成氢键显著地影响Yz残基的电子性质;同时,Glu离子在Yz残基附近存在有助于形成稳定的中间复合物M1,并有利于引导硝化试剂到达Yz·的-OH邻位C原子上,这些作用主要依赖于N_(17)…O_(15)相互作用(此作用与·NO_2平面垂直)。此外,Glu残基在Yz残基附近的存在还有助于复合物M2通过双质子协同迁移得到更稳定的复合物M3,其中Glu离子作为质子开关催化了质子迁移,从理论上证实了实验结果,即在Yz的附近存在负价态残基,是决定硝化位点的关键。
As is well-known, genetic information is stored and duplicated in nucleic acids which can thus be considered as one of the most important molecules in our life. Metal cations have significant influence on the structure, dynamics and function of nucleic acids. The interaction between metal ions or metal ion adducts with the nucleic acid bases is the base of discovery of antitumor drugs, make of spectrum probes and reaction probes, and development of nanometer scale DNA-based device technology. Thus, it is fundamentally important to understand the chemical nature of interactions between metal cations with nucleic acid bases.
In the present paper, we investigated the interaction between metal cations with DNA bases and DNA base pairs using the high-level quantum chemical computation methods. The main results are as follows:
1. The different affinity of the studied metal cations (Mg~(2+), Zn~(2+), Mn~(2+), and Ni~(2+)) for the N7 position of guanine in GC WC or GG rH base pair has been quantitatively characterized using density functional theory (DFT), highly correlated treatments, AIM analysis, and NBO analysis to explore the origin of difference of the melting temperature of DNA when presenting different metal cations. From comparing the difference of the molecular structures, topological analysis, NBO analysis, the total interaction energies, and the hydrogen-bond interactions in base pairs between isolated nucleobases and metalated nucleobases; the energy differences of formation of the ion-pair between isolated nucleobases and metalated nucleobases; the difference of energy penalty for changing the coordination number of different metal cations–GC complexes with one or two water molecules in the second shell, we propose that the energy penalty for changing the coordination number of metal cation-necleobases complex seems to be dominant to explain the difference of the melting temperature of DNA when presenting different metal cations.
2. We have numerically compared the changes of the hydrogen bonds in the AT base pair upon the hydrated metal cations(Na~+, Mg~(2+), and Zn~(2+))binding the adenine-N3 of AT or the adenine-N7 of AT base pair, using the electron density topological analysis and NBO analysis at B3LYP/6-31++G(d,p) level of theory, to discuss the differences of the hydrogen bonds when presenting the hydrated metal cations binding to major grooves or minor grooves of DNA. In comparison with the hydrogen bonds in the isolated AT case pair, the changes of the hydrogen bonds when presenting the hydrated metal cations at A-N3 position are different from those when presenting the hydrated metal cations at A-N7 position. Due to the much stronger hydrogen bond interaction when binding the hydrated metal cations to the N3 of adenine in AT, it is possible that the N3 position of adenine in minor groove of DNA can also be a potential target for platinum-based chemotherapy.
3. We have quantified the binding energies between cations and G tetrad in G4-M~(Z+)-G4 (inter) complexes (M~(Z+)=Li~+, Na~+, K~+, Rb+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+) using DFT, highly correlated treatments, AIM analysis, and NBO analysis, to discuss the effect when presenting metal ions both in stabilization and destabilization of G-tetrad complexes and the origin of metal ions selectivity. On the basis of theoretical results, we found the stability order of the metal cations in the G4-M~+-G4 complexes obtained from supermolecule calculation method, whether it is corrected by the hydration energy or not, obviously conflicts with the experimental observations. According the topological analysis and relaxation energy sequence of G4-M~+-G4 complexes (M~+=Li~+, Na~+, and K~+), we proposed that the ion selectivity in the G tetraplexes is still dominated by the optimal fit of the cations not by relative energies of hydration.
4. To gain insight into the effect of the electron density redistribution induced upon cation binding on the interaction between bases, we have compared the molecular electrostatic potential (ESP) computed by B3LYP/6-31++G(d,p) between GC Watson-Crick, GG r-Hoogsteen, and AT Watson-Crick base pairs with the counterpart metalated base pairs. According the ESP, there are many negative ESP sites around the isolated base pair where tend to bind with metal cations. After the hydrated metal cations binding with the N7 position of guanine in GC WC or GG rH base pair and the adenine-N7 of AT base pair, there are significant changes in ESP that the negative ESP charges are disappeared whereas the positive ESP charges are increased. It is worth noting that the changes of ESP in base pairing with hydrated metal cations may affect subtle environment of base pair and influence the structure, dynamics and function of nucleic acids.
5. The influence of the local environment (water, histidine, or glutamate anion) on the properties of tyrosine and the process of 3-nitrotyrosine formation with the presence of glutamate residue have been investigated in detail at the B3LYP/6- 31++G(d,p) theory level. The results show that the presence of glutamate anion within a few angstroms from the tyrosine residue (a) may help the tyrosine more likely to ionize and more easily to form radical by acting as a proton acceptor; (b) may stabilize the intermolecular complex M1 and direct the nitro reagent to the two equivalent ortho carbons of the aromatic ring of tyrosine residues mainly by the N…O interaction whose geometry is found to be vertical with the plane of nitro due to the electrostatic interaction between N atom of·NO_2 and O atom of glutamate anion; (c) may assist to form the more stable complex M3 through the concerted double proton transfer, in which the glutamate residue acts as a proton switch to catalyze the proton transfer.
本文以DNA为研究对象,采用高级别量子化学计算程序并结合化学理论基础知识,对金属离子与DNA碱基对相互作用中存在的某些实验现象及问题进行了理论研究,并讨论了这种相互作用在相关生命现象的意义,主要内容有:
1.从不同金属离子( Mg~(2+), Mn~(2+), Ni~(2+), Zn~(2+) )在GC Watson-Crick碱基对和GG r-Hoogsteen碱基对中鸟嘌呤碱基上金属离子最佳成键位点N7位成键的研究出发,采用密度泛函理论方法、高级电子相关方法以及AIM和NBO分析方法,较为深入探讨了这些金属离子存在下双螺旋DNA熔化温度Tm差异的根源。从金属离子作用前后碱基对结构、拓扑分析、电荷分布、相互作用能以及碱基对间氢键的差异、碱基对在不同金属离子作用前后形成碱基离子对能量的不同、不同金属离子在碱基骨架变化后配位数变化所需的能量补偿不同等方面的比较研究,结果表明决定不同金属离子存在下双螺旋DNA熔化温度Tm的差异主要是由于不同金属离子在碱基骨架变化后引起的配位数变化所需能量补偿不同所致。
2.采用密度泛函理论方法、高级电子相关方法以及AIM和NBO分析方法,比较了不同金属离子(Na+、Mg~(2+)和Zn~(2+))在DNA的AT Watson-Crick碱基对大沟金属最佳位点N7位和小沟金属最佳位点N3位上配位后碱基的几何结构、电荷分布以及碱基对间氢键能的差异,讨论了DNA螺旋结构碱基在大沟和小沟中不同金属位点作用后碱基间氢键作用的差异。结果显示与孤立AT碱基对中氢键比较,水合金属离子配位于A( N3 )位与配位于A( N7 )位时对AT碱基对氢键的影响明显不同。水合金属离子与AT碱基对的A( N3 )位作用能够有效地增加碱基对间氢键的强度,因而处于DNA小沟位置中碱基A的N3位也可能是一个有潜力的金属抗癌药物化学疗法成键位点。
3.采用密度泛函理论方法、高级电子相关方法以及AIM分析方法,从几何结构、相互作用能、临界点的电荷密度以及作用的净电荷等方面讨论了不同金属离子对G4聚合物结构稳定性的影响及G4聚合物对金属离子的选择性。通过在B3LYP/SDD以及MPWB95/6-31+G(d,p)和MP2/6-31G理论计算级别下,计算了金属离子在G4-MZ+-G4复合物(MZ+=Li~+、Na~+、K~+、Rb~+、Cs~+、Mg~(2+)、Ca~(2+)、Sr~(2+)、Ba~(2+))中分子间相互作用能的大小顺序,结果发现即使是采用水合能进行校正与否,都与实验结果相矛盾。对于G4-M~+-G4复合物,AIM分析表明在O-M~+相互作用临界点上电荷密度值ρb的大小顺序为K~+ > Na~+ > Li~+,也就意味着在G4-M~+-G4复合物中K~+比Na~+和Li~+要稳定,且与稳定性实验结果K~+ > Na~+ >> Li~+相一致,说明G4-MZ+-G4复合物对金属离子的选择性主要取决于“最佳适合尺寸”而不是相对水合自由能。
4.采用B3LYP/6-31++G(d,p)理论方法,就碱基对(GC Watson-Crick碱基对、GG r-Hoogsteen碱基对及AT Watson-Crick碱基对)在水合金属离子作用前后的静电势变化进行了计算。从碱基对的静电势可知,金属正离子与碱基对可在多个位点成键。金属离子在碱基对负电势位点成键后,基本观测不到碱基对的负电势区,而正电势区扩大且正电势值增加。由此可推测金属离子作用碱基对前后其静电势的变化必然会改变碱基周围的微环境,从而引起相应结构、动力学与相关性质的改变。5.采用B3LYP/6-31++G(d,p)理论方法以及AIM理论分析,探讨了谷氨酸离子在蛋白质酪氨酸(Yz)硝化中的作用。就谷氨酸离子的存在对Yz性质的影响、对Yz·的形成机理以及谷氨酸离子如何引导·NO_2至Yz·附近以形成NT后可能的质子迁移机理等方面进行了研究。结果表明,Yz残基附近Glu离子存在能通过它与Yz残基形成氢键显著地影响Yz残基的电子性质;同时,Glu离子在Yz残基附近存在有助于形成稳定的中间复合物M1,并有利于引导硝化试剂到达Yz·的-OH邻位C原子上,这些作用主要依赖于N_(17)…O_(15)相互作用(此作用与·NO_2平面垂直)。此外,Glu残基在Yz残基附近的存在还有助于复合物M2通过双质子协同迁移得到更稳定的复合物M3,其中Glu离子作为质子开关催化了质子迁移,从理论上证实了实验结果,即在Yz的附近存在负价态残基,是决定硝化位点的关键。
As is well-known, genetic information is stored and duplicated in nucleic acids which can thus be considered as one of the most important molecules in our life. Metal cations have significant influence on the structure, dynamics and function of nucleic acids. The interaction between metal ions or metal ion adducts with the nucleic acid bases is the base of discovery of antitumor drugs, make of spectrum probes and reaction probes, and development of nanometer scale DNA-based device technology. Thus, it is fundamentally important to understand the chemical nature of interactions between metal cations with nucleic acid bases.
In the present paper, we investigated the interaction between metal cations with DNA bases and DNA base pairs using the high-level quantum chemical computation methods. The main results are as follows:
1. The different affinity of the studied metal cations (Mg~(2+), Zn~(2+), Mn~(2+), and Ni~(2+)) for the N7 position of guanine in GC WC or GG rH base pair has been quantitatively characterized using density functional theory (DFT), highly correlated treatments, AIM analysis, and NBO analysis to explore the origin of difference of the melting temperature of DNA when presenting different metal cations. From comparing the difference of the molecular structures, topological analysis, NBO analysis, the total interaction energies, and the hydrogen-bond interactions in base pairs between isolated nucleobases and metalated nucleobases; the energy differences of formation of the ion-pair between isolated nucleobases and metalated nucleobases; the difference of energy penalty for changing the coordination number of different metal cations–GC complexes with one or two water molecules in the second shell, we propose that the energy penalty for changing the coordination number of metal cation-necleobases complex seems to be dominant to explain the difference of the melting temperature of DNA when presenting different metal cations.
2. We have numerically compared the changes of the hydrogen bonds in the AT base pair upon the hydrated metal cations(Na~+, Mg~(2+), and Zn~(2+))binding the adenine-N3 of AT or the adenine-N7 of AT base pair, using the electron density topological analysis and NBO analysis at B3LYP/6-31++G(d,p) level of theory, to discuss the differences of the hydrogen bonds when presenting the hydrated metal cations binding to major grooves or minor grooves of DNA. In comparison with the hydrogen bonds in the isolated AT case pair, the changes of the hydrogen bonds when presenting the hydrated metal cations at A-N3 position are different from those when presenting the hydrated metal cations at A-N7 position. Due to the much stronger hydrogen bond interaction when binding the hydrated metal cations to the N3 of adenine in AT, it is possible that the N3 position of adenine in minor groove of DNA can also be a potential target for platinum-based chemotherapy.
3. We have quantified the binding energies between cations and G tetrad in G4-M~(Z+)-G4 (inter) complexes (M~(Z+)=Li~+, Na~+, K~+, Rb+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+) using DFT, highly correlated treatments, AIM analysis, and NBO analysis, to discuss the effect when presenting metal ions both in stabilization and destabilization of G-tetrad complexes and the origin of metal ions selectivity. On the basis of theoretical results, we found the stability order of the metal cations in the G4-M~+-G4 complexes obtained from supermolecule calculation method, whether it is corrected by the hydration energy or not, obviously conflicts with the experimental observations. According the topological analysis and relaxation energy sequence of G4-M~+-G4 complexes (M~+=Li~+, Na~+, and K~+), we proposed that the ion selectivity in the G tetraplexes is still dominated by the optimal fit of the cations not by relative energies of hydration.
4. To gain insight into the effect of the electron density redistribution induced upon cation binding on the interaction between bases, we have compared the molecular electrostatic potential (ESP) computed by B3LYP/6-31++G(d,p) between GC Watson-Crick, GG r-Hoogsteen, and AT Watson-Crick base pairs with the counterpart metalated base pairs. According the ESP, there are many negative ESP sites around the isolated base pair where tend to bind with metal cations. After the hydrated metal cations binding with the N7 position of guanine in GC WC or GG rH base pair and the adenine-N7 of AT base pair, there are significant changes in ESP that the negative ESP charges are disappeared whereas the positive ESP charges are increased. It is worth noting that the changes of ESP in base pairing with hydrated metal cations may affect subtle environment of base pair and influence the structure, dynamics and function of nucleic acids.
5. The influence of the local environment (water, histidine, or glutamate anion) on the properties of tyrosine and the process of 3-nitrotyrosine formation with the presence of glutamate residue have been investigated in detail at the B3LYP/6- 31++G(d,p) theory level. The results show that the presence of glutamate anion within a few angstroms from the tyrosine residue (a) may help the tyrosine more likely to ionize and more easily to form radical by acting as a proton acceptor; (b) may stabilize the intermolecular complex M1 and direct the nitro reagent to the two equivalent ortho carbons of the aromatic ring of tyrosine residues mainly by the N…O interaction whose geometry is found to be vertical with the plane of nitro due to the electrostatic interaction between N atom of·NO_2 and O atom of glutamate anion; (c) may assist to form the more stable complex M3 through the concerted double proton transfer, in which the glutamate residue acts as a proton switch to catalyze the proton transfer.
引文
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