氨基酸与钙离子相互作用的理论研究
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摘要
在生物体中，钙离子有着重要的生理和生化功能，它通过与蛋白质等生物大分子相互作用，引起这些生物大分子构象的改变，在生物分子中产生活性中心或成为结构中心。从而参与到血液凝固、肌肉收缩、神经递质的释放等众多生理反应中，这些反应对所有的生命体来说都是不可或缺的。但蛋白质分子量较大，而氨基酸是构成生物体内蛋白质分子的基本单位，因此对氨基酸与钙离子相互作用的研究就显得尤为重要。通过这类研究我们可以确定在大生物分子中钙离子的最佳吸附位置，以及吸附强度。
(1)首先通过调研，我们设计了大量的氨基酸-钙离子络合物的初始结构，确保在这些结构尽可能形成较多的内部氢键。然后利用紧束缚（TB）方法对所有的结构进行初步优化，当得到能量较低的结构后，采用较高水平的微扰二阶近似法MP2/6-31G(d,p)对候选的低能结构进行进一步优化，从而确定其最稳定几何构型，并针对最稳定构型在同样的计算水平下进行了频率计算。又在MP2/6-311++G(d,p)水平下计算了稳定构型的单点能。我们发现，当侧链中不含有杂原子的脂肪族氨基酸与钙离子络合时，salt-bridge (SB)结构是最稳定的，但是当其他氨基酸与钙离子络合时，charge-solvated(CS)结构是最稳定的(除了谷氨酸、谷氨酰胺、精氨酸、赖氨酸以及色氨酸)。我们选取了谷氨酰胺(Gln)和天冬酰胺(Asn)与钙离子形成络合物的红外光谱进行了详细分析，并与相应的实验光谱进行对比，结果表明我们的理论结果与实验吻合的很好。
(2)很多的生物反应发生在有水环境中，水分子通过调解静电力场发挥了关键的作用。因此我们还对水溶液中所有20种α-种氨基酸与钙离子的相互作用进行了系统的理论研究。我们利用连续可极化溶剂模型(PCM)对氨基酸-钙离子络合物进行了几何构型优化、单点能计算以及NBO分析，设定介电常数为78.39，即溶剂为水。此外，我们在B3LYP/6-311++G(d,p)水平下应用TDDFT方法，计算了苯丙氨酸（Phe）、色氨酸（Trp）以及酪氨酸（Tyr）等芳香氨基酸与钙离子形成络合物的紫外吸收光谱。结果证明在水溶液中，所有20种氨基酸与钙离子络合的最稳定构型都是二配位的SB结构，在这种结构中Ca~(2+)同时与氨基酸主链羧基负离子中的两个O原子结合。通过对氨基酸-钙离子络合物的最稳定结构进行NBO分析，发现不足0.1e的电荷转移，这表明氨基酸与钙离子间主要为静电相互作用，它们之间的微弱键级也可以证明这一点。通过计算Phe-Ca~(2+)、Trp-Ca~(2+)以及Tyr Ca~(2+)三种络合物的紫外吸收光谱，我们可以发现钙离子的加入导致了Phe和Trp光谱的蓝移，但导致了Tyr的光谱发生了红移。
(3)相较于全溶剂化的研究，气相中水合团簇的研究可以更好地确定在第一水合层中，每个水分子的逐步加入所引起的改变。我们在MP2/6-31G(d,p)//MP2/6-311++G(d,p)水平下研究了三种水合团簇体系Gly-Ca~(2+)(H_2O)n、Thr-Ca~(2+)(H_2O)n和Phe-Ca~(2+)(H_2O)n，确定了在水合过程中它们结构的改变、稳定性顺序的变化、电荷转移以及最稳定结构的红外光谱。结果表明，不论是对于芳香氨基酸-钙离子络合物的水合团簇Phe-Ca~(2+)(H_2O)n，还是对于脂肪族氨基酸-钙离子络合物的水合团簇Gly-Ca~(2+)(H_2O)n、Thr-Ca~(2+)(H_2O)n，当钙离子周围第一水合层达到八配位时，这种结构的结合能最低，稳定性最好。并且上述构型中的键长与键角都十分接近全溶剂化条件下优化的结果。水分子对络合的稳定性顺序产生了很大影响。气相中它们的稳定性顺序为Phe-Ca~(2+)> Thr-Ca~(2+)> Gly-Ca~(2+)，而形成水合团簇后稳定顺序则变为Thr-Ca~(2+)(H_2O)n> Phe-Ca~(2+)(H_2O)n>Gly-Ca~(2+)(H_2O)n。
In living organisms, the complexation of metal cations to amino acid is one ofthe most important processes, especially for Ca~(2+). The binding of amino acid with~(2+)is involved in a large number of different physiological reactions taking place inall forms of life (ie., flagella movement, intracellular signaling, the complementsystem, blood coagulation, muscle contraction, and neurotransmitter release insynapses). The knowledge of the binding interactions of the Ca~(2+)and amino acidsystems is important to predict where the calcium ion attachment occurs preferentiallyin a macromolecule and how strong the binding at a particular site.
(1) By surveying the possible permutations of metal chelation and hydrogenbonding, a number of initial structures for the calcium–amino acids complexes, eachof them with maximum number of hydrogen bonds, were generated. All the structureswere initially optimized with the Tight-Binding method, and then optimized byhigher-level MP2/6-31G(d,p) method. For the gas-phase low-energy structures, thesingle-point energies were calculated at MP2/6-311++G(d,p). All the calculations atthe MP2level were performed using the Gaussian03package. We showed that in thegas phase the salt-bridge structure is the most preferred Ca~(2+)binding motif foraliphatic amino acids with no heteroatom in the side chain, while for other aminoacids they have charge-solvated structure except for glutamic acid, glutamine,arginine, lysine and tryptophane. IR spectra of Gln-Ca~(2+)and Asn-Ca~(2+)complexeswere calculated and compared well with the available experiments.
(2) Majority of biological processes occurs in aqueous environments and water molecules play a central role by moderating electrostatic forces. In our present study,NBO analysis, geometry optimizations and single point energies were also conductedin the PCM model at the same level using the Gaussian03package with a dielectricconstant of78.39(water). In addition, the vertical excitation energies were computedusing the time-dependent density functional theory (TDDFT) method at theB3LYP/6-311++G(d,p) level. The bidentate salt-bridge structure was determined tobe the most favorable for all the twenty kinds of amino acids by chelation of Ca~(2+)toboth oxygen atoms of the negatively carboxylate group in the backbone. The muchlower magnitude of charge transfer contribution (about0.1e) in calcium ioncoordinated complexes suggests that the interactions in these complexes areelectrostatic, which can also be shown by the very tiny wiberg bond indices. Thevertical excitation energies of the calcium ion-aromatic amino acid compounds havebeen discussed, the blue-shifts have been found for Phe-Ca~(2+)and Trp-Ca~(2+), but thepeculiar red-shift has been found for Tyr Ca~(2+), possibly because the p-conjugatedegree of hydroxyl with aromatic ring is enhanced by NH3+above the ring.
(3) Compared with the full solution studies, the gas-phase studies of hydratedclusters can provide much detailed insights into thermochemical and structuralchanges with the stepwise addition of water molecules in the first shell of biologicalmolecules. The structural changes triggered by hydration and the binding energies ofhydrated composites were studied for the three hydrated molecular clusters includingGly-Ca~(2+)(H_2O)n, Thr-Ca~(2+)(H_2O)nand Phe-Ca~(2+)(H_2O)nat the MP2/6-311++G(d,p)level. In the investigation on the hydration of all the three systems, the clusters withthe first hydration shell displaying an octacoordination configuration around calciumion are found to be most competitive in binding energy no matter for aromatic aminoacid clusters Phe-Ca~(2+)(H_2O)nor the aliphatic amino acid clusters Gly-Ca~(2+)(H_2O)nandThr-Ca~(2+)(H_2O)n. The bond lengths and bond angles of the above-mentioned structuresare close to the corresponding values from the PCM calculations. Water moleculeshave a considerable effect on the relative stability of individual complexes, withbinding energy decreasing in the order Phe-Ca~(2+)> Thr-Ca~(2+)> Gly-Ca~(2+)without waterand Thr-Ca~(2+)(H_2O)n> Phe-Ca~(2+)(H_2O)n> Gly-Ca~(2+)(H_2O)nupon hydration, respectively. Owning to the different nature of side chain of Gly, Thr and Phe, variousintermolecular hydrogen bonds appear in the three hydrated composites, which giverise to different vibrational absorption peaks.
(1)首先通过调研，我们设计了大量的氨基酸-钙离子络合物的初始结构，确保在这些结构尽可能形成较多的内部氢键。然后利用紧束缚（TB）方法对所有的结构进行初步优化，当得到能量较低的结构后，采用较高水平的微扰二阶近似法MP2/6-31G(d,p)对候选的低能结构进行进一步优化，从而确定其最稳定几何构型，并针对最稳定构型在同样的计算水平下进行了频率计算。又在MP2/6-311++G(d,p)水平下计算了稳定构型的单点能。我们发现，当侧链中不含有杂原子的脂肪族氨基酸与钙离子络合时，salt-bridge (SB)结构是最稳定的，但是当其他氨基酸与钙离子络合时，charge-solvated(CS)结构是最稳定的(除了谷氨酸、谷氨酰胺、精氨酸、赖氨酸以及色氨酸)。我们选取了谷氨酰胺(Gln)和天冬酰胺(Asn)与钙离子形成络合物的红外光谱进行了详细分析，并与相应的实验光谱进行对比，结果表明我们的理论结果与实验吻合的很好。
(2)很多的生物反应发生在有水环境中，水分子通过调解静电力场发挥了关键的作用。因此我们还对水溶液中所有20种α-种氨基酸与钙离子的相互作用进行了系统的理论研究。我们利用连续可极化溶剂模型(PCM)对氨基酸-钙离子络合物进行了几何构型优化、单点能计算以及NBO分析，设定介电常数为78.39，即溶剂为水。此外，我们在B3LYP/6-311++G(d,p)水平下应用TDDFT方法，计算了苯丙氨酸（Phe）、色氨酸（Trp）以及酪氨酸（Tyr）等芳香氨基酸与钙离子形成络合物的紫外吸收光谱。结果证明在水溶液中，所有20种氨基酸与钙离子络合的最稳定构型都是二配位的SB结构，在这种结构中Ca~(2+)同时与氨基酸主链羧基负离子中的两个O原子结合。通过对氨基酸-钙离子络合物的最稳定结构进行NBO分析，发现不足0.1e的电荷转移，这表明氨基酸与钙离子间主要为静电相互作用，它们之间的微弱键级也可以证明这一点。通过计算Phe-Ca~(2+)、Trp-Ca~(2+)以及Tyr Ca~(2+)三种络合物的紫外吸收光谱，我们可以发现钙离子的加入导致了Phe和Trp光谱的蓝移，但导致了Tyr的光谱发生了红移。
(3)相较于全溶剂化的研究，气相中水合团簇的研究可以更好地确定在第一水合层中，每个水分子的逐步加入所引起的改变。我们在MP2/6-31G(d,p)//MP2/6-311++G(d,p)水平下研究了三种水合团簇体系Gly-Ca~(2+)(H_2O)n、Thr-Ca~(2+)(H_2O)n和Phe-Ca~(2+)(H_2O)n，确定了在水合过程中它们结构的改变、稳定性顺序的变化、电荷转移以及最稳定结构的红外光谱。结果表明，不论是对于芳香氨基酸-钙离子络合物的水合团簇Phe-Ca~(2+)(H_2O)n，还是对于脂肪族氨基酸-钙离子络合物的水合团簇Gly-Ca~(2+)(H_2O)n、Thr-Ca~(2+)(H_2O)n，当钙离子周围第一水合层达到八配位时，这种结构的结合能最低，稳定性最好。并且上述构型中的键长与键角都十分接近全溶剂化条件下优化的结果。水分子对络合的稳定性顺序产生了很大影响。气相中它们的稳定性顺序为Phe-Ca~(2+)> Thr-Ca~(2+)> Gly-Ca~(2+)，而形成水合团簇后稳定顺序则变为Thr-Ca~(2+)(H_2O)n> Phe-Ca~(2+)(H_2O)n>Gly-Ca~(2+)(H_2O)n。
In living organisms, the complexation of metal cations to amino acid is one ofthe most important processes, especially for Ca~(2+). The binding of amino acid with~(2+)is involved in a large number of different physiological reactions taking place inall forms of life (ie., flagella movement, intracellular signaling, the complementsystem, blood coagulation, muscle contraction, and neurotransmitter release insynapses). The knowledge of the binding interactions of the Ca~(2+)and amino acidsystems is important to predict where the calcium ion attachment occurs preferentiallyin a macromolecule and how strong the binding at a particular site.
(1) By surveying the possible permutations of metal chelation and hydrogenbonding, a number of initial structures for the calcium–amino acids complexes, eachof them with maximum number of hydrogen bonds, were generated. All the structureswere initially optimized with the Tight-Binding method, and then optimized byhigher-level MP2/6-31G(d,p) method. For the gas-phase low-energy structures, thesingle-point energies were calculated at MP2/6-311++G(d,p). All the calculations atthe MP2level were performed using the Gaussian03package. We showed that in thegas phase the salt-bridge structure is the most preferred Ca~(2+)binding motif foraliphatic amino acids with no heteroatom in the side chain, while for other aminoacids they have charge-solvated structure except for glutamic acid, glutamine,arginine, lysine and tryptophane. IR spectra of Gln-Ca~(2+)and Asn-Ca~(2+)complexeswere calculated and compared well with the available experiments.
(2) Majority of biological processes occurs in aqueous environments and water molecules play a central role by moderating electrostatic forces. In our present study,NBO analysis, geometry optimizations and single point energies were also conductedin the PCM model at the same level using the Gaussian03package with a dielectricconstant of78.39(water). In addition, the vertical excitation energies were computedusing the time-dependent density functional theory (TDDFT) method at theB3LYP/6-311++G(d,p) level. The bidentate salt-bridge structure was determined tobe the most favorable for all the twenty kinds of amino acids by chelation of Ca~(2+)toboth oxygen atoms of the negatively carboxylate group in the backbone. The muchlower magnitude of charge transfer contribution (about0.1e) in calcium ioncoordinated complexes suggests that the interactions in these complexes areelectrostatic, which can also be shown by the very tiny wiberg bond indices. Thevertical excitation energies of the calcium ion-aromatic amino acid compounds havebeen discussed, the blue-shifts have been found for Phe-Ca~(2+)and Trp-Ca~(2+), but thepeculiar red-shift has been found for Tyr Ca~(2+), possibly because the p-conjugatedegree of hydroxyl with aromatic ring is enhanced by NH3+above the ring.
(3) Compared with the full solution studies, the gas-phase studies of hydratedclusters can provide much detailed insights into thermochemical and structuralchanges with the stepwise addition of water molecules in the first shell of biologicalmolecules. The structural changes triggered by hydration and the binding energies ofhydrated composites were studied for the three hydrated molecular clusters includingGly-Ca~(2+)(H_2O)n, Thr-Ca~(2+)(H_2O)nand Phe-Ca~(2+)(H_2O)nat the MP2/6-311++G(d,p)level. In the investigation on the hydration of all the three systems, the clusters withthe first hydration shell displaying an octacoordination configuration around calciumion are found to be most competitive in binding energy no matter for aromatic aminoacid clusters Phe-Ca~(2+)(H_2O)nor the aliphatic amino acid clusters Gly-Ca~(2+)(H_2O)nandThr-Ca~(2+)(H_2O)n. The bond lengths and bond angles of the above-mentioned structuresare close to the corresponding values from the PCM calculations. Water moleculeshave a considerable effect on the relative stability of individual complexes, withbinding energy decreasing in the order Phe-Ca~(2+)> Thr-Ca~(2+)> Gly-Ca~(2+)without waterand Thr-Ca~(2+)(H_2O)n> Phe-Ca~(2+)(H_2O)n> Gly-Ca~(2+)(H_2O)nupon hydration, respectively. Owning to the different nature of side chain of Gly, Thr and Phe, variousintermolecular hydrogen bonds appear in the three hydrated composites, which giverise to different vibrational absorption peaks.
引文
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