光谱与密度泛函研究金属硫蛋白的结构
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摘要
金属硫蛋白(metallothionein,简称为MT),是一类具有高半胱氨酸含量(占总氨基酸含量的30%)、无芳香氨基酸、广泛存在于生物体内的低分子量金属蛋白。MT具有解重金属毒性、清除自由基和烷基化试剂的作用,在金属药物的药理研究中也具有重要地位。MT的结构研究一直是生命科学领域的研究热点。基于重金属易与MT结合,本论文研究了硫蛋白结合三种重要的金属离子——Bi3+、Pb2+和As3+的结构特性,主要结果包括：
(1)采用基于密度泛函理论(Density functional theory)的B3LYP、 mPW1PW、OLYP和TPSSh方法,以及从头算(ab initio)的HF方法,对含主族金属铋、锑和砷的巯基小分子化合物M(SC6H5)3(M=Bi, Sb,As)的几何结构、振动频率和电子吸收光谱等进行了研究,并与文献报道的数据做了比较,确认适宜于各金属巯基化合物的最优化结构计算方法。结果显示：对于Sb(SC6H5)3和As(SC6H5)3, mPW1PW的计算精度明显高于其它四种计算方法；而对于复合物Bi(SC6H5)3, B3LYP方法能给出更高的计算精度。确定的最优计算方法将用于apo-MT结合Bi3+、Pb2+及As3+的结构研究。
(2)采用紫外吸收光谱和CD光谱,研究了Bi3+结合脱金属硫蛋白(apo-MT)的反应过程及最终产物。确认产物中Bi3+和apo-MT的计量比为7：1,即形成Bi7-MT。CD光谱结果显示Bi7-MT具有不同于Zn7-MT和Cd7-MT的蛋白质二级结构。采用活性位点模型,利用密度泛函理论研究了Bi7-MT中Bi3+的三种可能配位结构(BiS3O1(1)、 BiS3O1(2)和BiS3O1(3)),并计算了生成络合结构的结合自由能和紫外吸收光谱。通过比较计算结果与实验光谱,揭示了Bi7-MT的内核结构模型为BiS3O1(1),其中Bi-O键中的配体氧来源于MT侧链上天冬氨酸的羧基。
(3)采用紫外吸收光谱和圆二色光谱法研究了脱金属硫蛋白(apo-MT)及其单个结构域(apo-aMT, apo-βMT)、Zn7—MT在不同pH值下结合Pb2+的反应过程及最终产物。在pH5.4-7.0时,apo-MT结合Pb2+得到产物Pb7-MT;在pH5.4-4.0时,apo-MT结合Pb2+得到产物Pb7-MT', apo-αMT、apo-βMT及Zn7-MT结合Pb2+的产物与apo-MT相同。Pb7-MT和Pb7-MT'表现出不同的化学稳定性.Pb7-MT在pH2.5可完全脱去Pb2+,而Pb7-MT'在pH2.0时才能完全脱去Pb2+。Pb7-MT可以在低pH值转变为Pb7-MT,而Pb7-MT’具有较高的稳定性,即使在中性溶液中也能稳定存在。分别采用连续介质模型法及ONIOM分层方法处理蛋白质环境,探讨了Pb-MT和Pb7-MT'的结构及其电子吸收光谱。计算结果表明,相较于连续介质模型法,采用ONIOM方法获得的计算光谱更接近于实验光谱。中性条件下形成的产物Pb7-MT,其金属活性中心结构为Pb-S3三配位；酸性条件下形成的产物Pb7-MT',其金属活性中心结构较为复杂,同时含有Pb-S3三配位和Pb-S3O1的四配位结构,其中的配体O来自天冬氨酸残基上的羧基。Pb7-MT'较Pb7-MT更加稳定。
(4)采用连续介质模型法和ONIOM分层方法,成功预测As6-MT的金属活性中心结构为As-S3配位的结构,该配位结构不同于Zn2+在Zn7-MT的配位结构。As3+具有与zn2+完全不同的配位结构,生物体摄入As3+后导致起酶催化的一些含锌蛋白结构发生变化,而失去生物功能,这可能是As3+具有毒性的原因之一。
Metallothionein (MT) is a class of metal protein characterized by a high cysteines content (up to30%of the amino acid residues), low molar mass and lack of aromatic amino acid residues. Chemical and spectroscopic studies have shown that MT can bind a wide range of metal ions. MT can lower heavy metals toxicology, capture harmful oxidant radicals and alkylating agent. MT also plays a central role in the pharmacology of metal-containing medicines. Due to its unique physiological functions, MT has been a hot topic in the life science. Elucidating the structure of MT is important for understanding its physiological functions. Here, the structures of three kinds of MT (Bi-MT, Pb-MT and As-MT) were investigated using spectroscopy and theoretical calculation methods. The main results were shown in the following:
(1) The molecular geometry, vibration frequencies and electric absorption spectrum of metal thiolate complexes M(SC6H5)3(M=Bi, Sb or As) have been calculated with density functional (mPW1PW, B3LYP, TPSSh and OLYP) and ab initio method (HF), respectively. The theoretical results were compared to the available experimental data. It is demonstrated that mPW1PW functional is superior to other functionals (B3LYP, TPSSh and OLYP) and ab initio method (HF) in predicting molecular structures and vibration frequencies of Sb-thiolate and As-thiolate complexes. For Bi-thiolate complex, the hybrid density functional B3LYP gives better performance than other methods. The theoretical electric absorption spectra of Bi(SC6H5)3from B3LYP functional is similar to the available experimental data, which confirms the rationality of theoretical calculation method. The confirmed optimal theoretical calculation method for each complex will be helpful for our further understanding on the complexation structures of apo-MT binding Bi3+,Pb2+and As3+
(2) The coordination of Bi3+to rabbit liver metal-free metallothionein was investigated using both experimental and theoretical methods. Spectral results suggest that one apo-MT can bind7Bi3+ forming the product Bi7-MT. Circular dichroism spectra indicate that Bi-MT2has a different secondary structure from those of Zn-MT2and Cd-MT2. Three possible Bi3+coordination structures (BiS3O1(1), BiS3O1(2) and BiS3O1(3)) and their relative binding free energies in Bi7-MT2were calculated using the density functional theory by active-site modes. Absorption spectra corresponding to these coordination structures were evaluated by time-dependent density functional theory. By comparison of calculated results and experimental spectra, the coordination mode in Bi7-MT2was confirmed to be BiS3O1(1), and the carboxyl group in the aspartic acid residues contributes to the Bi-O bond formation. Furthermore, the theoretical method was successfully used to predict the formation process of Bi-O bond in Bi7-metallothionein, an important product in vivo on effectively reducing side effect of metal-containing drugs.
(3) The binding of apo-MT, its individual domains (apo-αMT, and apo-βMT) and Zn7-MT with Pb2+at different pH conditions have been studied by UV-vis and CD spectra. For apo-MT, the product Pb7-MT was obtained from apo-MT under pH5.4-7.0, while the product Pb7-MT' was formed under pH5.4-4.0. The spectra results from apo-αMT, apo-βMT and Zn7-MT were similar to those from apo-MT. Pb7-MT' showed better chemical stability than Pb7-MT. The structures of Pb7-MT and Pb7-MT' were investigated by continuum model method and ONIOM method, respectively. ONIOM method gave better prediction for the absorption spectra of Pb-containing MT. The consistency of computed and experimental spectra suggests that Pb2+binds thiol groups in Pb7-MT by Pb-S3coordination model and in Pb7-MT'by Pb-S3O1coordination model. The ligand O in Pb7-MT' is from the carboxyl group in the aspartic acid residues.
(4) The structure and absorption spectra of As6-MT were investigated by continuous medium model and ONIOM method, respectively. The calculation results indicate that ONIOM method can give better prediction for the absorption spectra of As6-MT. As3+binds thiol groups in As6-MT by As-S3coordination model, which is different from the coordination model of Zn2+in Zn-containing enzyme protein. That will change the structure of the enzyme protein structure. Therefore, after the replacement of Zn2+by As3+, the changed structures of Zn-containing enzyme proteins may induce the disability on their biological functions.
(1)采用基于密度泛函理论(Density functional theory)的B3LYP、 mPW1PW、OLYP和TPSSh方法,以及从头算(ab initio)的HF方法,对含主族金属铋、锑和砷的巯基小分子化合物M(SC6H5)3(M=Bi, Sb,As)的几何结构、振动频率和电子吸收光谱等进行了研究,并与文献报道的数据做了比较,确认适宜于各金属巯基化合物的最优化结构计算方法。结果显示：对于Sb(SC6H5)3和As(SC6H5)3, mPW1PW的计算精度明显高于其它四种计算方法；而对于复合物Bi(SC6H5)3, B3LYP方法能给出更高的计算精度。确定的最优计算方法将用于apo-MT结合Bi3+、Pb2+及As3+的结构研究。
(2)采用紫外吸收光谱和CD光谱,研究了Bi3+结合脱金属硫蛋白(apo-MT)的反应过程及最终产物。确认产物中Bi3+和apo-MT的计量比为7：1,即形成Bi7-MT。CD光谱结果显示Bi7-MT具有不同于Zn7-MT和Cd7-MT的蛋白质二级结构。采用活性位点模型,利用密度泛函理论研究了Bi7-MT中Bi3+的三种可能配位结构(BiS3O1(1)、 BiS3O1(2)和BiS3O1(3)),并计算了生成络合结构的结合自由能和紫外吸收光谱。通过比较计算结果与实验光谱,揭示了Bi7-MT的内核结构模型为BiS3O1(1),其中Bi-O键中的配体氧来源于MT侧链上天冬氨酸的羧基。
(3)采用紫外吸收光谱和圆二色光谱法研究了脱金属硫蛋白(apo-MT)及其单个结构域(apo-aMT, apo-βMT)、Zn7—MT在不同pH值下结合Pb2+的反应过程及最终产物。在pH5.4-7.0时,apo-MT结合Pb2+得到产物Pb7-MT;在pH5.4-4.0时,apo-MT结合Pb2+得到产物Pb7-MT', apo-αMT、apo-βMT及Zn7-MT结合Pb2+的产物与apo-MT相同。Pb7-MT和Pb7-MT'表现出不同的化学稳定性.Pb7-MT在pH2.5可完全脱去Pb2+,而Pb7-MT'在pH2.0时才能完全脱去Pb2+。Pb7-MT可以在低pH值转变为Pb7-MT,而Pb7-MT’具有较高的稳定性,即使在中性溶液中也能稳定存在。分别采用连续介质模型法及ONIOM分层方法处理蛋白质环境,探讨了Pb-MT和Pb7-MT'的结构及其电子吸收光谱。计算结果表明,相较于连续介质模型法,采用ONIOM方法获得的计算光谱更接近于实验光谱。中性条件下形成的产物Pb7-MT,其金属活性中心结构为Pb-S3三配位；酸性条件下形成的产物Pb7-MT',其金属活性中心结构较为复杂,同时含有Pb-S3三配位和Pb-S3O1的四配位结构,其中的配体O来自天冬氨酸残基上的羧基。Pb7-MT'较Pb7-MT更加稳定。
(4)采用连续介质模型法和ONIOM分层方法,成功预测As6-MT的金属活性中心结构为As-S3配位的结构,该配位结构不同于Zn2+在Zn7-MT的配位结构。As3+具有与zn2+完全不同的配位结构,生物体摄入As3+后导致起酶催化的一些含锌蛋白结构发生变化,而失去生物功能,这可能是As3+具有毒性的原因之一。
Metallothionein (MT) is a class of metal protein characterized by a high cysteines content (up to30%of the amino acid residues), low molar mass and lack of aromatic amino acid residues. Chemical and spectroscopic studies have shown that MT can bind a wide range of metal ions. MT can lower heavy metals toxicology, capture harmful oxidant radicals and alkylating agent. MT also plays a central role in the pharmacology of metal-containing medicines. Due to its unique physiological functions, MT has been a hot topic in the life science. Elucidating the structure of MT is important for understanding its physiological functions. Here, the structures of three kinds of MT (Bi-MT, Pb-MT and As-MT) were investigated using spectroscopy and theoretical calculation methods. The main results were shown in the following:
(1) The molecular geometry, vibration frequencies and electric absorption spectrum of metal thiolate complexes M(SC6H5)3(M=Bi, Sb or As) have been calculated with density functional (mPW1PW, B3LYP, TPSSh and OLYP) and ab initio method (HF), respectively. The theoretical results were compared to the available experimental data. It is demonstrated that mPW1PW functional is superior to other functionals (B3LYP, TPSSh and OLYP) and ab initio method (HF) in predicting molecular structures and vibration frequencies of Sb-thiolate and As-thiolate complexes. For Bi-thiolate complex, the hybrid density functional B3LYP gives better performance than other methods. The theoretical electric absorption spectra of Bi(SC6H5)3from B3LYP functional is similar to the available experimental data, which confirms the rationality of theoretical calculation method. The confirmed optimal theoretical calculation method for each complex will be helpful for our further understanding on the complexation structures of apo-MT binding Bi3+,Pb2+and As3+
(2) The coordination of Bi3+to rabbit liver metal-free metallothionein was investigated using both experimental and theoretical methods. Spectral results suggest that one apo-MT can bind7Bi3+ forming the product Bi7-MT. Circular dichroism spectra indicate that Bi-MT2has a different secondary structure from those of Zn-MT2and Cd-MT2. Three possible Bi3+coordination structures (BiS3O1(1), BiS3O1(2) and BiS3O1(3)) and their relative binding free energies in Bi7-MT2were calculated using the density functional theory by active-site modes. Absorption spectra corresponding to these coordination structures were evaluated by time-dependent density functional theory. By comparison of calculated results and experimental spectra, the coordination mode in Bi7-MT2was confirmed to be BiS3O1(1), and the carboxyl group in the aspartic acid residues contributes to the Bi-O bond formation. Furthermore, the theoretical method was successfully used to predict the formation process of Bi-O bond in Bi7-metallothionein, an important product in vivo on effectively reducing side effect of metal-containing drugs.
(3) The binding of apo-MT, its individual domains (apo-αMT, and apo-βMT) and Zn7-MT with Pb2+at different pH conditions have been studied by UV-vis and CD spectra. For apo-MT, the product Pb7-MT was obtained from apo-MT under pH5.4-7.0, while the product Pb7-MT' was formed under pH5.4-4.0. The spectra results from apo-αMT, apo-βMT and Zn7-MT were similar to those from apo-MT. Pb7-MT' showed better chemical stability than Pb7-MT. The structures of Pb7-MT and Pb7-MT' were investigated by continuum model method and ONIOM method, respectively. ONIOM method gave better prediction for the absorption spectra of Pb-containing MT. The consistency of computed and experimental spectra suggests that Pb2+binds thiol groups in Pb7-MT by Pb-S3coordination model and in Pb7-MT'by Pb-S3O1coordination model. The ligand O in Pb7-MT' is from the carboxyl group in the aspartic acid residues.
(4) The structure and absorption spectra of As6-MT were investigated by continuous medium model and ONIOM method, respectively. The calculation results indicate that ONIOM method can give better prediction for the absorption spectra of As6-MT. As3+binds thiol groups in As6-MT by As-S3coordination model, which is different from the coordination model of Zn2+in Zn-containing enzyme protein. That will change the structure of the enzyme protein structure. Therefore, after the replacement of Zn2+by As3+, the changed structures of Zn-containing enzyme proteins may induce the disability on their biological functions.
引文
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