蛋白质的分子动力学模拟和催化机理的理论研究
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摘要
本文利用同源模建、分子力学、分子动力学模拟和量子化学计算等方法,对六种蛋白质体系进行了理论研究。主要内容包括:
1.利用同源模建和分子动力学模拟,构建了人类N-乙酰唾液酸酶(hNAL)的三维结构。在此基础上进行了其与配体唾液酸、抑制剂KDO的分子对接研究。验证了hNAL对KDO的水解能力较弱,并阐明了引起水解能力差异的原因,同时指出了形成复合物过程中的关键氨基酸残基。
2.通过同源模建和分子动力学方法,进行了人类2-氨基-3-羧基粘康酸-6-半醛脱羧酶(hACMSD)的理论研究。确定了开环形式的底物ACMS更容易与酶相互作用,并进入到酶活性位点的中心部位,并且Zn2+在酶与配体的作用过程中起到非常重要的作用。
3.通过谷胱甘肽硫转移酶M5(GSTM5)的同源模建及分子对接研究,分别考察了五羟黄酮和利尿酸与GSTM5的结合方式,发现抑制剂五羟黄酮的抑制作用要强于利尿酸。
4.通过天冬氨酸酰基转移酶-2(hASPA-2)的分子动力学模拟研究,并与hASPA-1结果进行比较发现形成酶与底物复合物过程中,起主要作用的为保守氨基酸残基。量子化学计算结果表明当水分子配位到锌离子后,NAA与hASPAs之间的相互作用变强。
5.利用分子动力学和量子化学计算方法,研究了α-磷酸甘露糖酶1催化的α-D-甘露糖-1-磷酸与D-甘露糖-6-磷酸异构的反应机理。计算结果表明磷酸基团转移过程中,不同的质子化状态拥有不同的反应路径,但都同样伴有质子的迁移,并且非质子化状态更有利于产物的释放。
6.通过同源模建和分子力学优化,得到了ScFv-B3的三维结构,预测了底物GSH的两个可能结合部位。通过分子对接研究发现,Site1相对于Site2是更有可能的GSH结合位点,并且在不含有丝氨酸的结合位点中,预测Site1的Ala180和Site2的Ala44作为潜在的可突变位点。
In recent years, along with the development of homology, molecule mechanics, dynamics, and quantum mechanics theories, and the process of calculator technique, molecule simulations have already become a main research method in the fields of biology science to analyze the interaction between receptor and ligand and to describe the catalytic mechanism.
In our thesis, homology modeling, molecule mechanics, dynamics, and quantum mechanics methods were used to theoretically study on the potency and selectivity ligands of the proteins, the reaction mechanism ofα-Phosphomannomutase1 in both protonated and deprotonated state, and improving the GPX activity of the human single-chain Fv antibody. The main results are summarized as follows:
1. Homology modeling and Molecular dynamics study on N-acetylneuraminate lyase
N-acetyl-neuraminic acid (sialic acid) is an interesting high carbon sugar with important pharmaceutical implications. It plays a prominent role in numerous biological functions, including virus infections.
In this investigation, the 3D structure of hNAL was built by homology modeling, which was based on the known crystal structure of N-acetylneuraminate lyase from E.coli. And then energy minimization and molecular dynamics were used to refine the structure. With this model, a flexible docking study was performed and the docking results indicate that the AcHN group in sialic acid can stabilize the position and orientation in active site of hNAL. Thr51 and Tyr143 may be the key amino acids residues interacting with the substrates, and Asp176 and Ser218 may help sialic acid interact with hNAL steady.
2. Theoretical Studies on Interaction Mode Between human 2-Amino 3-carboxymuconate 6-semialdehyde Decarboxylase and Substrate and Inhibitor
2-amino 3-carboxymuconate 6-semialdehyde Decarboxylase (hACMSD) occupies a key positition at the branching point of ACMS metabolic pathways and control the final fate of the metabolites in both pathway.
The three dimensional structure of hACMSD was modeled and refined by using Homology modeling and Molecular dynamics. The complex structures of the substrate or inhibitor with hACMSD were obtained and investigated through ligand-receptor docking studies by means of Affinity. The binding pattern predicted by the affinity module reveals Arg47, Val48 and the catalytic Zn2+ interacted with substrate or inhibitor. By contrasting the results of the ACMS and QA, ACMS interacts more easy with ACMSD than QA.
3. Molecular Simulation on Interaction between Glutathione S-transferase M5 and Substrate or Inhibitors
The three dimensional structure of glutathione S-transferase (GSTM5) was modeled and refined by using Homology modeling and Molecular dynamics. The complex structures of the substrate and inhibitor, ethacrynic acid and pentahydroxyflavone, with GSTM5 were obtained and investigated through ligand-receptor docking studies by means of Affinity. The complex of GSTM5 and ligands predicted by the affinity module reveals Tyr7,Trp8,Leu13,His108,Val112 interacted with substrate or inhibitors. And the inhibition of pentahydroxyflavone is more than ethacrynic acid.
4. 3D Structure and Catalytic Mechanism Potency Study on Aspartoacylase
Deficiency in aspartoacylase (ASPA) is the established cause of Canavan disease (CD), a fatal progressive leukodystrophy affecting young children.
The 3D model of the aspartoacylase-2 from human is constructed based on the crystal structure of the aspartoacylase-1. With this model, a flexible docking study is performed and the results indicate that Asp68, Asn70, Asp168, Glu178, Tyr288 and zinc ion play major roles in catalysis of hASPA-2. By contrasting the result, aspartoacylase-1 are performed the same operation. Quantum chemistry calculations show after the water coordinated to the zinc ion, the interactions between the NAA and hASPA become stronger.
5. DFT Investigation on the Reaction Mechanism Catalyzed byα-Phosphomannomutase1 in Protonated/Deprotonated state
Congenital disorder of glycosylation type 1a (CDG-1a) which is a congenital disease, is caused by mutations inα-Phosphomannomutase1 (α-PMM1).
The reaction mechanism of theα-PMM1 enzyme has been investigated by means of density functional theory using the hydrid functional B3LYP.α-PMM1 catalyzes the interconversion of theα-D-mannose 1-phosphate to D-mannose 6-phosphate via a mannose-1, 6-(bis) phosphate intermediate. The quantum chemical models, which were chosen in protonated/deprotonated states models, were built on the basis of the docking result. The process of the phosphoryl group transfer from Asp19 to the mannose 6-phosphate is in different steps in the two states, but are both coupled with the protons transfer. In addition, our results support the hypothesis that the Asp19 as a nucleophile plays an important role in theα-PMM1 biology function, indicate Gln62 helps to stabilize the phosphoryl group and the structure of the substrate, and the deprotonated states is more suitable for product release.
6. Improving GPX activity of selenium-containing human single-chain Fv antibody by site-directed mutation based on the structural analysis
GPX is a well-known antioxidant selenoenzyme which can catalyze the reduction of a variety of hydroperoxides and consequently protect cells and other biological tissues against oxidative damage.
In this investigation, the 3D structure of ScFv-B3 was built by homology modeling. And then energy minimization and molecular dynamics were used to refine the structure. With this model, two active sites were obtained and the Affinity was performed to obtain the complexes of the substrate GSH. Through interaction analysis, it was determined that the total interaction energy in Site 1 is more negative than that in Site 2, thus Site1 is the more likely binding site. Ala180 in Site 1 and Ala44 in Site 2 were the optimal choices for the candidate according to the principles above to improve the GPX activity. Our calculation results are good agreement with the experiment results made by the experimental cooperate team.
1.利用同源模建和分子动力学模拟,构建了人类N-乙酰唾液酸酶(hNAL)的三维结构。在此基础上进行了其与配体唾液酸、抑制剂KDO的分子对接研究。验证了hNAL对KDO的水解能力较弱,并阐明了引起水解能力差异的原因,同时指出了形成复合物过程中的关键氨基酸残基。
2.通过同源模建和分子动力学方法,进行了人类2-氨基-3-羧基粘康酸-6-半醛脱羧酶(hACMSD)的理论研究。确定了开环形式的底物ACMS更容易与酶相互作用,并进入到酶活性位点的中心部位,并且Zn2+在酶与配体的作用过程中起到非常重要的作用。
3.通过谷胱甘肽硫转移酶M5(GSTM5)的同源模建及分子对接研究,分别考察了五羟黄酮和利尿酸与GSTM5的结合方式,发现抑制剂五羟黄酮的抑制作用要强于利尿酸。
4.通过天冬氨酸酰基转移酶-2(hASPA-2)的分子动力学模拟研究,并与hASPA-1结果进行比较发现形成酶与底物复合物过程中,起主要作用的为保守氨基酸残基。量子化学计算结果表明当水分子配位到锌离子后,NAA与hASPAs之间的相互作用变强。
5.利用分子动力学和量子化学计算方法,研究了α-磷酸甘露糖酶1催化的α-D-甘露糖-1-磷酸与D-甘露糖-6-磷酸异构的反应机理。计算结果表明磷酸基团转移过程中,不同的质子化状态拥有不同的反应路径,但都同样伴有质子的迁移,并且非质子化状态更有利于产物的释放。
6.通过同源模建和分子力学优化,得到了ScFv-B3的三维结构,预测了底物GSH的两个可能结合部位。通过分子对接研究发现,Site1相对于Site2是更有可能的GSH结合位点,并且在不含有丝氨酸的结合位点中,预测Site1的Ala180和Site2的Ala44作为潜在的可突变位点。
In recent years, along with the development of homology, molecule mechanics, dynamics, and quantum mechanics theories, and the process of calculator technique, molecule simulations have already become a main research method in the fields of biology science to analyze the interaction between receptor and ligand and to describe the catalytic mechanism.
In our thesis, homology modeling, molecule mechanics, dynamics, and quantum mechanics methods were used to theoretically study on the potency and selectivity ligands of the proteins, the reaction mechanism ofα-Phosphomannomutase1 in both protonated and deprotonated state, and improving the GPX activity of the human single-chain Fv antibody. The main results are summarized as follows:
1. Homology modeling and Molecular dynamics study on N-acetylneuraminate lyase
N-acetyl-neuraminic acid (sialic acid) is an interesting high carbon sugar with important pharmaceutical implications. It plays a prominent role in numerous biological functions, including virus infections.
In this investigation, the 3D structure of hNAL was built by homology modeling, which was based on the known crystal structure of N-acetylneuraminate lyase from E.coli. And then energy minimization and molecular dynamics were used to refine the structure. With this model, a flexible docking study was performed and the docking results indicate that the AcHN group in sialic acid can stabilize the position and orientation in active site of hNAL. Thr51 and Tyr143 may be the key amino acids residues interacting with the substrates, and Asp176 and Ser218 may help sialic acid interact with hNAL steady.
2. Theoretical Studies on Interaction Mode Between human 2-Amino 3-carboxymuconate 6-semialdehyde Decarboxylase and Substrate and Inhibitor
2-amino 3-carboxymuconate 6-semialdehyde Decarboxylase (hACMSD) occupies a key positition at the branching point of ACMS metabolic pathways and control the final fate of the metabolites in both pathway.
The three dimensional structure of hACMSD was modeled and refined by using Homology modeling and Molecular dynamics. The complex structures of the substrate or inhibitor with hACMSD were obtained and investigated through ligand-receptor docking studies by means of Affinity. The binding pattern predicted by the affinity module reveals Arg47, Val48 and the catalytic Zn2+ interacted with substrate or inhibitor. By contrasting the results of the ACMS and QA, ACMS interacts more easy with ACMSD than QA.
3. Molecular Simulation on Interaction between Glutathione S-transferase M5 and Substrate or Inhibitors
The three dimensional structure of glutathione S-transferase (GSTM5) was modeled and refined by using Homology modeling and Molecular dynamics. The complex structures of the substrate and inhibitor, ethacrynic acid and pentahydroxyflavone, with GSTM5 were obtained and investigated through ligand-receptor docking studies by means of Affinity. The complex of GSTM5 and ligands predicted by the affinity module reveals Tyr7,Trp8,Leu13,His108,Val112 interacted with substrate or inhibitors. And the inhibition of pentahydroxyflavone is more than ethacrynic acid.
4. 3D Structure and Catalytic Mechanism Potency Study on Aspartoacylase
Deficiency in aspartoacylase (ASPA) is the established cause of Canavan disease (CD), a fatal progressive leukodystrophy affecting young children.
The 3D model of the aspartoacylase-2 from human is constructed based on the crystal structure of the aspartoacylase-1. With this model, a flexible docking study is performed and the results indicate that Asp68, Asn70, Asp168, Glu178, Tyr288 and zinc ion play major roles in catalysis of hASPA-2. By contrasting the result, aspartoacylase-1 are performed the same operation. Quantum chemistry calculations show after the water coordinated to the zinc ion, the interactions between the NAA and hASPA become stronger.
5. DFT Investigation on the Reaction Mechanism Catalyzed byα-Phosphomannomutase1 in Protonated/Deprotonated state
Congenital disorder of glycosylation type 1a (CDG-1a) which is a congenital disease, is caused by mutations inα-Phosphomannomutase1 (α-PMM1).
The reaction mechanism of theα-PMM1 enzyme has been investigated by means of density functional theory using the hydrid functional B3LYP.α-PMM1 catalyzes the interconversion of theα-D-mannose 1-phosphate to D-mannose 6-phosphate via a mannose-1, 6-(bis) phosphate intermediate. The quantum chemical models, which were chosen in protonated/deprotonated states models, were built on the basis of the docking result. The process of the phosphoryl group transfer from Asp19 to the mannose 6-phosphate is in different steps in the two states, but are both coupled with the protons transfer. In addition, our results support the hypothesis that the Asp19 as a nucleophile plays an important role in theα-PMM1 biology function, indicate Gln62 helps to stabilize the phosphoryl group and the structure of the substrate, and the deprotonated states is more suitable for product release.
6. Improving GPX activity of selenium-containing human single-chain Fv antibody by site-directed mutation based on the structural analysis
GPX is a well-known antioxidant selenoenzyme which can catalyze the reduction of a variety of hydroperoxides and consequently protect cells and other biological tissues against oxidative damage.
In this investigation, the 3D structure of ScFv-B3 was built by homology modeling. And then energy minimization and molecular dynamics were used to refine the structure. With this model, two active sites were obtained and the Affinity was performed to obtain the complexes of the substrate GSH. Through interaction analysis, it was determined that the total interaction energy in Site 1 is more negative than that in Site 2, thus Site1 is the more likely binding site. Ala180 in Site 1 and Ala44 in Site 2 were the optimal choices for the candidate according to the principles above to improve the GPX activity. Our calculation results are good agreement with the experiment results made by the experimental cooperate team.
引文
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