基于分子动力学模拟的两种重要蛋白结构与功能研究
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摘要
分子动力学模拟是一种能够揭示生物大分子结构与功能物质基础的重要方法。运用分子动力学模拟的方法，我们可以提供以时间为顺序单个粒子运动的最终细节。因此，利用此种方法构建模型来研究某个体系的具体性能问题，往往比实际实验来的容易。
本论文分别通过两个实例来展示分子动力学模拟应用于生物大分子研究中的直观优势。首先是对耐热脂肪酶T1在不同温度条件下的模拟。T1脂肪酶是来源于GeobacilluszalihaeT1菌株的恒温嗜碱酶，具有很好的稳定性，而稳定性是集约型可持续化工业运行的重要标准。因此我们通过分子动力学模拟揭示了为什么T1脂肪酶在高温条件下具有如此好的稳定性和活性，实验结果表明，T1脂肪酶在60℃和70℃下的蛋白结构相比30℃时更加稳定，尤其是构成活性口袋的两个α螺旋之间的距离可以稳定在一定的范围内，使水分子能够长时间停留在活性中心附近，为水解反应提供必须的水。通过分析我们还得到，疏水作用是导致T1脂肪酶在不同温度下有不同结构变化的主要作用力。最后，我们对另一种耐热脂肪酶L1进行了模拟，得到了与T1脂肪酶相似的结论，由此推测相同的催化机理可能存在于多种耐热脂肪酶中。
另一则实例是关于成纤维细胞生长因子9的模拟。成纤维细胞生长因子9（fibroblastgrowth factor,FGF9）是成纤维细胞生长因子家族的成员之一。在骨骼发育早期，FGF9的作用是促进软骨细胞肥大；在骨骼发育后期，其主要作用是调节生长板的血管化和成骨过程。生化研究发现FGF9的99位的丝氨酸突变为天冬酰胺是多发性骨性连接综合征（Multiple synostoses syndrome,SYNS）的发病原因，因此我们利用分子模拟的方法分别研究FGF9的野生型与突变型的模拟结果，比对FGF9的野生型和突变型的3D结构，发现FGF9碳端具有一个秩序井然的结构，这个结构在成纤维细胞生长因子的信号传递过程中诱导其形成同源二聚体，从而打破单体与二聚体的动态平衡。这一平衡被认为是成纤维细胞生长因子信号传递过程中，调节胞外基质亲和与组织扩散的关键环节。由于野生型形成同源二聚体的自由能相对较低，因此它优先形成有生理活性的同源二聚体。而突变体S99N的单体更愿意与受体结合，形成没有活性的复合体，导致信号传导受阻。成纤维细胞生长因子信号的衰减是人类骨性连接综合症的潜在原因，因此模拟结果成功的揭示了成纤维细胞生长因子9的致病机理。本论文中的这两个实例充分的证明了在未来的研究中，分子动力学模拟技术在生物学领域将会有更广泛的应用。
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. MD simulations can provide the ultimate detail concerning individual particle motions as a function of time. Thus, they can be used to address specific questions about the properties of a model system, often more easily than experiments on the actual system.
In this thesis, we use two examples to show the applications of MD simulations on biology investigations. One is simulating the T1lipase at different temperatures. T1lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1and it was with a perfect stability that is an important criterion for a sustainable industrial operation economically. So we want to find out why the T1lipase is so stable and high active at high temperature. By analysis, the structure of T1lipase at60℃and70℃is more stable, especially the distance between the two a helixes making up the active pocket could maintain in a specific range. This could keep water for the hydrolysis reaction near the active site for a long time. We also found that the hydrophobic interaction is main force to cause the different structural changes of T1lipase at diferernt temperature. Finally, another thermostable enzyme named L1lipase was simulated, and yielded a similar Conclusion with T1lipase. It is presumed that the same catalytic mechanism may exist widely in various thermostable enzymes.
The other instance is the simulation of the fibroblast growth factor9(FGF9). Fibroblast growth factor9(FGF9) is one of the members of fibroblast growth factors'family. In the early stages of skeletal growth, the function of FGF9is to enlarge the area of the cartilage; In the later stages of skeletal growth, the major function of FGF9is to adjust vascularization for growth plate and osteogenetic process. Biochemical analysis reveals that the identified FGF9mutation (Ser99Asn) as a potential cause of multiple synostoses syndrome (SYNS). So we performed computational studies on wild-type and mutant FGF9separately. From the correlation of the3D structure of the wild-type and mutant FGF9, We found that the FGF9has a well-ordered C-terminal structure, which can reduce its homodimerization ability so as to break the monomer-dimer equilibrium in the FGF signaling, which is considered as a key factor to regulate extracellular matrix affinity and tissue diffusion in the FGF signaling pathway. FGF9WT monomer can preferentially form a homodimer owe to its comparatively lower binding free energy. In contrast, FGF9S99N monomer is preferred to bind with FGFR3c receptor to form an inactive complex, leading to impair FGF signaling. The impaired FGF signaling is believed to be a potential cause of human synostoses syndrome. So the result from the simulation successfully revealed the pathogenic mechanism on FGF9. To sum up the above arguments, these results available from this thesis make clear that the applications of molecular dynamics will play an even more important role for our understanding of biology in the future.
本论文分别通过两个实例来展示分子动力学模拟应用于生物大分子研究中的直观优势。首先是对耐热脂肪酶T1在不同温度条件下的模拟。T1脂肪酶是来源于GeobacilluszalihaeT1菌株的恒温嗜碱酶，具有很好的稳定性，而稳定性是集约型可持续化工业运行的重要标准。因此我们通过分子动力学模拟揭示了为什么T1脂肪酶在高温条件下具有如此好的稳定性和活性，实验结果表明，T1脂肪酶在60℃和70℃下的蛋白结构相比30℃时更加稳定，尤其是构成活性口袋的两个α螺旋之间的距离可以稳定在一定的范围内，使水分子能够长时间停留在活性中心附近，为水解反应提供必须的水。通过分析我们还得到，疏水作用是导致T1脂肪酶在不同温度下有不同结构变化的主要作用力。最后，我们对另一种耐热脂肪酶L1进行了模拟，得到了与T1脂肪酶相似的结论，由此推测相同的催化机理可能存在于多种耐热脂肪酶中。
另一则实例是关于成纤维细胞生长因子9的模拟。成纤维细胞生长因子9（fibroblastgrowth factor,FGF9）是成纤维细胞生长因子家族的成员之一。在骨骼发育早期，FGF9的作用是促进软骨细胞肥大；在骨骼发育后期，其主要作用是调节生长板的血管化和成骨过程。生化研究发现FGF9的99位的丝氨酸突变为天冬酰胺是多发性骨性连接综合征（Multiple synostoses syndrome,SYNS）的发病原因，因此我们利用分子模拟的方法分别研究FGF9的野生型与突变型的模拟结果，比对FGF9的野生型和突变型的3D结构，发现FGF9碳端具有一个秩序井然的结构，这个结构在成纤维细胞生长因子的信号传递过程中诱导其形成同源二聚体，从而打破单体与二聚体的动态平衡。这一平衡被认为是成纤维细胞生长因子信号传递过程中，调节胞外基质亲和与组织扩散的关键环节。由于野生型形成同源二聚体的自由能相对较低，因此它优先形成有生理活性的同源二聚体。而突变体S99N的单体更愿意与受体结合，形成没有活性的复合体，导致信号传导受阻。成纤维细胞生长因子信号的衰减是人类骨性连接综合症的潜在原因，因此模拟结果成功的揭示了成纤维细胞生长因子9的致病机理。本论文中的这两个实例充分的证明了在未来的研究中，分子动力学模拟技术在生物学领域将会有更广泛的应用。
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. MD simulations can provide the ultimate detail concerning individual particle motions as a function of time. Thus, they can be used to address specific questions about the properties of a model system, often more easily than experiments on the actual system.
In this thesis, we use two examples to show the applications of MD simulations on biology investigations. One is simulating the T1lipase at different temperatures. T1lipase is a thermoalkalophilic enzyme derived from Geobacillus zalihae strain T1and it was with a perfect stability that is an important criterion for a sustainable industrial operation economically. So we want to find out why the T1lipase is so stable and high active at high temperature. By analysis, the structure of T1lipase at60℃and70℃is more stable, especially the distance between the two a helixes making up the active pocket could maintain in a specific range. This could keep water for the hydrolysis reaction near the active site for a long time. We also found that the hydrophobic interaction is main force to cause the different structural changes of T1lipase at diferernt temperature. Finally, another thermostable enzyme named L1lipase was simulated, and yielded a similar Conclusion with T1lipase. It is presumed that the same catalytic mechanism may exist widely in various thermostable enzymes.
The other instance is the simulation of the fibroblast growth factor9(FGF9). Fibroblast growth factor9(FGF9) is one of the members of fibroblast growth factors'family. In the early stages of skeletal growth, the function of FGF9is to enlarge the area of the cartilage; In the later stages of skeletal growth, the major function of FGF9is to adjust vascularization for growth plate and osteogenetic process. Biochemical analysis reveals that the identified FGF9mutation (Ser99Asn) as a potential cause of multiple synostoses syndrome (SYNS). So we performed computational studies on wild-type and mutant FGF9separately. From the correlation of the3D structure of the wild-type and mutant FGF9, We found that the FGF9has a well-ordered C-terminal structure, which can reduce its homodimerization ability so as to break the monomer-dimer equilibrium in the FGF signaling, which is considered as a key factor to regulate extracellular matrix affinity and tissue diffusion in the FGF signaling pathway. FGF9WT monomer can preferentially form a homodimer owe to its comparatively lower binding free energy. In contrast, FGF9S99N monomer is preferred to bind with FGFR3c receptor to form an inactive complex, leading to impair FGF signaling. The impaired FGF signaling is believed to be a potential cause of human synostoses syndrome. So the result from the simulation successfully revealed the pathogenic mechanism on FGF9. To sum up the above arguments, these results available from this thesis make clear that the applications of molecular dynamics will play an even more important role for our understanding of biology in the future.
引文
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