碳纳米材料与PTP1B和纤维素酶作用机制的分子动力学模拟

发布时间：2018-10-08 14:00

【摘要】：近些年来纳米材料由于其独特物理化学性质,得到科学界的广泛关注和研究。纳米尺度的微粒可以高效地在体内运输,从而实现其在生物医学、纳米药物储存以及药物递送释放等领域的应用,这些独特的性质使纳米材料与传统宏观材料相比,具有更加明显的优势。与此同时,纳米科学与其他学科融合形成的交叉学科也随之成为研究热点,成为新兴的研究领域。富勒烯及其衍生物具有特殊的物理结构和化学性质,在生物医学领域的应用最为广泛。早期就有文献指出富勒烯衍生物对HIV蛋白酶具有良好的抑制效果,在此研究的基础上,有实验报道几种特殊修饰的富勒烯衍生物对蛋白质酪氨酸磷酸酶家族的多种酶都呈现较好的抑制活性,但是具体的作用机理却不明朗。因此,本研究采用分子优化,分子对接,分子动力学模拟以及结合自由能计算等手段从理论的角度对富勒烯抑制剂在Protein tyrosine phosphatase 1B(PTP1B)中的结合模式以及抑制机理进行考察。研究发现富勒烯抑制剂的尺寸和PTP1B的活性口袋大小相近,可以很好的结合在活性口袋中。并且,两种富勒烯抑制剂可能都作为竞争性抑制剂起作用,通过结合在活性位点阻止底物的结合从而达到抑制效果。来自富勒烯修饰基团上的负电亲水基团和P-loop上的残基Arg221,识别环区上的Lys116和Lys120形成强烈的静电作用,这可能是富勒烯抑制剂进入活性中心的主要驱动力,而周围的非极性残基对富勒烯碳笼的范德华贡献也是其能稳定在活性口袋的重要原因。另外,富勒烯抑制剂结合在活性中心之后,会引起WPD loop的偏转,造成催化酸Asp181远离活性中心,可能是富勒烯抑制剂优秀抑制活性的一个原因。对富勒烯抑制剂抑制模式的探究可以为高效、新型抑制剂的设计和改造提供指导。此外,我们还使用分子动力学模拟考察了纤维素酶Cel48F在石墨烯等碳纳米材料上的固载作用,以及固载前后对纤维素酶体系催化活性的影响。研究发现,除了Glu55和Asp230的作用之外,Glu44对纤维素酶活性的影响有重要影响。水解过程中Glu44可以维持底物构象并且可能作为催化碱促进水解的顺利进行,在水解之后Glu44协助产物从蛋白中解离。拉伸分子动力学模拟研究表明,产物解离初期,Glu44,Glu55,Asp494和Trp611等参与氢键重排作用,有效地降低产物的滑行能垒,促进产物的解离。而在解离后期,产物解离的主要动力来自于溶剂,由于溶剂的无序性运动使得底物解离的方向并不确定。再此基础上,我们考察了其在石墨烯上固载化的可能性,研究发现Cel48F可以通过一些非极性作用和堆积作用力靠近石墨烯层。综上两方面,利用分子模拟手段研究生物体系的基本性质及其在纳米材料中的应用机理,对碳纳米材料的生物应用和改进具有理论指导意义。
[Abstract]:In recent years, nanomaterials have received extensive attention and research in the scientific community because of their unique physical and chemical properties. Nanoscale particles can be transported in vivo efficiently, thus achieving their applications in biomedicine, nanopharmaceutical storage and drug delivery and release. These unique properties allow nanomaterials to compare with traditional macro materials. Have more obvious advantage. At the same time, the interdiscipline of nanoscience and other disciplines has become a research hotspot and a new research field. Fullerene and its derivatives have special physical structure and chemical properties and are widely used in biomedical field. Fullerene derivatives have been shown to have a good inhibitory effect on HIV protease in the early days. It has been reported that several special modified fullerene derivatives have good inhibitory activity on protein tyrosine phosphatase family enzymes, but the specific mechanism is not clear. Therefore, molecular optimization, molecular docking, molecular dynamics simulation and binding free energy calculation were used to investigate the binding mode and inhibition mechanism of fullerene inhibitors in Protein tyrosine phosphatase 1B (PTP1B) from the theoretical point of view. It was found that the size of fullerene inhibitor was similar to that of active pocket of PTP1B. Moreover, both fullerene inhibitors may act as competitive inhibitors, which can inhibit the binding of substrates by binding to active sites. The negative hydrophilic group from fullerene modified group and the residue Arg221, on P-loop recognize Lys116 and Lys120 on the ring region to form a strong electrostatic interaction, which may be the main driving force for fullerene inhibitors to enter the active center. The nonpolar residues around contribute to the van der Waals contribution of fullerene carbon cages, which is also an important reason for the stability in the active pockets of fullerene carbon cages. In addition, the binding of fullerene inhibitor to the active center will cause the deflection of WPD loop, which may cause the catalytic acid Asp181 to stay away from the active center, which may be one of the reasons for the excellent inhibitory activity of fullerene inhibitor. The study of the inhibition mode of fullerene inhibitors can provide guidance for the design and modification of new and efficient inhibitors. In addition, we also investigated the immobilization of cellulase Cel48F on graphene and other carbon nanomaterials by molecular dynamics simulation, and the effect of immobilization on the catalytic activity of cellulase system before and after immobilization. In addition to the effects of Glu55 and Asp230, the effect of Glu44 on cellulase activity was found to be significant. During hydrolysis, Glu44 can maintain the conformation of the substrate and may be used as a catalytic base to facilitate the hydrolysis. After hydrolysis, Glu44 assists in the dissociation of the product from the protein. The results of tensile molecular dynamics simulation show that Glu44-Glu55Asp494 and Trp611 are involved in hydrogen bond rearrangement, which can effectively reduce the gliding barrier of the product and promote the dissociation of the product. In the later stage of dissociation, the main motive force of product dissociation comes from solvent, and the direction of substrate dissociation is uncertain due to the disordered movement of solvent. On this basis, we investigated the possibility of its immobilization on graphene. It was found that Cel48F can close to the graphene layer through some nonpolar effects and stacking forces. In summary, molecular simulation is used to study the basic properties of biological system and its application mechanism in nanomaterials, which is of theoretical significance for the biological application and improvement of carbon nano-materials.
【学位授予单位】：吉林大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q55;TB383.1

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