| Summary: |
本研究利用分子動態模擬(molecular dynamics simulations,簡稱MD)探討生長因子受體蛋白2(growth factor receptor bound protein 2,簡稱Grb2)結構域(domain)與胜肽(peptide)之間的作用模式。分子動態模擬可用來研究蛋白質進行其功能時,隨著時間變化於結構中各原子間交互作用會如何影響蛋白質的調控,提供一個可觀察的蛋白質交互作用情況,進而了解蛋白質作用機制。Grb2在細胞中所扮演的角色是透過不同的機制間接調控細胞的生長、分化、遷移和死亡。Grb2是一種銜接蛋白(adaptor protein),負責訊號的傳遞,透過磷酸化的酪氨酸(phosphorylated tyrosine)和下游細胞事件之間的信號傳遞。Grb2 SH2 domain藉由磷酸化的酪氨酸結合至受體蛋白使生物體內訊號傳遞,近年來已有相關的研究。目前Grb2-SH2 domaim的結構已被解析完成,利用Grb2 SH2 domain的monomer結構與具有域交換(domain swapping)的dimer結構,研究蛋白質-配體交互作用對於Grb2 SH2 domain的影響,以結構生物學、計算化學與熱力學加以分析Grb2 SH2 domain於生物系統內的結構運動情況。將Grb2 SH2 domain swapping的dimer和monomer與磷酸化tripeptide (pYVN)進行結合模擬。發現dimer的兩個結合位點表現出不同的親和力,並且和monomer相比亦有不同的親和力。由Grb2 SH2 domain與peptide結合得到複合形式的dimer和monomer結構,胺基酸W121可能影響複合物的親和力,故認為可發生重要的交互作用在Grb2 SH2 domain。在此進行以下研究:一、 比較Grb2 SH2 domain結構域交換的dimer、monomer與pYVN結合模式。由模擬結果得知pYVN與dimer、monomer結合模式非常相似,然而結合時的親和力卻不相同,其主要原因為有相互作用力的胺基酸其提供的作用力強度的不同。二、 探討Grb2 SH2 domain上的關鍵胺基酸W121對dimer和monomer之影響,推論胺基酸W121的扭轉角度會對dimer和monomer之結合位附近的胺基酸提供的親和力有影響。並推論對於Grb2 SH2蛋白質-配體結合為是否有最適當的扭轉角,以及扭轉角的模擬變化進而了解殘基W121對於Grb2 SH2 Domain的重要性。 Grb2, an adaptor protein, plays a role in regulating cell growth, differentiation, migration, and death. Grb2 SH2 domain delivers messages to the downstream cells when the phosphorylated tyrosine combines with the receptor protein. In this work, molecular dynamics (MD) simulations were applied to shed light on the interaction between Grb2 SH2 domain and a pYVN tripeptide. Currently there are two types of Grb2 SH2-pYVN complexes available. One is a monomeric SH2 bound with a pYVN peptide; another one is dimeric SH2 bound with two pYVN peptides. Moreover, it is noteworthy that in the dimeric form the two Grb2 SH2 domains are intertwined with their extended {212441}B helixes to form domain swapping. Thermodynamic experiment conducted by Benfield et al. suggested that the monomer Grb2 SH2 bound with pYVN with a higher affinity (Ka = 6.1×105) whereas the Grb2 SH2 dimer possesses two different affinities toward pYVN, i.e., Ka = 1.5×105 for the first binding site and Ka = 4.7×104 for the second binding site, and both are lower than the monomer’s binding site. Herein, our aims are to explain the structural, energetic, and dynamic causes for the aforementioned binding affinity discrepancy. Furthermore, we evaluated the different rotamers of W121, which sits in the beginning of the swapping region, to discuss its role in domain swapping in Grb2 SH2. |