Structural Characterization of the Phosphotyrosine Binding of A High Affinity SH2 domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations

• Main Authors: Feng, Ming-Hsiang, 馮銘祥
• Other Authors: Carmay Lim
• Format: Others
• Language: en_US
• Online Access: http://ndltd.ncl.edu.tw/handle/08493661268504672669

碩士 === 國立清華大學 === 化學學系 === 84 === SH2 domain是一種在細胞內訊號傳遞過程中扮演很重要角色的蛋白質基本 組成單位之一。它的功能乃是去調節控制這些細胞質訊號分子彼此的作用 ，俾使正常細胞功能得以運作。為了要了解這些訊號的傳遞機制，甚至於 進一步控制或修飾其功能，第一步就是了解這些訊號分子彼此之間準確的 作用力。因此，本文乃是利用分子動力學模擬來修飾優化NMR結構以獲取 更高解析度的結構，進而可提供我們一個清楚的分子之間精確作用的圖像 ，並且利用核磁共振化學位移的量子力學計算來進一步確認MD結構的優越 性。我們所感興趣的分子是磷酸解脂酵素(phospholipase C上C端的SH2 domain，它是血小板生長因子接受器的一個受質，會和1021位置上的pTyr 產生結合而將訊號往下傳遞。雖然這個複合物的NMR結構已被解出，但是 由於一些因素，包括pTyr的結合元素，Arg，的脂肪基因微秒 (ms) 的運 動而使NMR訊號容易變胖變弱而不易決定及 pTyr磷酸根上缺氫等等的影響 ，使得pTyr結合口袋並不具有很高的NOE密度進而影響這一區域的結構品 質。雖然MD模擬以NMR結構為出發點，但很快就收歛到一個新的組態 (conformation)，而這個組態很明顯地比原來的NMR結構更能解釋實驗看 到的核磁共振化學位移光譜，並且也提供一些不同於原作者的解釋。總而 言之，本研究是一個很好的示範用來說明MD的優點一方面不但可用來增強 從NMR結構中所獲取的 息，包括氫鍵分佈及其它的作用力；另一方面也可 從原子尺度蚖異U解釋實驗化學位移的數據。 hree molecular dynamics simulations of the free,hosphate-ion- bound and phosphopeptide-bound-terminal SH2 domain of phospholipase C have beenerformed to aid in the interpretation of chemical shift data and lucidation of interatomic interactions at the phosphotyrosine inding region of PLCC. The simulation of the phosphopeptideomplex has been carried out with newly developed CHARMMorce-field parameters for the pTyr residue, optimized againstxperimental and ab initio data. The lack of NOEsnvolving phosphate in the binding pocket has recently hemical shift analysis of the pTyr binding region for a more haracterization of the hydrogen bonding interactions involvingTyr. Although most of these interactions are not present in theMR structure used as the simulation starting point, the systemonverges early in the simulation to a structure more compatible he chemical shift data.he simulation structure of the PLCC.pY complex reveals a moreomplete picture of inter-atomic interactions in the pTyr bindingocket than is possible with current chemical shift and NOEpproaches alone, thereby permitting the identification of therimary pTyr-recognition residues. In particular, this pattern ofnteractions is strikingly similar to those of crystal structures elated SH2 domains. Moreover, ab initio evaluation of chemicalhifts of the three arginines in the pTyrinding pocket based on the current PLCC.pY MD structuren general agrees well with experimental values,hich in turn validate the MD structure.he simulations also suggest several alternative interpretationsf the chemical shift data to those suggested in the experimentalnvestigation. This demostrates the power of MD serving to refine tructure as well as aiding in the interpretation of chemical