PPARγ部分促進機制之結構生物資料探勘研究及其分子入塢電腦模擬

Structural Bioinformatics Data Mining and Molecular Docking for the PPARγ Partial Agonism

李家豪(Jia-Hau Li)

指導教授 ： 林盈廷

高雄醫學大學/生命科學院/生物科技學系碩士班/碩士(2014年)

https://doi.org/10.6832/KMU.2014.00143

摘要

在蓬勃發展的網路空間世界，電腦可以模擬及分析所有領域的資料。生物資訊學運用了許多科學的學科，像是電腦科學、數學、生物學。人們可以用生物資訊工具去處理各種生物學的訊息。在這裡我們旨在探索PPARγ的部份促進機制。PPAR蛋白是一系列的核受體蛋白，功能是用做調控基因表現的轉錄因子。PPAR蛋白在細胞的分化、發育、代謝和高等生物體的癌化都扮演了很重要的角色。目前主要已知的PPAR蛋白有三種亞型：PPARα、PPARδ和PPARγ，而我們只聚焦在PPARγ。一些熟悉的PPARγ促進劑例如：Rosiglitazone和Pioglitazone，已經被用來治療第二型糖尿病、高血脂和高血糖，且由先前文獻得知促進劑啟動PPARγ蛋白提升轉錄最大效能是藉由促進劑結合到PPARγ的AF2 (Activation Function 2) 位置上所引發，然而它們卻會造成一些嚴重的副作用。事實上由促進轉錄的活性差異，可將促進劑區分為全促進劑以及部份促進劑。而有科學家推測部份促進劑可能會比全促進劑更適合當作糖尿病的藥物。我們從實驗室的工具中挑選其中兩個工具－Chimera和Discovery Studio (DS) 來分析PPARγ蛋白和促進劑。第一個工具－Chimera，這是一套可以高度擴充的軟體，可用作互動式視覺觀察、分子結構和相關資料的分析，這套軟體是由Python程式語言包裝且可由Python來進行擴充或使軟體自動運作。第二個工具－DS，DS是廣為人知的套裝軟體，可用作模擬小分子和大分子的。除此之外DS也提供了很多功能、分析方法，讓我們能做生物資訊的研究。為了瞭解PPARγ促進劑的部份促進機制，我們檢查了促進劑的X光繞射蛋白結構位置、計算B因子的平均、確認電子密度圖且以分子入塢模擬促進劑的入塢構形。我們的實驗結果暗示著：一、AF2是一個很重要的活化域，從蛋白質結晶裡配位小分子頂端的原子與AF2的距離與基因轉錄的最大效能有高度的相關性 (R = -0.94)。二、配位小分子的B因子和基因轉錄的最大效能也有高度個相關性 (R = -0.87)。三、最後在分子入塢模擬的部份，入塢的配位小分子頂端原子與AF2的距離和基因轉錄的最大效能也有著不錯的相關性 (R = -0.69)。總和了以上的結果，這暗示著小分子滑離AF2的程度能夠藉由B因子來表示，且對於PPARγ部份促進機制，促進劑和AF2的結晶距離扮演了很重要的角色。

關鍵字

部份促進劑 ； 結構生物資料探勘 ； 分子入塢

並列摘要

In the blossomed world of cyberspace, computer can simulate and analyze data of almost all area. Bioinformatics uses multiple disciplines of sciences, like computer science, mathematics and biology. One can use bioinformatics tools to deal with variety biological information. Here, we aim to explore the partial agonism of PPARγ. The peroxisome proliferator-activated receptors (PPARs) are a group of nuclear receptor proteins that function as transcription factors regulating the expression of genes. PPARs play essential roles in the regulation of cellular differentiation, development, metabolism (carbohydrate, lipid, protein), and tumorigenesis of higher organisms. Three subtypes of PPARs are known: PPARα, PPARγ, and PPARδ, and we focus on PPARγ. Some well-known PPARγ agonists, like rosiglitazone or pioglitazone, have been used in the treatment of type 2 diabetes, hyperlipidaemia and hyperglycemia, and previously we know that PPARγ is activated by agonists binding to activation function 2 (AF2), however they show some advert side effects. Actually, the agonists have two different translational activations, as classified to full and partial. People suspect that the partial agonist could be a suitable drug for diabetes than the full one. Then we use two of many tools in our lab, Chimera and Discovery Studio (DS) to analyze PPARγ and agonists. First tools, Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, it's packed by python programming language and the function can be expanded or operated automatically by Python programming language. Second, DS is a well-known suite of software for simulating small molecule and macromolecule systems. Discovery Studio provides many functions and method let us to do bioinformation research. To know the causes of partial agonism of PPARγ agonist, we examined the co-crystal pose of agonist, calculated the averaged B-factor, checked density map and obtain docked pose of agonist by molecular docking. Our results suggested that: 1. The activation function 2 (AF2) is an important activated domain, and the distance between co-crystal ligand head and the AF2 is highly correlated with PPARγ gene transcription efficacy maximum, r = -0.94. 2. The ligand B-factor is another influential element as exhibiting highly correlated to the efficacy maximum, r = -0.87. 3. Moreover, in molecular docking simulation, the distance between docked ligand head and the AF2 is well correlated with PPARγ gene transcription efficacy maximum, r = -0.69. Taken together, the above results suggest that the degree of slipping away from the AF2, indicated by B-factor and the distance from the AF2 of agonists, plays the crucial role to the PPARγ partial agonism.

並列關鍵字

Structural Bioinformatics Data Mining ； Molecular Docking ； Partial Agonism

參考文獻

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