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研究生(外文):Nai-Wan Hsiao
論文名稱(外文):The Studies of Structure, Stability and Function on the SOX9 High-Mobility Group
指導教授(外文):Ping-Chiang Lyu
外文關鍵詞:EMSAHMG: High Mobility Groupinstability indexpImutationBioinformatics
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高移動區段(HMG: High Mobility Group)為一具八十個胺基酸的蛋白質,其認識非典型DNA結構或序列專一的DNA及一般典型雙股DNA。SOX9蛋白質是包含HMG區段的蛋白質家族,與特殊序列DNA(5’-AGAACAATGG-3’)之minor groove結合,和性別決定以及脊椎動物骨骼發育有關。SOX9 HMG區段的三級結構模型是利用已解出結構之SOX5 HMG區段模擬而來。HMG區段包含三條helix,摺疊成L形狀,helices 1和helices 2在短臂軸, helices 3在長臂軸。本篇主要利用斑馬魚的SOX9 HMG區段來研究其功能與結構的關係並提出其與DNA結合機制的模型。利用圓二色旋光儀(circular dichroism spectroscopy)偵測蛋白質的二級結構,並用熱變性實驗和化學變性實驗,研究蛋白質的穩定性。以丙胺酸取代法研究胺基酸在蛋白質中的重要性,使用電泳膠移動分析法(EMSA)來測試斑馬魚SOX9 HMG區段蛋白質結合DNA探針的親合力。實驗中分析兩個不同DNA探針“S9WT (5-TAAGAACAATGGGA-3)和COL2C1 (5-CCCACAATGCC-3)”,兩者皆能結合斑馬魚SOX9 HMG蛋白質。此研究為第一篇序列專一性結合的HMG區段丙胺酸分析報告。在多樣的突變斑馬魚SOX9 HMG蛋白質之中,F12A被發現在熱變性及化學變性上較原型蛋白質差,造成結構上較不穩定,因而使結合DNA探針的能力下降甚至到不會結合DNA,此外將F12作修飾加上一個-OH基到側基的苯環上成為Y12,將大大的減低結合DNA的能力,但其二級結構及穩定性並無改變。推測蛋白質上的F12、N10和M13的側基對結合DNA而言非常重要。以生物資訊分析其DNA結合時的結構改變,等電點(pI)高低,不穩定指數(instability index)高低及DNA結合區域的分子多寡均可解釋其生理功能與DNA專一性結合的機制。另一方面,利用結構生物資訊的分析推測出SOX9 HMG區段具有出核訊息(Nuclear Export Signal),並已利用實驗證明其功能。
A unique class of proteins, containing High Mobility Group domain(s) (HMG), recognizes unusual DNA structures and/or bends specific AT-rich linear double strand DNA. The DNA binding feature of these proteins is exhibited in the HMG domain(s). Although the sequence specific and non-sequence specific HMG domains exhibit very high sequence similarities, the reasons for the difference between their DNA recognition mechanisms are unclear. A series of zebra fish SOX9 HMG domain mutants was prepared to elucidate the importance of various residues on protein stability and DNA binding. This study is the first of a comprehensive mutagenesis study on a sequence specific HMG domain. Comparing how various residues influence sequence specific and non-sequence specific HMG domains helps us to rationalize their mode of action. Positively charged amino acids concentrated at the surface of sequence specific HMG domains recognize specific, linear AT-rich DNA segments. After the negative charges at the surface of the DNA are neutralized, the hydrophobic residues of the protein may intercalate DNA. Phenylalanine at position 12 plays a crucial role in sequence specific HMG domain. The differences in pI values, instability index and DNA contact regions between sequence and non-sequence specific HMG domains are associated with their functional modes.
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