博碩士論文 101223013 詳細資訊




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姓名 溫珮辰(Pei-chen Wen)  查詢紙本館藏   畢業系所 化學學系
論文名稱
(An Understanding of the O2-Iron Protoporphyrin IX Binding in Human Serum Albumin and its Engineered Mutant from the O2 Diffusion Pathways and Escape Routes)
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摘要(中) 人血清白蛋白HSA (Human serum albumin)是在人體的血液循環系統之血漿中含量最多的蛋白質。許多研究闡明人血清白蛋白是一種多功能蛋白,其中它具有與高鐵血紅素hemin (iron-(III) protoporphyrin IX) 較高的結合常數,以防止其參與Fenton’s reaction而產生對身體有劇毒的羥基自由基。 人血清白蛋白對血紅素具有強親和力的特性,能將人血清白蛋白用來開發作為人造血紅素蛋白(hemoprotein),可以仿效血紅蛋白(Hb)和肌紅蛋白(Mb)與O2的結合能力。小松博士等人根據此特性,開發出了三個雙突變體,這些人造血紅素蛋白能在室溫下與氧氣可逆得結合和釋放。在這些雙突變體中以HF(I142H/Y161F)具有最高的O2親和力,由於以下原因:(i) Ile-142  His可產生類似於血紅素蛋白中血紅素之Fe2 +離子的軸向配位及(ii) Tyr-161Phe可讓Fe2 +離子的第六配位位置空出以供O2鍵結。在本研究中,使用Temperature-controlled locally enhanced sampling (TLES)方法,去探討氧氣在HSA和HF中擴散的網絡 (diffusion network)。此方法大幅提高了模擬氣體擴散的效率。我們清楚得鑑定HSA及HF的氧氣擴散腔 (diffusion cavities)及門戶網絡(portals),我們發現HSA及HF之氧氣擴散腔的網絡有明顯的不同。在HF中,所有擴散腔之間的通道是相通的,這顯示O2擴散到和heme-O2 結合有重要關係之遠端擴散腔 (distal diffusion cavity)的機率較高。然而,在HSA中擴散腔II (diffusion cavity II)到遠端擴散腔以及擴散腔I (diffusion cavity I)的通道是被禁止的。這些結果表明擴散腔II在HSA中扮演著“O2儲存槽”的角色,導致O2擴散到遠端擴散腔的機率變低。HSA和HF擴散腔的網絡結果支持HF 有較高的氧氣親和力的實驗結果。
摘要(英) Human serum albumin (HSA) is the most prominent plasma protein in our circulatory system. Many studies have revealed that HSA is a versatile protein, which has a high binding constant for hemin to prevent it participates in Fenton’s reaction to produce hydroxyl radicals, highly toxic for our body. This strong affinity of HSA for hemin has stimulated efforts to develop albumin as an artificial hemoprotein which can mimic the O2 binding capability of Hb and myoglobin(Mb). Komatsu et al. have engineered three double mutants, which can reversibly bind and release O2 at room temperature. Among these mutants, HF (I142H/Y161F)-heme has the highest O2 binding affinity, which can be ascribed to the following reasons: (i) Ile-142  His mutation creating an axially coordinated to the central Fe2+ ion of the heme similar to that of hemoprotein and (ii) Tyr-161  Phe mutation making the sixth coordinate position of Fe2+ ion available. In this study, we investigate the O2 diffusion network (diffusion cavities and portals) of HSA and HF by employing temperature-controlled locally enhanced sampling (TLES) method to greatly enhance the simulation efficiency. We have identified the O2 diffusion cavities and portals of HSA and HF. The networks of O2 diffusion cavities of HSA and HF are distinct different. In the HF, the channels between all diffusion cavities are all allowed indicating the high probability of O2 molecules diffused to the distal diffusion cavity, the key cavity for heme- O2 binding. In the wild-type HSA, the channels of distal diffusion cavity and diffusion cavity I to diffusion cavity II are allowed, however, the channels of diffusion cavity II to distal diffusion cavity and diffusion cavity I are forbidden. These results indicate the diffusion cavity II in HSA plays a role like “O2 storage” leading to low probability of O2 molecules diffused to the distal diffusion cavity. These results support the experimental results of O2-heme binding affinities of HSA and HF in terms of the network of diffusion cavities.
關鍵字(中) ★ 人血清白蛋白 關鍵字(英)
論文目次 摘要 i
Abstract ii
誌謝 iii
Table of contents iv
List of Figures vi
List of Tables viii
Chapter 1 – Introduction 1
Chapter 2 − Computational Methods 9
Chapter 3 − Results 12
3.1 Method Validation 12
3.2 Characterization of Cavities in Subdomain IB 14
3.3 O2 Diffusion in HSA 18
3.4 O2 Diffusion in HF 29
Chapter 4 − Discussion 38
Chapter 5 −Conclusion and Summary 46
References: 47
Appendix A 53
Appendix B 54
Appendix C 55
Appendix D 56
Appendix E 57
Appendix F 58
Appendix G 59
Appendix H 60
Appendix I 61
Appendix J 62
Appendix K 63
Appendix L 64
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指導教授 蔡惠旭(Hui-Hsu Gavin Tsai) 審核日期 2014-7-10
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