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論文中文名稱:以分子動態模擬探討來自人類胰島素的VEALYL與LYQLEN胜肽結構穩定性與聚集行為 [以論文名稱查詢館藏系統]
論文英文名稱:Molecular Dynamics Simulations to Gain Insights into the Structural Stability and Aggregation Behavior of the VEALYL and LYQLEN Peptides Derived from Human Insulin [以論文名稱查詢館藏系統]
院校名稱:臺北科技大學
學院名稱:工程學院
系所名稱:生物科技研究所
畢業學年度:97
出版年度:98
中文姓名:林業峰
英文姓名:Yeh-Fon Lin
研究生學號:96688026
學位類別:碩士
語文別:英文
口試日期:2009-07-28
論文頁數:112
指導教授中文名:劉宣良
口試委員中文名:蔡偉博;黃志宏;林忻怡
中文關鍵詞:胰島素VEALYL胜肽LYQLEN 胜肽類澱粉纖維立體拉鍊分子動態模擬
英文關鍵詞:InsulinVEALYL peptideLYQLEN peptideamyloid-like fibrilssteric zippermolecular dynamics (MD) simulation
論文中文摘要:來自胰島素的A鏈(13-18號胺基酸)與B鏈(12-17號胺基酸)上的LYQLEN與VEALYL胜肽已被證實會形成類澱粉纖維。最近,X射線顯微晶體攝相已決定了LYQLEN與VEALYL寡聚體的分子結構,並且發現在相鄰的β-sheet之間有一個無水溶液存在並且緊密互補的結構,稱之為”立體拉鍊”。本研究利用分子動態模擬來探討不同聚集數量的LYQLEN和VEALYL胜肽與它們的glycine單點突變在水溶液環境下的結構穩定性及聚集行為。在單層模型的結果中顯示LYQLEN與VEALYL寡聚體的結構穩定性會隨著β-strand數目的增加而明顯地更為穩定。我們進而推測形成LYQLEN與VEALYL類澱粉纖維的最低成核數為三或四聚。我們的結果也指出對於LYQLEN與VEALYL寡聚體而言,glutamate與tyrosine之間的疏水作用力對於穩定同層內的相鄰β-strand扮演重要的角色。對於VEALYL寡聚體而言,V1、A3、L4、Y5和L6的側鏈形成疏水立體拉鍊並在結合鄰近的β-sheet方面扮演重要角色。突變實驗顯示V1、A3、L4、 Y5或L6如果被glycine取代則會直接破壞兩相鄰β-sheet之間的立體拉鍊,進而造成VEALYL寡聚體的結構不穩定。然而對於LYQLEN寡聚體而言,立體拉鍊則是透過L1、Q3、L4和N6的側鏈將相鄰的β-sheet結合在一起的。突變實驗顯示Y2或E5被glycine取代時會造成同層內的β-strand之間不穩定,但是L1、Q3、L4或N6被glycine取代時則會直接破壞兩相鄰β-sheet之間的立體拉鍊,而使得LYQLEN寡聚體不穩定。本篇研究的結果提供了原子尺度下穩定LYQLEN與VEALYL寡聚體的因素與它們的聚集動態行為,這將提供有用的資訊來設計新的或是修改已知的抑制劑來防止胰島素蛋白的纖維化。
論文英文摘要:The LYQLEN and VEALYL peptides from the A chain (residues 13-18) and B chain (residues 12-17) of insulin has been shown to form amyloid-like fibrils. Recently, the atomic structures of the LYQLEN and VEALYL oligomers have been determined by x-ray microcrystallography and reveal a dry, tightly self-complementing structure between the neighboringβ-sheet layers, termed as “steric zipper”. In this study, several molecular dynamics simulations with all-atom explicit water were conducted to investigate the structural stability and aggregation behavior of the LYQLEN and VEALYL peptides with various sizes and their single glycine replacement mutations. The results of our single-layer models showed that the structural stability of the LYQLEN and VEALYL oligomers increases significantly with increasing the number ofβ-strands. We further suggested that the minimal nucleus seed for LYQLEN and VEALYL fibril formation could be as small as trimer or tetramer. Our results also revealed that the hydrophobic interaction between glutamate and tyrosine plays an important role in stabilizing the adjacentβ-strands within the same layer for LYQLEN and VEALYL oligomers. For the case VEALYL oligomers, the hydrophobic steric zipper formed via the side chains of V1, A3, L4, Y5, and L6 plays a critical role in holding the two opposingβ-sheets together. Mutation simulations showed that single glycine substitution at V1, A3, L4, Y5 and L6 directly destroyed the steric zipper, leading to the destabilization of the VEALYL oligomers. For the case of LYQLEN oligomers, the steric zipper via the side chains of L1, Q3, L4, and N6 associates two neighbouringβ-sheet layers together. Mutation simulations showed that the replacement of Y2 or E5 by a single glycine residue exhibits strong destabilizing effects on the adjacentβ-strands within the same layer; whereas single glycine substitution at L1, Q3, L4, and N6 directly disrupts the steric zipper between the two neighbouringβ-sheet layers, resulting in the destabilization of the entire LYQLEN oligomers. The results of this study provide detailed atomistic insights into the factors stabilizing the LYQLEN and VEALYL oligomers and the aggregation behaviour of these two peptides. It may also provide helpful information for designing new or modified inhibitor able to prevent the fibrillization of the insulin protein.
論文目次:ABSTRACT i
ACKNOWLEDGEMENTS v
CONTENTS vi
TABLE CONTENTS x
FIGURE CONTENTS xi
Chapter 1 GENERAL INTRODUCTION 1
Chapter 2 LITERATURE REVIEW 3
2.1 Amyloid 3
2.1.1 Pathogenesis of Disease-Related Proteins 4
2.1.2 Non-Pathogenic Peptides and Proteins 5
2.1.3 The Hallmarks of Amyloid Fibrils 6
2.2 Insulin 9
2.2.1 Previous Experimental Studies of Insulin Fibrillation 11
2.2.2 Amyloidogenic Region of Insulin 14
2.3 Steric Zipper 16
2.3.1 Eight Theoretically Possible Classes of Steric Zippers 16
2.3.2 Steric Zipper Structure of Insulin Peptide Fragment 20
Chapter 3 MOLECULAR MODELING 22
3.1 Overview 22
3.2 Force Fields 23
3.2.1 Overview Several Classical Force Fields 24
3.2.2 The Parameters in the Force Field 26
3.2.3 Functional Form of the CVFF Force Field 31
3.3 Minimization 33
3.4 Equilibration 36
3.5 Molecular Dynamics 37
3.5.1 Constraints during Dynamics Simulations 39
3.5.2 Temperature Jump Techniques 41
3.6 Structure Analysis 43
3.6.1 Definition of Three Geometrical Parameters: Twist Angle, Interstrand and Intrasheet Distance 44
3.6.2 Definition of Side-Chain Contact 45
3.6.3 Radius of Gyration 46
Chapter 4 Structural Stability and Aggregation Behavior of the VEALYL Peptide Derived from Human Insulin: A Molecular Dynamics Simulation Study 47
4.1 Abstract 47
4.2 Introduction 48
4.3 Materials and Methods 51
4.3.1 Model Building 51
4.3.2 Simulation Protocol 52
4.3.2 Structural Analysis 54
4.4 Results and discussion 54
4.4.1 The Structural Stability of the VEALYL Oligomers with Various Sizes 54
4.4.2 The Role of the Hydrophobic Interaction between E2 and Y5 in the Stability of the VEALYL Oligomers 58
4.4.3 The Role of the Intersheet Hydrophobic Interactions in Stabilizing the VEALYL Oligomers 61
4.4.4 The Effects of a Single-Glycine Replacement on the Stability of the VEALYL Oligomers 63
4.4.5 The Biological Implications of this Study 67
4.5 References 69
Chapter 5 Molecular Dynamics Simulations to Investigate the Structural Stability and Aggregation Behavior of the LYQLEN Peptide Derived from 72
5.1 Abstract 72
5.2 Introduction 73
5.2.1 Introduction of Amyloid Fibrils 73
5.2.2 Previous Studies of Insulin Protein 74
5.2.3 Introduction of Steric Zipper 75
5.2.4 Purpose 76
5.3 Materials and Methods 77
5.3.1 Model Building 77
5.3.2 Simulation Protocol 78
5.3.3 Structural Analysis 80
5.4 Results and discussion 80
5.4.1 The Structural Stability of the LYQLEN Oligomers with Various Sizes 80
5.4.2 The Role of Interstrand Hydrophobic Interaction between Y2 and E5 in the Stability of the LYQLEN Oligomers 83
5.4.3 The Role of the Steric Zipper in Stabilizing the LYQLEN Oligomers 84
5.4.4 The Effects of a Single-Glycine Replacement on the Structural Stability of the LYQLEN Oligomers 87
5.4.5 The Twisting β-Sheet Conformation in Explicit Water 90
5.4.6 The Biological Implications of this Study 93
5.5 References 96
Chapter 6 GENERAL CONCLUSIONS 103
Chapter 7 GENERAL REFERENCES 105
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