臺灣博碩士論文加值系統

細胞穿越胜肽是一小段胺基酸序列，通常有著多組精胺酸及賴胺酸，此種胜肽有著穿越各種類型細胞膜的能力。TAT胜肽是HIV-1 Tat蛋白質的48到60胺基酸序列，亦是一種細胞穿越胜肽，常用來攜帶貨物(ex: drug)進入細胞膜中。此種細胞穿越胜肽的特性引起了科學家的高度興趣，其穿越的機制是科學家們一直持續在進行的研究。而HBV的L蛋白質的9到18胺基酸序列也被實驗研究發現可以穿越脂質細胞膜。我們的研究利用分子動力學模擬致力於此兩種可以穿越的胜肽與POPC脂質細胞膜的交互作用。我們也連結此兩種胜肽建立成新的人工胜肽像是：HBVpreS – TAT胜肽，用來與單一的胜肽做比較，試著找出穿越效率更好的胜肽。而我們做了一系列的傘取樣模擬用來計算胜肽進入細胞膜內的平均力能。在我們的結果中，人工胜肽與我們預期的一樣，降低了跨越細胞膜邊界的能量。此外我們亦建立環肽研究其性質。

Cell-penetrating peptides (CPPs) consist of a short sequence of amino acids which is rich in arginines and lysines and has the ability to penetrate almost all types of membranes. TAT peptide, amino acid 48 to 60 of Tat sequence from HIV-1, is a kind of CPPs and used to carry cargo across the membrane into the cell. The properties of cell-penetrating peptides integrating into membranes, makes them highly interesting in science and applied research. Similarly, HBVpreS peptide, amino acids 9 to 18 of the L protein of HBV, is found to cross the lipid membrane observed in experiment studies.
Our work uses molecular dynamic simulations focusing on the interaction between each of the two peptides and POPC lipids bilayers. In addition, artificial peptides linking both peptides, e.g. HBVperS - TAT peptides, are constructed and the results compared with those of the individual peptides. The potential of mean force (PMF) is calculated from a series of umbrella sampling simulations to evaluate the energy of peptides integrating into the lipid membrane. It is found, that the artificial peptide lowers the energy barrier. Also, the cyclic peptide is build. The capability to penetrate into membrane is investigated.

Content
Acknowlegement 4
Abstract 5
論文摘要 6
Chapter 1
Introduction 7
1.1 Background 7
Cell-penetrating peptide 7
TAT 8
HBVpreS 8
Cyclic peptide 9
Molecular dynamics simulation 9
1.2 Objective 11
Chapter 2
Materials and Methods 12
2.1 Peptide sequence 12
2.2 Lipid 12
2.3 Software 12
2.4 Simulation method 14
2.5 Data analysis 16
Chapter 3
Results 17
3.1 Individual peptide 17
In water box 17
Approach membrane 18
On the surface of membrane 19
In the center of membrane 21
3.2 Artificial peptide 23
In water box 23
Approach membrane 24
On the surface of membrane 25
In the center of membrane 26
3.2 Umbrella sampling simulation 27
3.3 Cyclic peptide 29
Chapter 4
Discussion 31
4.1 Individual peptide 31
4.2 Artificial peptide 33
4.2 Umbrella sampling simulation 34
Chapter 5
Conclusions 35
Reference 36

Figures
Fig. 1 The step of our simulation 14
Fig. 2 The Schematic of pulling peptide in to membrane 15
Fig. 3 Individual peptide in a water box 18
Fig. 4 Individual peptide approach membrane 19
Fig. 5 Individual peptide on the surface of membrane 20
Fig. 6 Individual peptide in the center of membrane 22
Fig. 7 Artificial peptide in a water box 23
Fig. 8 Artificial peptide approach membrane 24
Fig. 9 Artificial peptide on the surface of membrane 25
Fig. 10 Artificial peptide in the center of membrane 26
Fig. 11 Potential of mean force 28
Fig. 12 Type 1 cyclic peptide 29
Fig. 13 Type 2 cyclic peptide 30

Tables
Table 1. Compare the natural of TAT peptide and HBVpreS peptide 9
Table 2. The ratio of the number of peptide, lipids, water molecules 13

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