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研究生:Rivo Kristian Suoth
研究生(外文):Rivo Kristian Suoth
論文名稱:The Relationship between Solvent Accessibility and Evolutionary Rate in Human Protein
論文名稱(外文):The Relationship between Solvent Accessibility and Evolutionary Rate in Human Protein
指導教授:陳玉菁陳玉菁引用關係
指導教授(外文):Yu-Ching, Chen
學位類別:碩士
校院名稱:亞洲大學
系所名稱:生物資訊學系碩士班
學門:工程學門
學類:生醫工程學類
論文種類:學術論文
畢業學年度:99
語文別:英文
外文關鍵詞:Solvent accessibilityHomo sapiensdeterminant factor of evolutionary ratealignment length
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Previous studies have established the factors, including solvent accessibility of protein, that determine the protein evolutionary rate. However, in human, this accessibility’s relationship to protein evolutionary rate remains unclear due to discrepancy of previous studies' results. Following the study done by Lin et al. (2007) which involved Saccharomyces cerevisiae as the model organism, in the recent work, we study Homo sapiens as the model organism to find out the influence of solvent accessible residues on the rate of protein evolution. The present study's result suggested that solvent accessibility of residues in human protein significantly yet weakly correlates with synonymous substitution rates, and there is some correlation change when the dataset was divided into six groups, confirming the account of alignment length in the correlation. Moreover, this study establishes that synonymous substitution rates of human protein are stable whatever the alignment lengths are.
Table of Contents
.
Abstract .......................................................................................................................... ii
Acknowledgements ...................................................................................................... iii
Chapter 1 Introduction ................................................................................................... 7
1.1 Background .......................................................................................................... 7
1.2 Research problem ................................................................................................. 9
1.3 Research aim ...................................................................................................... 10
1.4 Research hypotheses .......................................................................................... 10
Chapter 2 Materials and Methods ................................................................................ 11
2.1 Dataset ................................................................................................................ 11
2.2 Relative solvent accessibility measurement ....................................................... 12
2.3 Codon Adaptation Index .................................................................................... 14
2.4 Protein evolutionary rate estimation .................................................................. 14
2.5 Statistical analyses.............................................................................................. 16
Chapter 3 Results ......................................................................................................... 18
3.1 Difference in mean ranks of 5 variables among alignment length groups ......... 20
3.2 Correlation between solvent accessibility and protein evolutionary rate ........... 22
3.3 Relationship between protein evolutionary rate and solvent accessibility changes as alignment threshold changes .................................................................. 24
3.4 Partial correlation analyses................................................................................. 27
Chapter 4 Discussions .................................................................................................. 28
Chapter 5 Conclusions ................................................................................................. 36
References .................................................................................................................... 37
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