Structural and functional studies on stem cell transcription factors-an integrated in silico approach : in silico analysis of Oct4, Sox2 and Nanog
- 주제(키워드) Thesis Submission
- 발행기관 아주대학교
- 지도교수 Sangdun Choi
- 발행년도 2018
- 학위수여년월 2018. 2
- 학위명 박사
- 학과 및 전공 일반대학원 분자과학기술학과
- 실제URI http://www.dcollection.net/handler/ajou/000000027012
- 본문언어 영어
- 저작권 아주대학교 논문은 저작권에 의해 보호받습니다.
초록/요약
Reprogramming of human somatic cells into induced pluripotent stem cells (iPSCs) signifies the advancement in biological principles and technologies that have been developed over the last decades [1]. The transcription factors (TFs) such as Oct4 and Sox2 and their interactions in biological systems are considered as the key factors in reprogramming process [2]. Despite the fact that Oct4 and Sox2 have independent roles in defining other cell types, their function in reprogramming cells is due to the cooperative interaction between them that drives the transcription of target genes [3, 4]. There are ample amount of biochemical studies available for these proteins, whereas structural mechanism behind their cooperative interactions are not clear. Explicit structural knowledge of protein-protein and protein-DNA interaction among Oct4, and Sox2 can support to analyze the structure-function relationship of these TFs and reprogramming process. The availability of Oct4 and Sox2 atomic structures has improved our understanding about their binding preferences [5-7]; however, there is no experimental evidence that shows how binding of one protein to DNA is necessary to incorporate other proteins, or what conformational alterations in DNA/protein perpetuate such allosteric mechanisms. Thus, in our first study we focused on Oct4/Sox2 cooperative interactions in undifferentiated embryonic cell transcription factor 1 (Utf1) and fibroblast growth factor 4 (Fgf4) promoter regions, in order to identify the structural mechanism behind its distinct efficiency during reprogramming process. TFs bind to DNA in a sequence-specific manner and function to regulate the transcription of target genes. Thus, it is valuable to study the unique characteristics of such specific DNA binding pattern for each TF. Hence, in our second study, the specificity and affinity of Sox2 protein for its distinct DNA binding patterns were analyzed using computational techniques.
more목차
CHAPTER I INTRODUCTION 1
1.1 Induced pluripotent stem cells (iPSCs) 1
1.2 Yamanaka factors 2
1.3 Cooperative binding of TFs 3
1.4 Characteristics of Oct4 and Sox2 6
1.5 Interrogation in stem cell TF regulation 7
CHAPTER II METHODS 9
2.1 Protein preparation for Oct4/Sox2 interaction study 9
2.2 Molecular Dynamic (MD) simulation 10
2.3 Protein-DNA preparation for Sox2 binding affinity analysis. 11
2.4 Steered MD and umbrella sampling 12
2.5 Principal Component Analysis (PCA) 13
2.6 Energy calculation for protein-DNA complex 14
2.7 DNA conformational Analysis 15
2.8 Base stacking energy calculation 16
CHAPTER III RESULTS (EXTENDED ABSTRACTS OF MANUSCRIPTS) 17
3.1 Research Article 1: Structural mechanism behind distinct efficiency of Oct4/Sox2 proteins in differentially spaced DNA complexes 17
3.2 Research Article 2: Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation 22
CHAPTER IV CONCLUSION AND FUTURE PROSPECTS 28
4.1 Conclusion 28
4.2 Future prospects 29
BIBLIOGRAPHY 30
Appendix I 36
Appendix II 58
