TEMPO-Assisted Free-Radical-Initiated Fragmentation of Arginine–Alanine Peptides : Effects of Terminal Arginine Position Revealed by Mass Spectrometry and Molecular Dynamics
- 주제어 (키워드) Polyalanine Peptide Structure Analysis , TEMPO-Assisted Mass Spectrometry , Peptide fragmentation , GROMACS-Based Molecular Dynamics
- 발행기관 서강대학교 일반대학원
- 지도교수 오한빈
- 발행년도 2025
- 학위수여년월 2025. 8
- 학위명 석사
- 학과 및 전공 일반대학원 화학과
- 실제 URI http://www.dcollection.net/handler/sogang/000000081893
- UCI I804:11029-000000081893
- 본문언어 영어
- 저작권 서강대학교 논문은 저작권 보호를 받습니다.
목차
Ⅰ. Introduction 6
Ⅱ. Materials and Methods 10
1. Materials 10
2. Synthesis of p-TEMPO-Bn-Sc-NHS 10
3. Peptide conjugated with p-TEMPO-Bn-Sc-NHS 13
4. Mass Spectrometry and Analysis 14
5. Survival Fraction Calculation 15
6. Molecular Dynamics Simulations 16
Ⅲ. Result and Discussion 19
1. Confirmation of Successful TEMPO Conjugation to Model Peptides
19
2. Fragmentation Behavior of TEMPO-Labeled Peptides with Terminal
Arginine (N- and C-Terminal) in HCD-MS/MS 24
2.1 Fragmentation Characteristics of TEMPO–Arg–Ala₇: Localized
Cleavage via N-Terminal Arginine 24
2.2 Fragmentation Characteristics of TEMPO–Ala₇–Arg: Extended
Radical Migration via C-Terminal Arginine 27
2.3 Effect of Arginine Position on Radical Propagation and
Fragmentation Selectivity 29
2.4 Survival Behavior of TEMPO-Labeled Peptides 32
2.5 Energetic Thresholds and Fragmentation Mechanisms of
TEMPO-Labeled Peptides in HCD-MS/MS 35
3. Structural Stability from MD Simulations Using GROMACS 36
3.1 Simulation Setup and Parameterization 36
3.2 Global Structural Stability Assessed by RMSD and Radius of
Gyration 44
3.3 Hydrogen Bond Network Disruption and Helix Loss 49
3.4 Ramachandran Plot-Based Evaluation of Helix Stability and
TEMPO-Induced Structural Changes 53
3.5 Structural Mechanisms of TEMPO-Induced Destabilization 57
3.6 Correlating Structural Destabilization with Fragmentation
Behavior in HCD-MS 60
Ⅳ. Conclusion 63
Reference 66
