Theoretical Analysis of the Spin-label ESR Spectra for the Confined Polypeptides within Nanochannels Using Tether-in-a-cone Model

• Main Authors: Chien, Chia-Lung, 錢家隆
• Other Authors: Chiang, Yun-Wei
• Format: Others
• Language: zh-TW
• Published: 2012
• Online Access: http://ndltd.ncl.edu.tw/handle/90169664988113714842

碩士 === 國立清華大學 === 化學系 === 100 === Spin-labeled electron spin resonance (ESR) in recent years has been combined together with mesoporous materials and demonstrated as a new biophysical methodology. Upon encapsulation of the spin-labeled biomolecules into the nanochannel of the mesoporous materials, the nano-confinement effects were proved to be effective in reducing isotropic tumbling motions of the spin-labeled molecules and, consequently, enhancing the ESR spectroscopic resolutions in the anisotropy of the local environment. These spectroscopic improvements made it possible for ESR techniques to study protein dynamics at room/physiological temperatures in the absence of viscosity agents that could possibly disrupt protein dynamical structure. However, a theoretical model for analyzing the ESR spectra of confined biomolecules has yet to be developed. To gain the benefits of the nano-confinement effects, it is urgently necessary to apply a more rigorous theoretical model of ESR lineshape theory to the analysis of the spectra collected under nano-confinement. This study incorporates the tether-in-a-cone (TIAC) model into the analysis of the inter-spin distance distribution of cw-ESR spectra. TIAC was previously developed by Eric J. Hustedt and applied to ESR spectra of a disordered system in a frozen solution state. The analysis was found to be very limited due to the poor cw-ESR resolution in the disordered system. In the TIAC model, a detailed molecular model describing the magnetic and molecular frames of each single nitroxide spin, the relative orientations of each spin pairs, and the magnitude of nitroxide side-chain disordering in terms of the cone width is taken into consideration in the spectral simulations. In this study, we follow the theoretical work of Eric J. Hustedt and develop a home-written Matlab program of the TIAC model calculation. In Chapter 1, we give a brief introduction concerning spin-label ESR techniques, the MSU mesoporous material, and the studied model peptide n3, which is a 26-residue-long polypeptide derived from prion protein. In Chapter 2, we give theoretical background and detailed descriptions as well as equation derivations of the TIAC model. In the first part of Chapter 3, a series of numerical model experiments are performed to demonstrate the validity of the program and the feasibility of the TIAC model for analyzing the spectra of spin-labeled biomolecules in nanochannels. In the second part of Chapter 3, a study of the real experimental data analysis using the TIAC model is presented. The TIAC program is utilized to extract the inter-spin distance distributions of the doubly labeled n3 polypeptides. A comparison of the TIAC results and the previous study based on point-to-point assumption is provided. With this sophisticated model, we demonstrate in both the studies of the model and experimental analyses that the use of the TIAC model is useful for revealing the relative orientational information that is essential to understanding the biomolecular conformations in the nanochannels. A concluding remark and summary of the improvements and perspective are given in Chapter 4.