Probing the Protein Backbone Dynamics of the HATH Domain of Human Hepatoma-Derived Growth Factor in Monomer and Dimer

• Main Authors: Shih-Chi Tien, 田世齊
• Other Authors: Tai-Huang Huang
• Format: Others
• Language: en_US
• Published: 2006
• Online Access: http://ndltd.ncl.edu.tw/handle/30791707606816822961

碩士 === 國立清華大學 === 生物資訊與結構生物研究所 === 94 === Human hepatoma-derived growth factor (hHDGF) is a member of HRPs (HDGF-related proteins) family of proteins. HRPs belong to a new protein family that has been known in nephrogenesis, tumorigenesis, vascular development, cell proliferation and transcriptional activation. All the HRPs have the conserved N-terminal homologous to the amino terminal of HDGF (HATH) domain, but vary in the C-terminal domain. hHDGF is a 240-amino acid protein, which can be divided into two parts: the first is the well-structured HATH domain, from residues 1-100 and the structure has been determined by NMR; the second is the C-terminal domain, from residues 101-240 , which is disorder. HATH domain has been shown to bind to heparin and heparin sulfate located outside the surface of cell membrane and facilitated internalization of the protein into cell. The C-terminal domain may help translocate the protein from cytoplasm to nucleus, and serve as a signal to stimulate cell growth. Previous studies showed that HATH domain monomer shares a portion of structure with each other to form the particular dimer called the domain-swapped dimer. Dimer has much higher heparin-binding affinity to heparin than that of the monomer. My thesis work is aimed at determining the difference in dynamics by NMR relaxation method between monomer and the homo-dimer of the HATH domain. 15N spin relaxation rates and heteronuclear NOE determined at 600 MHz field were analyzed by Modelfree approach to extract the dynamic parameter: S2 (order parameter), τe (effective correlation time) and Rex (chemical exchange rate). I also use Reduced Spectral Density Mapping to determine the spectral density functions: J(ω0.87H), J(0) and J(ωN). The results showed that the domain swapped semi-dimer packs similar in spatial and orientation compares to the monomer by order parameters and spectral density function, J(0.87H). Besides fast local fluctuation loop motions act similar in both monomer and dimer, there were much more micro- to millisecond motions in monomer. Both in monomer and dimer, the L2 loop region acts more complicated dynamic motions with fitting to effective correlation times and exchange rates. We demonstrated the dynamic similarity and differences in monomer and dimer of HATH domain in wide-ranged time scale by using NMR relaxation experiments.