Application of Small Angle X-ray Scattering on Multi-domain Protein Trigger Factor and Knotted Proteins

• Main Authors: Shih, Po-Min, 施博閔
• Other Authors: Hsu, Ban-Dar
• Format: Others
• Language: en_US
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/42023970220115444563

碩士 === 國立清華大學 === 生物資訊與結構生物研究所 === 102 === Abstract Small angle X-ray scattering (SAXS) is a powerful methods in observing particles’ shapes. To our knowledge, trigger factor (TF) has a non-native dimer form from crystal packinf artifact; Knotted protein YibK conatains the knot in chemically denatured state; UCHL1 wild type (WT) and its mutantion I93M have almost the same crystal structure but the different behaviors. We use SAXS to investigate these phenomena with ATSAS programs. Rigid body modeling reveals the reorientational TF domains’ positions to fit experimental data. With mixture and flexibility system, we analyzed the Rg distribution of YibK to understand the structural information in chemically denatured condition. Combination of SAXS and molecular dynamic (MD) simulation reveals how the local structural effect on the global conformation. We found that the new orientation of TF individual domains have a better predicted SAXS data than crystal structures. Applied Flory’s theory on experimental SAXS results, knotted proteins have similar global conformation with those unknotted proteins.