Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Poster Session I

14 – POS Board 14 Random Coil-like Behaviour of Chemically Denatured Topologically Knotted Protein Monitored by Small Angle X-ray Scattering Po-Min Shih 1,3 , Liang-Wei Wang 1,2,3 , Shu-Ju M. Hsieh 1 , Chih-Ting Huang 1,3 , Iren Wang 1 , Chih- Ta H. Chien 1,2 , Szu-Yu Chen 1 , Ping-Chiang Lyu 3 , Ban-Dar Hsu 3 , Shang-Te Danny Hsu 1,2,3 . 1 Academia Sinica, Taipei, Taiwan, 2 National Taiwan University, Taipei, Taiwan, 3 National Tsing Hua University, Hsinchu, Taiwan. Recent studies on the mechanisms by which topologically knotted proteins attain their natively knotted structures have intrigued theoretical and experimental biophysicists in the field of protein folding. Despite the lack of spectral signatures to identify the presence of residual secondary and tertiary structures, cyclization-coupled refolding data provided strong biochemical evidence to indicate that YibK and YbeA, two best-studied knotted proteins, remain knotted in their chemically denatured states. Using small angle X-ray scattering, we ask the question of whether these chemically denatured knotted proteins possess any unique structural features that would set them apart from typical random coils. Radius of gyration (R g ) is used to monitor global conformational changes associated with the chemical denaturation of the knotted proteins and the unfolding transitions are in line with previously reported data extracted by spectroscopic methods. By revisiting the scaling law of R g as function of polypeptide chain length for chemically denatured proteins, and compiling a new empirical scaling law for the natively folded proteins, we find that the chemically denatured knotted proteins in fact follow the same random coil-like behaviour. The results suggest that the formation of topological protein knots do not necessarily require global compaction while the loosely knotted polypeptide chains are capable of maintaining the correct chirality without defined secondary and/or tertiary structures.

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