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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