title: Random-Coil Behavior of Chemically Denatured Topologically Knotted Proteins Revealed by Small-Angle X-ray Scattering.
abstract: Recent studies on the mechanisms by which topologically knotted proteins attain their natively knotted structures have intrigued theoretical and experimental biophysicists. Of particular interest is the finding that YibK and YbeA, two small trefoil knotted proteins, remain topologically knotted in their chemically denatured states. Using small-angle X-ray scattering (SAXS), we examine whether these chemically denatured knotted proteins are different from typical random coils. By revisiting the scaling law of radius of gyration (Rg) as a function of polypeptide chain length for chemically denatured proteins and natively folded proteins, we find that the chemically denatured knotted proteins in fact follow the same random coil-like behavior, suggesting 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 or tertiary structures.
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|‡Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
authors.forename: Po-Min
authors.initials: PM
authors.lastname: Shih
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.
authors.forename: Iren
authors.initials: I
authors.lastname: Wang
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|§Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
authors.forename: Yun-Tzai Cloud
authors.initials: YT
authors.lastname: Lee
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|‡Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
authors.forename: Shu-Ju
authors.initials: SJ
authors.lastname: Hsieh
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.
authors.forename: Szu-Yu
authors.initials: SY
authors.lastname: Chen
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|‡Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.|§Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
authors.forename: Liang-Wei
authors.initials: LW
authors.lastname: Wang
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|‡Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
authors.forename: Chih-Ting
authors.initials: CT
authors.lastname: Huang
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|∥Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
authors.forename: Chih-Ta
authors.initials: CT
authors.lastname: Chien
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|§Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
authors.forename: Chia-Yun
authors.initials: CY
authors.lastname: Chang
authors.affiliation: †Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan.|‡Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.|§Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
authors.forename: Shang-Te Danny
authors.initials: ST
authors.lastname: Hsu
mesh_terms: D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011489:Protein Denaturation / Q000187:drug effects*; D017433:Protein Structure, Secondary; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D064267:Intrinsically Disordered Proteins