Research focus 研究方向


Our research interests are primarily focused on the investigation of the structures and properties of biological molecules, especially proteins and quadruplex-forming G-rich oligonucleotides, in the context of folding dynamics and their relationship to biological evolution and disease. We are working on the folding of knotted proteins, in particular, human ubiquitin C-terminal hydrolayses (UCHs), which have one of the most complex protein knots identified to date. A variety of biophysical, biochemical and computational approaches are employed to help understand how disease-associated mutations and post-translational modifications of various proteins affect their folding properties, thereby causing disorders.
Recent publications


Our recent paper (Sriramojou et al., Sci. Rep. (2018) 8, 7076) demonstrated the unprecedented mechanostabilities of 52-knotted human ubiquitin C-terminal hydrolases (UCHs). The ClpXP-dependent proteolysis of the human proteasome-associated UCH-L5, in particular, was 10000 times slower than that of GFP, which is chemically and thermally far more stable than any of the four UCHs. This finding hinted the functional benefits of being topologically knotted, at least for UCH-L5 that needs to work in a tug of war against the proteasome to compete for the same poly-ubiquitinated substrates.


Through comparative folding analyses of unknotted versus trefoil-knotted ornithine transcarbamylases by using hydrogen-deuterium exchange mass spectrometry (HDX-MS) in conjunction with small angle X-ray scattering and intrinsic fluorescence spectroscopy, we proposed that, in addition to substrate specificity, the knotted structures in XcAOTC and BfSOTC may play an important role in stabilising the folding dynamics, particularly around the knotted structural elements. (Sriramoju, Yang & Hsu, Biochem. Biophys. Res. Commun. (2018) in press).

SELECTED PUBLICATIONS

Folding dynamics and functions of topologically knotted proteins
  • M. K. Sriramojou, T. J. Yang & S.-T.D. Hsu* "Comparative folding analyses of unknotted versus trefoil-knotted ornithine transcarbamylases suggest stabilizing effects of protein knots" (2018) Biochem. Biophys. Res. Common. in press
  • Y.T.C. Lee & S.-T.D. Hsu* "A natively monomeric deubiquitinase UCH-L1 forms highly dynamic but defined metastable oligomeric folding intermediates" (2018) J. Phys. Chem. Lett. 9, 2433
  • M. K. Sriramojou, Y. Chen, Y.T.C. Lee & S.-T.D. Hsu* "Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease" (2018) Sci. Rep. 8, 7076
  • Y.T.C. Lee, C.Y. Chang, S.Y. Chen, Y.R. Pan, M.R. Ho & S.-T.D. Hsu* "Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome" (2017) Sci. Rep. 7, 45174
  • S.-T.D. Hsu*  "Protein knotting through concatenation significantly reduces folding stability." (2016) Sci. Rep. 6, 39357  
  • I. Wang, S.Y. Chen & S.-T.D. Hsu*  "Folding analysis of the most complex Stevedore's protein knot." (2016) Sci. Rep. 6, 31514  
  • S.C. Lou, S. Wetzel, H. Zhang, E.W. Crone, Y.T. Lee, S.E. Jackson & S.-T.D. Hsu “The knotted protein UCH-L1 exhibits partially unfolded forms under native conditions that share common structural features with its kinetic folding intermediates” J. Mol. Biol. (2016) 428, 2507-20 
  • L.W. Wang, Y.N. Liu, P.C. Lyu, S.E. Jackson, S.-T.D. Hsu*. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori. (2015) J. Phys. Condens. Matter 27(35), 354106
  • P.M. Shih, I. Wang, Y.T. Lee, S.J. Hsieh, S.Y. Chen. L.W. Wang, C.T. Huang, C.T. Chien, C.Y. Chang & S.-T.D. Hsu “Random coil behavior of chemically denatured topologically proteins revealed by small angle X-ray scattering” J. Phys. Chem. B (2015) 119, 5437-43 
  • I. Wang, S.Y. Chen & S.-T.D. Hsu “Unraveling the folding mechanism of the smallest knotted protein, MJ0366” J. Phys. Chem. B (2015) 119, 4359-70 
  • F. I. Andersson, E.F. Werrell, L. McMorran, W. J. Crone, C. Das, S.-T.D. Hsu & S. E. Jackson "The Effect of Parkinson's Disease Associated Mutations on the Deubiquitinating Enzyme UCH-L1" J. Mol. Biol. (2011) 407, 261-72
G-quadruplexes 
  • Z.F. Wang, M.H. Li, W.W. Chen, S.-T.D. Hsu* & T.C. Chang* “A novel transition pathway of ligand-induced topological conversion from hybrid forms to parallel forms of human telomeric G- quadruplexes” Nucleic Acids Res., (2016) 44, 3958-68
  • M. Kuo, Z.F. Wang, T.Y. Tseng, M.H. Li, S.T.D. Hsu, J.J. Lin and T.C. Chang* "The Conformational transition of hairpin structure to G-quadruplex within the WNT1 gene promoter" J. Am. Chem. Soc. (2014) 137(1), 210-8
  • Z.F. Wang, M.H. Li, S.-T.D. Hsu, & T.C. Chang "Structural basis of sodium-potassium exchange of a human telomeric DNA quadruplex without topological conversion" Nucleic Acid Res. (2014) 42, 4723-33
  • M.H. Li, Z.F. Wang, M. Kuo, S.-T.D. Hsu*, & T.C. Chang* "Unfolding kinetics of human telomeric G-quadruplexes studied by NMR Spectroscopy" J. Phys. Chem. B. (2014) 118, 931-6
  • A. Bugaut, R. Rodriguez, S. Kumari, S.-T.D. Hsu, and S. Balasubramanian* “Small molecule-mediated inhibition of translation by targeting a native RNA G-quadruplex” Org. Biomol. Chem. (2010) 8, 2771-6
  • S.-T.D. Hsu, P. Varnai, A. Bugaut, A.P. Reszka, S. Neidle, and S. Balasubramanian “A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics” J. Am. Chem. Soc. (2009) 131, 13399-409
  • Z.A.E. Waller, S.A. Sweitz, S.-T.D. Hsu and S. Balasubramanian* “A small molecule that disrupts G-quadruplex DNA and enhances gene expression” J. Am. Chem. Soc. (2009) 131, 12628-33
  • J. Dash, P.S. Shirude,S.-T.D. Hsu and S. Balasubramanian “Diarylethynyl amides that recognise the parallel conformation of genomic promoter DNA G-quadruplexes” J. Am. Chem. Soc., (2008) 130, 15950-6
Co-translational folding and chaperones 
  • E. Barbet-Massin, C.T. Huang, V. Daebe, S.-T.D. Hsu, B. Reif* "Site-specific solid-state NMR Studies of "trigger factor" in complex with the large ribosomal subunit 50S." (2015) Angewandte Chimie Int'l Ed. 54(14), 4367-9
  • L.D. Cabrita, S.-T.D. Hsu, H. Launay, C.M. Dobson* and J. Christodoulou* “Probing ribosome-nascent chain complexes produced in vivo by NMR spectroscopy” PNAS  (2009) 106, 22239-44
  • S.-T.D. Hsu, L.D. Cabrita, P. Fucini, J. Christodoulou and C.M. Dobson “Probing side-chain dynamics of a ribosome-bound nascent chain using methyl NMR spectroscopy“ J. Am. Chem. Soc. (2009) 131, 8366-7
  • S.-T.D. Hsu, C.W. Bertoncini and C.M. Dobson “The use of protonless NMR spectroscopy to alleviate the loss of information resulting from exchange-broadening“ J. Am. Chem. Soc. (2009) 131, 7222-3
  • S.-T.D. Hsu, P. Fucini, L.D. Cabrita, H. Launay, C.M. Dobson and J. Christodoulou “Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy” PNAS (2007) 104, 16516-16521 / Must Read by F1000 
Drug discovery and biotechnology 
  • T.J. Hsieh, H.Y. Lin, Z. Tu, T.C. Lin, S.C. Wu, Y.Y. Tseng, F.T. Liu, S.-T. D. Hsu* & C.H. Lin* "Dual binding modes of thio-digalactosides with human galectins-1, -3 and -7 as the structural basis of potent and selective inhibitors” Sci. Rep., (2016) 6, 29457
  • J.H. Liao, C.T. Chien, H.Y. Wu, K.F. Huang, I. Wang, M.R. Ho, I.F. Tu, I.M. Lee, W. Li, Y.L. Shih, C.Y. Wu, P. Lukyanov, S.-T.D. Hsu* & S.H. Wu* “A multivalent marine lectin from Crenomytilus grayanus possesses anti-cancer activity through recognizing globotriose Gb3” J. Am. Chem. Soc., (2016) 138, 4787-96
  • S.-T.D. Hsu, E. Breukink, E. Tischenko, B. de Kruijff, M.A.G. Lutters, R. Kaptein, A.M.J.J. Bonvin and N.A.J. van Nuland "The nisin–lipid II complex reveals a pyrophosphate cage provides a blueprint for novel antibiotics" Nat. Struc. Mol. Biol. (2004) 11, 963-967 / Must Read by F1000 
FULL PUBLICATION LIST [click here] or [find the entries in PubMed]
Supported by the International Human Frontier Science Program