Alzheimer Disease; Membrane Proteins; Pharmacology; Crystallography, X-Ray; Chemicals and Drugs
Public Health Interests
In our laboratory we are interested in the structure and mechanism of a class of integral membrane proteins called intramembrane proteases. These proteases are involved in many important biological pathways responsible for metabolic regulation and cell signaling. The x-ray structures of rhomboid protease and GxGD protease, both solved first in our laboratory, have revealed general architectural principles for the two protease families, enabling us to ask specific questions about their mechanism of action. One question concerns how the protease changes conformation during catalysis. Since the active site of the protease is filled with water, it has to be closed initially to minimize unfavorable contact with lipids. Then how does transmembrane substrate, whose diffusion is restricted to the membrane plane, gain access to the active site? The crystal structures showed that the proteases have narrow transmembrane domains, suggesting that the lipid bilayer is severely constricted around the protein. Can this affect the presentation of buried cleavage sites to the protease? Finally, how does the protease achieve specificity? To study these questions we apply a wide array of biochemical and biophysical techniques to the two protease systems described above. The knowledge generated from these studies has both theoretical and practical significance because many membrane proteases are potential targets for pharmacological intervention.
Speciailzed Terms: Membrane protein; X-ray crystallography; Enzyme mechanism
Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S’ subsites.
Xue, Y., Chowdhury, S., Liu, X., Akiyama, Y., Ellman, J. & Ha, Y. (2012) Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S’ subsites. Biochemistry 51, 3723-3731.
The catalytic mechanism of rhomboid protease GlpG probed by 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate.
Xue, Y. & Ha, Y. (2012) The catalytic mechanism of rhomboid protease GlpG probed by 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate. J. Biol. Chem. 287, 3099-3107.
The crystal structure of GXGD membrane protease FlaK.
Hu, J., Xue, Y., Lee, S. & Ha, Y. (2011) The crystal structure of GXGD membrane protease FlaK. Nature 475, 528-531.
Open-cap conformation of intramembrane protease GlpG.
Wang, Y. & Ha, Y. (2007) Open-cap conformation of intramembrane protease GlpG. Proc. Natl. Acad. Sci. U.S.A. 104,2098-2102.
The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG.
Wang, Y., Maegawa, S., Akiyama, Y. & Ha, Y. (2007) The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J. Mol. Biol. 374, 1104-1113.
Crystal structure of a rhomboid family intramembrane protease.
Wang, Y. Zhang, Y. & Ha, Y. (2006) Crystal structure of a rhomboid family intramembrane protease. Nature 444,179-183.
Full List of PubMed Publications
- Muftuoglu Y, Xue Y, Gao X, Wu D, Ha Y: Mechanism of substrate specificity of phosphatidylinositol phosphate kinases. Proc Natl Acad Sci U S A. 2016 Aug 2; 2016 Jul 20. PMID: 27439870
- Hu J, Yuan Q, Kang X, Qin Y, Li L, Ha Y, Wu D: Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled. Nat Commun. 2015 Sep 14; 2015 Sep 14. PMID: 26365782
- Kuo IY, Hu J, Ha Y, Ehrlich BE: Presenilin-like GxGD membrane proteases have dual roles as proteolytic enzymes and ion channels. J Biol Chem. 2015 Mar 6; 2015 Jan 21. PMID: 25609250
- Xue Y, Ha Y: Large lateral movement of transmembrane helix S5 is not required for substrate access to the active site of rhomboid intramembrane protease. J Biol Chem. 2013 Jun 7; 2013 Apr 22. PMID: 23609444
- Ha Y, Akiyama Y, Xue Y: Structure and mechanism of rhomboid protease. J Biol Chem. 2013 May 31; 2013 Apr 12. PMID: 23585569
- Xue Y, Chowdhury S, Liu X, Akiyama Y, Ellman J, Ha Y: Conformational change in rhomboid protease GlpG induced by inhibitor binding to its S' subsites. Biochemistry. 2012 May 8; 2012 Apr 24. PMID: 22515733
- Xue Y, Ha Y: Catalytic mechanism of rhomboid protease GlpG probed by 3,4-dichloroisocoumarin and diisopropyl fluorophosphonate. J Biol Chem. 2012 Jan 27; 2011 Nov 29. PMID: 22130671
- Xue Y, Lee S, Ha Y: Crystal structure of amyloid precursor-like protein 1 and heparin complex suggests a dual role of heparin in E2 dimerization. Proc Natl Acad Sci U S A. 2011 Sep 27; 2011 Sep 19. PMID: 21930949
- Xue Y, Lee S, Wang Y, Ha Y: Crystal structure of the E2 domain of amyloid precursor protein-like protein 1 in complex with sucrose octasulfate. J Biol Chem. 2011 Aug 26; 2011 Jun 29. PMID: 21715329
- Hu J, Xue Y, Lee S, Ha Y: The crystal structure of GXGD membrane protease FlaK. Nature. 2011 Jul 17; 2011 Jul 17. PMID: 21765428
- Lee S, Xue Y, Hu J, Wang Y, Liu X, Demeler B, Ha Y: The E2 domains of APP and APLP1 share a conserved mode of dimerization. Biochemistry. 2011 Jun 21; 2011 May 26. PMID: 21574595
- Hoopes JT, Liu X, Xu X, Demeler B, Folta-Stogniew E, Li C, Ha Y: Structural characterization of the E2 domain of APL-1, a Caenorhabditis elegans homolog of human amyloid precursor protein, and its heparin binding site. J Biol Chem. 2010 Jan 15; 2009 Nov 10. PMID: 19906646
- Ha Y: Structure and mechanism of intramembrane protease. Semin Cell Dev Biol. 2009 Apr; 2008 Nov 19. PMID: 19059492
- Wang Y, Maegawa S, Akiyama Y, Ha Y: The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J Mol Biol. 2007 Dec 7; 2007 Oct 11. PMID: 17976648
- Ha Y: Structural principles of intramembrane proteases. Curr Opin Struct Biol. 2007 Aug; 2007 Aug 21. PMID: 17714936
- Wang Y, Ha Y: Open-cap conformation of intramembrane protease GlpG. Proc Natl Acad Sci U S A. 2007 Feb 13; 2007 Feb 2. PMID: 17277078
- Wang Y, Zhang Y, Ha Y: Crystal structure of a rhomboid family intramembrane protease. Nature. 2006 Nov 9; 2006 Oct 11. PMID: 17051161
- Wang Y, Ha Y: The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain. Mol Cell. 2004 Aug 13. PMID: 15304215
- Ha Y, Stevens DJ, Skehel JJ, Wiley DC: X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus. Virology. 2003 May 10. PMID: 12758169