Professor, Department of Biochemistry and Biomedical Sciences

4H25A Health Sciences Centre McMaster University
Tel: 905-525-9140 ext. 22455
Email: yang@mcmaster.ca

Research

• Structural Biology
• Protein/Nucleic Acid Structure/Function

 

Molecular modeling of protein - protein and protein - ligand interactions

The focus of my current research is in using computational tools to investigate molecular interactions. The main tool is the ZMM program suite and the molecular systems being investigated are ice - antifreeze, ion channels - toxin and cellulose - cellulases. I am also working with Professor Zhorov in using molecular modeling tools to teach biochemistry.

Selected Publications

• Solvent Accessibility Properties of Complex Proteins, Sprang, S, Yang, D.S.C. and Fletterick, R.J. (1979),Nature, 280, 333‑5.
• Crystal Structure Of An Antifreeze Polypeptide And Its Mechanistic Implications, Yang, D.S.C., Sax, M., Chakrabartty, A. and Hew, C.L. (1988) Nature, 333, 232-237.
• Antifreeze Protein Produced Endogenously by an Overwintering Plant, Griffith, M., Ala, P., Yang, D.S.C. and Moffatt, B.A. (1992) Plant Physiology 100, 593-596.
• Ice binding structure and mechanism of an antifreeze from winter flounder,  Sicheri, F. and Yang, D.S.C.  (1995) Nature 375, 427-431.
• Antifreeze proteins in winter rye are similar to pathogenesis-related proteins,  Hon. W.-C., Griffith, M., Mlynarz, A., Kwok, Y.C. and Yang, D.S.C. (1995) Plant Physiol. 109, 879-889.
• Structure of an enzyme required for aminoglycoside antibiotic resistance reveals homology to eukaryotic protein kinases, Hon, W.C., McKay, G.A., Thompson, P.R., Sweet, R.M., Yang, D.S.C., Wright, G.D. and Berghuis, A.M. (1997). Cell, 89, 887-895.
• Identification of the ice-binding surface on a type III AFP with a “flatness function” algorithm, Yang,D.S.C., Hon, W.-C., Bubanko,S., Xue,Y.Q., Seetharaman,J., Hew,C.L. & Sicheri,F. (1998). Biophysical Journal, 74: 2142-2151.
• Bone recognition mechanism of porcine osteocalcin from crystal structure. Hoang QQ, Sicheri F, Howard AJ, Yang DS. (2003).  Nature. 425(6961):977-80.
• Theoretical study of interaction of winter flounder antifreeze protein with ice. Jorov A, Zhorov BS, Yang DS. (2004). Protein Sci. 13(6):1524-37.
• Self-cleavable stimulus responsive tags for protein purification without chromatography. Ge X, Yang DS, TrabbicCarlson K, Kim B, Chilkoti A, Filipe CD. (2005) JACS. 127(32): 11228-9.
• Characterization of the C-terminal Domain of a Potassium Channel from Streptomyces lividans (KcsA). Pau VP, Zhu Y, Yuchi Z, Hoang QQ,  Yang DS. (2007) J. Biol. Chem. 282(40):29163-9.
• GCN4 enhances the stability of the pore domain of potassium channel KcsA. Yuchi Z, Pau VP, Yang DS. (2008) FEBS J. 275(24):6228-36.
• An engineered right-handed coiled coil domain imparts extreme thermostability to the KcsA channel. Yuchi Z, Pau VP, Lu BX, Junop M, Yang DS. (2009) FEBS J. 276(21):6236-46.